876 results on '"Base sequence"'
Search Results
2. Identification of the novel HLA-DPB1*14:01:15 allele in a Brazilian bone marrow donor.
- Author
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de Oliveira AML, Molinari IF, Massi FP, Pinto LDB, and Visentainer JEL
- Subjects
- Humans, Brazil, Sequence Analysis, DNA methods, Bone Marrow, Sequence Alignment, Codon, Bone Marrow Transplantation, HLA-DP beta-Chains genetics, Alleles, Exons, Tissue Donors, Histocompatibility Testing, Base Sequence
- Abstract
The novel HLA-DPB1*14:01:15 allele differs from DPB1*14:01:01:01 by change of C > T in exon 3., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
3. Characterisation of the novel HLA-A*33:01:21 allele, first identified in a Brazilian individual.
- Author
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Cunha M, Andrade G, Vianna R, Porto LC, and Secco D
- Subjects
- Humans, Base Sequence, Bone Marrow Transplantation, Brazil, Histocompatibility Testing, Sequence Analysis, DNA methods, Tissue Donors, Alleles, Exons, HLA-A Antigens genetics
- Abstract
The novel HLA-A*33:01:21 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
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- 2024
- Full Text
- View/download PDF
4. The novel non-classical HLA-F*01:12 allele identified in a Brazilian individual.
- Author
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Romero M, Stelet VN, Binato R, and Abdelhay E
- Subjects
- Humans, Brazil, Base Sequence, Sequence Analysis, DNA methods, Codon, Sequence Alignment, Alleles, Exons, Histocompatibility Antigens Class I genetics, Histocompatibility Antigens Class I immunology, Histocompatibility Testing
- Abstract
Non-classical HLA-F*01:12 differs from F*01:01:01:09 at one position in exon 3., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
5. The novel non-classical HLA-G*01:46 identified in a Brazilian individual.
- Author
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Romero M, Stelet VN, Binato R, and Abdelhay E
- Subjects
- Humans, Brazil, Histocompatibility Testing, Base Sequence, Sequence Analysis, DNA methods, HLA-G Antigens genetics, Exons, Alleles
- Abstract
Non-classical HLA-G*01:46 differs from G*01:01:03:03 at one position in exon 3., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
6. Characterisation of the novel HLA-C*01:273 allele, first identified in a Brazilian individual.
- Author
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Secco D, Cunha M, Andrade G, Vianna R, and Porto LC
- Subjects
- Humans, Brazil, Histocompatibility Testing, Base Sequence, Tissue Donors, Sequence Analysis, DNA methods, Sequence Alignment, Codon, HLA-C Antigens genetics, Alleles, Exons
- Abstract
The novel HLA-C*01:273 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
7. Characterisation of the novel HLA-DQB1*03:01:61 allele, first identified in a Brazilian individual.
- Author
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Secco D, Oliveira V, Cunha M, Vianna R, and Porto LC
- Subjects
- Humans, Base Sequence, Brazil, Codon, Sequence Analysis, DNA, Tissue Donors, Alleles, Exons, Histocompatibility Testing, HLA-DQ beta-Chains genetics
- Abstract
The novel HLA-DQB1*03:01:61 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
8. Characterisation of the novel HLA-A*02:1140 allele, first identified in a Brazilian individual.
- Author
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Secco D, Oliveira V, Cunha M, Vianna R, and Porto LC
- Subjects
- Humans, Brazil, Histocompatibility Testing, Exons, Tissue Donors, Base Sequence, Sequence Analysis, DNA methods, Sequence Alignment, Alleles, HLA-A2 Antigen genetics, HLA-A2 Antigen immunology
- Abstract
The novel HLA-A*02:1140 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
9. Characterisation of the novel HLA-B*35:593 allele using short and long-read sequencing technologies.
- Author
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Secco D, Santos A, Cunha M, Vianna R, and Porto LC
- Subjects
- Humans, Alleles, Base Sequence, Brazil, High-Throughput Nucleotide Sequencing methods, Histocompatibility Testing methods, HLA-B35 Antigen genetics, Sequence Analysis, DNA methods, Tissue Donors, Exons, HLA-B Antigens genetics
- Abstract
The novel HLA-B*35:593 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
10. Characterisation of the novel HLA-A*30:218 allele using two different sequencing technologies.
- Author
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Secco D, Lopes G, Santos A, Vianna R, and Porto LC
- Subjects
- Humans, Tissue Donors, Base Sequence, Brazil, Sequence Alignment, Alleles, HLA-A Antigens genetics, Exons, Sequence Analysis, DNA methods, Histocompatibility Testing methods
- Abstract
The novel HLA-A*30:218 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
11. Characterisation of the novel HLA-C*08:275 allele, first identified in a Brazilian individual.
- Author
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Secco D, Lopes G, Andrade G, Vianna R, and Porto LC
- Subjects
- Humans, Brazil, Histocompatibility Testing, Tissue Donors, Base Sequence, Sequence Analysis, DNA methods, Sequence Alignment, Codon, HLA-C Antigens genetics, Alleles, Exons
- Abstract
The novel HLA-C*08:275 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
12. Characterisation of the novel HLA-C*15:274 allele using short and long-read sequencing technologies.
- Author
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Oliveira V, Andrade G, Porto LC, Vianna R, and Secco D
- Subjects
- Humans, Sequence Analysis, DNA methods, Tissue Donors, Brazil, High-Throughput Nucleotide Sequencing methods, Base Sequence, HLA-C Antigens genetics, Alleles, Exons, Histocompatibility Testing methods
- Abstract
The novel HLA-C*15:274 allele, first described in a potential bone marrow donor from Brazil., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)
- Published
- 2024
- Full Text
- View/download PDF
13. Elucidating the life cycle of opossum parasites: DNA sequences reveal the involvement of planorbid snails as intermediate hosts of Rhopalias spp. (Trematoda: Echinostomatidae) in Brazil.
- Author
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López-Hernández D, Valadão MC, de Melo AL, Tkach VV, and Pinto HA
- Subjects
- Animals, Opossums, Base Sequence, Brazil, Life Cycle Stages, Larva, Cercaria, Echinostomatidae, Parasites, Trematoda, Biomphalaria
- Abstract
Echinostomatid digeneans belonging to the genus Rhopalias are intestinal trematodes found mainly in opossums in the New World. The genus comprises seven species, but their life cycles and intermediate hosts have been unknown until now. During our long-term study carried out in freshwater habitats within the state of Minas Gerais, Southeast Brazil, echinostomatid cercariae lacking collar spines were found in planorbid snails Biomphalaria glabrata, Biomphalaria straminea, Drepanotrema lucidum and Gundlachia ticaga in six different batches of snail samples collected between 2010 and 2019. Morphologically, the larvae reported herein are morphologically consistent with each other and characterized by the presence of 2-3 large ovoid or spherical corpuscles in each main duct of the excretory system, resembling to Cercaria macrogranulosa previously described from the same region of Brazil. Partial sequences of the ITS (ITS1-5.8S-ITS2) region and 28S gene of the nuclear ribosomal RNA operon, and partial sequences of mitochondrial nad1 and cox1 genes were obtained and compared with the data available for members of the family Echinostomatidae. Nuclear markers indicate that all samples of cercariae evaluated in the present study can be assigned to Rhopalias, but distinct from North American isolates of Rhopalias macracanthus, Rhopalias coronatus and Rhopalias oochi (divergence 0.2-1.2% in 28S and 0.8-4.7% in ITS). The lack of differences verified in both 28S and ITS in 5 out 6 studied samples suggested that they belong to the same species. However, nad1 sequences revealed that our cercariae correspond to three distinct species of Rhopalias (interspecific divergence: 7.7-9.9%), named here as Rhopalias sp. 1, found in B. straminea and G. ticaga, Rhopalias sp. 2 found in B. glabrata and D. lucidum, and Rhopalias sp. 3 also found in D. lucidum. They also differ by 10.8-17.2% from a North American isolate of R. macracanthus sequenced in this study. The cox1 sequences obtained for Rhopalias sp. 1 and Rhopalias sp. 2 (but not Rhopalias sp. 3) reveal that they are distinct from North American isolates of R. macracanthus (genetic divergence 16.3-16.5% and 15.6-15.7%, respectively), R. coronatus (9.2-9.3% and 9.3-9.5%) and Rhopalias oochi (9.0% and 9.5-10.1%). Encysted metacercariae with general morphology similar to that of the body of cercariae were found in tadpoles of Rhinella sp. from the same stream where snails harbored Rhopalias sp. 2, suggesting that the amphibians could act as second intermediate hosts of species of Rhopalias. Data obtained provide the first insights into the life cycle of this unusual echinostomatid genus., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 López-Hernández et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2023
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14. Plastome sequencing of South American Podocarpus species reveals low rearrangement rates despite ancient gondwanan disjunctions.
- Author
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Quiroga MP, Zattara EE, Souza G, Pedrosa-Harand A, and Premoli AC
- Subjects
- Phylogeny, Base Sequence, Brazil, Genomics, Chloroplasts
- Abstract
Background: Historical reconstructions within Podocarpaceae have provided valuable information to disentangle biogeographic scenarios that begun 65 Mya. However, early molecular phylogenies of Podocarpaceae failed to agree on the intergeneric relationships within the family. The aims of this study were to test whether plastome organization is stable within the genus Podocarpus, to estimate the selective regimes affecting plastome protein-coding genes, and to strengthen our understanding of the phylogenetic relationships and biogeographic history., Methods and Results: We sequenced the plastomes of four South American species from Patagonia, southern Yungas, and Brazilian subtropical forests. We compared their plastomes to those published from Brazil, Africa, New Zealand, and Southeast Asia, along with representatives from other genera within Podocarpaceae as outgroups. The four newly sequenced plastomes ranged in size between 133,791 bp and 133,991 bp. Gene content and order among chloroplasts from South American, African and Asian Podocarpus were conserved and different from the plastome of P. totara, from New Zealand. Most genes showed substitution patterns consistent with a conservative selective regime. Phylogenies inferred from either complete sequences or protein coding regions were mostly congruent with previous studies, but showed earlier branching of P. salignus, P. totara and P. sellowii., Conclusions: Highly similar and conserved plastomes of African, South American and Asian species suggest that P. totara plastome should be revised and compared to other species from Oceanic distribution. Furthermore, given such structural conservation, we suggest plastome sequencing is not useful to test whether genomic order can be climatically or geologically structured., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)
- Published
- 2023
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15. New records, neotype designation and DNA sequences of three species of Chaetonotus (Gastrotricha: Chaetonotidae) from Brazil.
- Author
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Salgado KFA, Minowa AK, and Garraffoni ARS
- Subjects
- Animals, Brazil, Base Sequence, Fresh Water
- Abstract
Gastrotrichs are aquatic microinvertebrates (less than 1 mm long) commonly found in freshwater and marine environments worldwide. The taxonomy of gastrotrichs is mainly based on external morphological characters, such as body shape and size of the different body regions, presence and distribution of adhesive tubules, or the microstructure of the external cuticle (e.g. scales, spines, cephalic plates). The diversity of Gastrotricha is still poorly known, especially in tropical regions. The aim of this study is to use integrative taxonomy to report new records of Chaetonotus dadayi, C. paucisquamatus and C. furcatus from the states of São Paulo and Minas Gerais, Brazil. In this study we present 1) new records of C. dadayi in Brazil with new morphological information and a first-time comprehensive diagnosis of the species; 2) the redescription of C. paucisquamatus based on material collected at the type locality and the neotype designation; and 3) the first record of C. furcatus outside its type locality. We also discuss the actual occurrence of C. paucisquamatus and C. furcatus in Poland, given that both species were found in artificial environments with flora imported from South America.
- Published
- 2022
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16. Characterization of insect-specific Culex flavivirus (Flaviviridae) nucleotide sequences in mosquitoes from urban parks in São Paulo, Brazil.
- Author
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Coletti TM, Romano CM, Urbinatti PR, Teixeira RS, Pedrosa LWA, Nardi MS, Natal D, Costa ACD, Jesus JG, Claro IM, Sabino EC, Witkin SS, Marrelli MT, and Fernandes LN
- Subjects
- Animals, Base Sequence, Brazil epidemiology, Parks, Recreational, Phylogeny, Culex genetics, Culicidae, Flaviviridae genetics, Flavivirus genetics
- Abstract
Background: Despite their worldwide occurrence, the distribution and role of insect-specific flaviviruses (ISFs) remain unclear., Methods: We evaluated the presence of ISFs in mosquitoes collected in São Paulo, Brazil, using reverse transcription and semi-nested polymerase chain reaction (PCR). Some of the positive samples were subjected to nanopore sequencing., Results: Twelve mosquito pools (2.8%) tested positive for flavivirus infection. Nanopore sequencing was successfully performed on six samples. Phylogenetic analysis grouped these sequences into genotype 2 of Culex flavivirus (CxFV)., Conclusions: The identification of CxFV genotype 2 at new locations in São Paulo highlights the importance of understanding the role of ISFs in mosquito vector competence.
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- 2022
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17. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus.
- Author
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Cunha RL, Nicastro KR, Zardi GI, Madeira C, McQuaid CD, Cox CJ, and Castilho R
- Subjects
- Animals, Base Sequence, Brazil, Mytilidae genetics, Perna, Genome, Mitochondrial genetics
- Abstract
Background: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna ., Methods: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus . This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship., Results: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1., Competing Interests: Rita Castilho is an Academic Editor for PeerJ., (© 2022 Cunha et al.)
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- 2022
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18. Description of Porphyrosela arachisella sp. nov. (Lepidoptera: Gracillariidae), the first report of Lithocolletinae for Brazil.
- Author
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Fochezato J, Brito R, Gonalves GL, Specht A, Becker VO, and Moreira GRP
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- Animals, Base Sequence, Brazil, Ecosystem, Moths
- Abstract
During a recent survey of leaf-mining microlepidoptera in the Cerrado biome, mines of an undescribed Porphyrosela Braun (Lepidoptera: Gracillariidae: Lithocolletinae) were found associated with the forage peanut, Arachis pintoi Krapov. W.C. Greg. (Fabaceae). Consequently, adults, immature stages and the leaf mine of Porphyrosela arachisella sp. nov. are herein described based on light and scanning electron microscopy. A preliminary analysis of DNA barcode sequences including putative members of other lithocolletine species and all BINs (Barcode Index Numbers) available for Porphyrosela supports P. arachisella as an independent cluster, with 8 to 11% divergence. Its nearest neighbour was the cluster formed by three BINs (BOLD: ADT2137, BOLD: AAG1161 and BOLD: ADU9985) that includes specimens from Australia, Vietnam and Bangladesh. This is the first report of a lithocolletine gracillariid for Brazil, and the third species recognized for the genus in the Neotropical region.
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- 2022
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19. Genomic surveillance of SARS-CoV-2 Spike gene by sanger sequencing.
- Author
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Salles TS, Cavalcanti AC, da Costa FB, Dias VZ, de Souza LM, de Meneses MDF, da Silva JAS, Amaral CD, Felix JR, Pereira DA, Boatto S, Guimarães MAAM, Ferreira DF, and Azevedo RC
- Subjects
- Base Sequence, Brazil epidemiology, COVID-19 virology, Diagnostic Tests, Routine methods, Electrophoresis, Agar Gel methods, Epidemiological Monitoring, Humans, Mutation, RNA, Viral genetics, RNA, Viral isolation & purification, COVID-19 diagnosis, COVID-19 epidemiology, COVID-19 Nucleic Acid Testing methods, Genes, Viral, Pandemics prevention & control, Reverse Transcriptase Polymerase Chain Reaction methods, SARS-CoV-2 genetics, Sequence Analysis, RNA methods, Spike Glycoprotein, Coronavirus genetics
- Abstract
The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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20. Full nucleotide sequencing of ribosomal DNA internal transcribed spacer of Leishmania species causing cutaneous leishmaniasis in Brazil and its potential for species typing.
- Author
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Espada CR, Ferreira BA, Ortiz PA, Uliana SRB, and Coelho AC
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- Base Sequence, Brazil, Humans, Leishmaniasis, Cutaneous, Nucleotides, Phylogeny, DNA, Protozoan genetics, DNA, Ribosomal Spacer genetics, Leishmania classification, Leishmania genetics
- Abstract
Species-specific diagnosis still represents a challenge in leishmaniasis management, particularly in regions with multiple endemic species. In Brazil, seven species have been recognized as etiological agents of cutaneous leishmaniasis. The disease comprises complex clinical presentation patterns, classified as localized, diffuse, disseminated and mucocutaneous leishmaniasis. In this study, we characterized the full nucleotide sequence of a region comprising the ribosomal DNA internal transcribed spacers 1 and 2 and 5.8 S gene of reference strains of Leishmania (Viannia) species reported as causative agents of human leishmaniasis in Brazil. The analysis of the nucleotide sequence of this region was able to discriminate species in the Leishmania (Viannia) subgenus and to determine intra- and interspecies phylogenetic relationships., (Copyright © 2021. Published by Elsevier B.V.)
- Published
- 2021
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21. Genetic structure of allopatric populations of Lutzomyia longipalpis sensu lato in Brazil.
- Author
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Sousa-Paula LC, da Silva LG, da Silva Junior WJ, Figueirêdo Júnior CAS, Costa CHN, Pessoa FAC, and Dantas-Torres F
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- Animals, Base Sequence, Brazil, Male, Phylogeny, Polymorphism, Single Nucleotide, Genetics, Population, Psychodidae genetics
- Abstract
Lutzomyia longipalpis sensu lato is a complex of phlebotomine sand fly species, which are widespread in the Neotropics. They have a great medico-veterinary importance due their role as vectors of Leishmania infantum, the causative agent of visceral leishmaniasis. Morphological variations of Lu. longipalpis s.l. males were reported in the late 1960s in Brazil. Male populations can present either one pair of spots on third abdominal tergites or two pairs on third and fourth ones, namely 1S and 2S phenotypes, respectively. Since then, there has been much interest on the taxonomic status of Lu. longipalpis s.l. Thereafter, several lines of evidence have been congruent in suggesting the existence of an uncertain number of cryptic species within Lu. longipalpis s.l. in Brazil. Herein, a 525 bp-fragment of the period gene was used for assessing the genetic structure and phylogenetic relationship of Lu. longipalpis s.l. populations in Brazil. We performed two set of analyses, first we originally sequenced three populations (Passira, Santarém and Teresina) of Lu. longipalpis s.l. and compared them. Thereafter, we performed a global analysis including in our dataset other three pairs of sympatric populations of Lu. longipalpis s.l. from three Brazilian localities available in GenBank. Fixed single nucleotide polymorphisms (SNPs) sharing, maximum likelihood inference, genetic structure and haplotype analyses revealed the presence of two genetic groups, one composed of Teresina population, and the other encompassing Passira and Santarém populations. The global analysis reflected the first of its kind, and two prominent groups were observed: the clade I comprising Teresina 1S, Bodocó 1S, Caririaçu 1S and Sobral 1S; and the clade II encompassing Passira 2S, Santarém 1S, Bodocó 2S, Caririaçu 2S and Sobral 2S. Genetic differentiation data suggested a limited gene flow between populations of the clade I versus clade II. Our results disclosed the presence of two prominent genetic groups, which could reasonably represent populations of Lu. longipalpis s.l. whose males produce the same courtship song., (Copyright © 2021 Elsevier B.V. All rights reserved.)
- Published
- 2021
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22. Occurrence of Leishmania infection in the immediate geographic region of Ji-Paraná, Rondônia State, Brazil.
- Author
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Almeida AP, Paulo PFM, Pereira Júnior AM, Gujanwski CA, Ferreira V, Costa GDS, Rodrigues MMS, Ferreira RGM, and Medeiros JF
- Subjects
- Base Sequence, Brazil epidemiology, Humans, Male, Rural Population, Leishmania braziliensis genetics, Leishmaniasis, Cutaneous diagnosis, Leishmaniasis, Cutaneous epidemiology
- Abstract
Introduction: This study evaluated the epidemiology of American cutaneous leishmaniasis in the immediate region of Ji-Paraná, Rondônia State., Methods: Samples and epidemiological data were collected from 105 patients., Results: Leishmania infection was observed in 58 (55.2%) patients, and Leishmania braziliensis was present in 82.9% of the 41 sequenced samples. Infected patients were predominantly male (93.1%). Leishmania infection was twice as prevalent among rural inhabitants versus urban inhabitants. Lesions were more frequent in the upper limbs (arms/hands, 41.82%)., Conclusions: The present data corroborate the zoonotic profile of cutaneous leishmaniasis; this information could help to improve surveillance and control strategies.
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- 2021
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23. First complete genome sequence and molecular characterization of Canine morbillivirus isolated in Central Brazil.
- Author
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da Costa VG, Saivish MV, de Oliveira PG, Silva-Júnior A, Moreli ML, and Krüger RH
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- Amino Acid Sequence, Animals, Base Sequence, Brazil, Distemper virology, Genes, Viral, Genotype, Glycosylation, Phylogeny, Recombination, Genetic genetics, Selection, Genetic, Viral Proteins chemistry, Viral Proteins genetics, Distemper Virus, Canine genetics, Distemper Virus, Canine isolation & purification, Dogs virology, Genome, Viral
- Abstract
The Brazilian regions are still highly endemic areas for Canine morbillivirus [canine distemper virus (CDV)]. However, little is known regarding the genetic variability of the strain circulating in several Brazilian regions. Here, we report the first full-length genome and molecular characterization of CDV isolated from domestic dogs in the Brazilian Center-West region. Sequence alignment and phylogenetic analyses based on deduced amino acid and nucleotide sequences showed that the isolated strain is characterized as the South America-I/Europe genotype. However, it segregates into a CDV subgenotype branch. Interestingly, both H and F proteins have a gain of a potential N-glycosylation sites compared to the Onderstepoort vaccine strain. Therefore, this study provides a reference to further understand the epidemic and molecular characteristics of the CDV in Brazil.
- Published
- 2021
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24. Amazonocrinis nigriterrae gen. nov., sp. nov., Atlanticothrix silvestris gen. nov., sp. nov. and Dendronalium phyllosphericum gen. nov., sp. nov., nostocacean cyanobacteria from Brazilian environments.
- Author
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Alvarenga DO, Andreote APD, Branco LHZ, Delbaje E, Cruz RB, Varani AM, and Fiore MF
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- Base Composition, Base Sequence, Brazil, Cyanobacteria cytology, Cyanobacteria genetics, DNA, Bacterial genetics, DNA, Intergenic genetics, Genome, Bacterial, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Cyanobacteria isolation & purification, Ecosystem, Environmental Microbiology
- Abstract
The cyanobacterial genus Nostoc is an important contributor to carbon and nitrogen bioavailability in terrestrial ecosystems and a frequent partner in symbiotic relationships with non-diazotrophic organisms. However, since this currently is a polyphyletic genus, the diversity of Nostoc -like cyanobacteria is considerably underestimated at this moment. While reviewing the phylogenetic placement of previously isolated Nostoc -like cyanobacteria originating from Brazilian Amazon, Caatinga and Atlantic forest samples, we detected 17 strains isolated from soil, freshwater, rock and tree surfaces presenting patterns that diverged significantly from related strains when ecological, morphological, molecular and genomic traits were also considered. These observations led to the identification of the evaluated strains as representative of three novel nostocacean genera and species: Amazonocrinis nigriterrae gen. nov., sp. nov.; Atlanticothrix silvestris gen. nov., sp. nov.; and Dendronalium phyllosphericum gen. nov., sp. nov., which are herein described according to the rules of the International Code of Nomenclature for algae, fungi and plants. This finding highlights the great importance of tropical and equatorial South American ecosystems for harbouring an unknown microbial diversity in the face of the anthropogenic threats with which they increasingly struggle.
- Published
- 2021
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25. A new highly divergent copiparvovirus in sheep.
- Author
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Mosena ACS, da Silva MS, Lorenzett MP, Cibulski SP, Weber MN, Budaszewski RF, Mayer FQ, Henker LC, de Cecco BS, Pavarini SP, Driemeier D, and Canal CW
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Brazil epidemiology, DNA, Viral genetics, Female, Genome, Viral genetics, Male, Parvoviridae Infections epidemiology, Parvoviridae Infections virology, Parvovirinae classification, Phylogeny, Sheep, Sheep Diseases epidemiology, Viral Proteins genetics, Parvoviridae Infections veterinary, Parvovirinae genetics, Sheep Diseases virology
- Abstract
The subfamily Parvovirinae within the family Parvoviridae consists of viruses that can infect a wide range of vertebrate hosts and cause effects ranging from severe disease to asymptomatic infection. In the present study, high-throughput sequencing (HTS) was utilized to analyze samples obtained from an abortion outbreak in a sheep flock to identify a putative viral etiology. A highly divergent nearly complete parvovirid genome sequence, approximately 4.9 kb in length, was determined. The nonstructural protein (NS1) amino acid (aa) sequence of this virus shared less than 30% identity with those of other copiparvoviruses and less than 22% identity with those of members of other genera in the subfamily Parvovirinae. Phylogenetically, this virus, which we have provisionally named "sheep copiparvovirus 1", formed a cluster with copiparvovirus sequences and should be classified as a member of a new species in the genus Copiparvovirus.
- Published
- 2021
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26. Description of optochin-resistant Streptococcus pneumoniae due to an uncommon mutation in the atpA gene and comparison with previously identified atpC mutants from Brazil.
- Author
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Souza ARV, de Pina SECM, Costa NS, Neves FPG, Merquior VLC, Peralta JM, Pinto TCA, and Teixeira LM
- Subjects
- Base Sequence, Brazil, Computer Simulation, Drug Resistance, Bacterial drug effects, Microbial Sensitivity Tests, Models, Molecular, Phenotype, Phylogeny, Protein Subunits chemistry, Quinine pharmacology, Drug Resistance, Bacterial genetics, Genes, Bacterial, Mutation genetics, Quinine analogs & derivatives, Streptococcus pneumoniae drug effects
- Abstract
Optochin susceptibility testing is a major assay used for presumptive identification of Streptococcus pneumoniae. Still, atypical optochin-resistant (Opt
r ) pneumococci have been reported and this phenotype has been attributed to nucleotide substitutions in the genes coding for the F0 F1 ATPase. While substitutions in the atpC gene (c-subunit of ATPase) are more common and better characterized, data on mutations in the atpA (a-subunit) are still limited. We have characterized five Optr isolates presenting alterations in the atpA (Trp206Cys in four isolates and Trp206Ser in one isolate), constituting the first report of such mutations in Brazil. Most of the Optr isolates consisted of heterogeneous populations. Except for Opt MICs and the nucleotide changes in the atpA gene, Optr and Opts subpopulations originating from the same culture had identical characteristics. In addition, we compared phenotypic and genetic characteristics of these atpA mutants with those of atpC mutants previously identified in Brazil. No structural alterations were detected among predicted proteins, regardless of mutations in the coding gene, suggesting that, despite the occurrence of mutations, protein structures tend to be highly conserved, ensuring their functionalities. Phylogenetic analysis revealed that atypical Optr strains are true pneumococci and Opt resistance does not represent any apparent selective advantage for clinical isolates.- Published
- 2021
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27. Norovirus strains in patients with acute gastroenteritis in rural and low-income urban areas in northern Brazil.
- Author
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Tinker RJ, da Costa AC, Tahmasebi R, Milagres FAP, Dos Santos Morais V, Pandey RP, José-Abrego A, Brustulin R, Rodrigues Teles MDA, Cunha MS, Araújo ELL, Gómez MM, Deng X, Delwart E, Sabino EC, Leal E, and Luchs A
- Subjects
- Base Sequence, Brazil epidemiology, Cross-Sectional Studies, Feces virology, Gastroenteritis virology, Genetic Variation genetics, Genotype, High-Throughput Nucleotide Sequencing, Humans, Molecular Epidemiology, Norovirus classification, Phylogeny, RNA, Viral genetics, Caliciviridae Infections epidemiology, Gastroenteritis epidemiology, Norovirus genetics, Norovirus isolation & purification, Poverty statistics & numerical data
- Abstract
From 2010-2016, a total of 251 stool samples were screened for norovirus using next-generation sequencing (NGS) followed by phylogenetic analysis to investigate the genotypic diversity of noroviruses in rural and low-income urban areas in northern Brazil. Norovirus infection was detected in 19.9% (50/251) of the samples. Eight different genotypes were identified: GII.4_Sydney[P31] (64%, 32/50), GII.6[P7] (14%, 7/50), GII.17[P17] (6%, 3/50), GII.1[P33] (6%, 3/50), GII.3[P16] (4%, 2/50), GII.2[P16] (2%, 1/50), GII.2[P2] (2%, 1/50), and GII.4_New Orleans[P4] (2%, 1/50). Distinct GII.6[P7] variants were recognized, indicating the presence of different co-circulating strains. Elucidating norovirus genetic diversity will improve our understanding of their potential health burden, in particular for the GII.4_Sydney[P31] variant.
- Published
- 2021
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28. Molecular detection of Histoplasma capsulatum in bats of the Amazon biome in Pará state, Brazil.
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da Silva JA, Scofield A, Barros FN, de Farias DM, Riet-Correa G, Bezerra Júnior PS, Santos TFS, Tavares GSF, Trevelin LC, da Paz GS, and Cerqueira VD
- Subjects
- Animals, Base Sequence, Brazil epidemiology, Cities, DNA Primers, DNA, Fungal analysis, DNA, Fungal genetics, Ecosystem, Histoplasma genetics, Histoplasmosis diagnosis, Histoplasmosis epidemiology, Humans, Phylogeny, Polymerase Chain Reaction veterinary, Chiroptera microbiology, Histoplasma isolation & purification, Histoplasmosis veterinary
- Abstract
Histoplasma capsulatum, the fungus causing histoplasmosis, has a strong impact on public health. Histoplasmosis is one of the most prevalent systemic mycoses in the Americas and occurs in several mammalian species. Bats are important in the epidemiological cycle of histoplasmosis because they disseminate the fungus throughout the environment. The aim of the present study was to investigate natural H. capsulatum infection in bats located in forested areas, which have undergone anthropogenic perturbations, as well as in the urban areas of the state of Pará. Twenty-two species of bats were captured in 18 municipalities of Pará; the samples obtained from these animals were subjected to nested PCR for amplification of H. capsulatum DNA. The HCI/HCII and HCIII/HCIV primers were used, and the final 210-pb fragment was amplified. Of the 100 bats analysed, two were confirmed to be positive for H. capsulatum. Samples amplified by nested PCR were sequenced and found to share identity and have 100% match with H. capsulatum DNA. H. capsulatum was detected in the area of study: the state of Pará has a wide diversity of bat species, and the region under investigation is situated in the north of the state, which suffers the most severe environmental and climatic changes. Therefore, it is essential to elucidate the distribution of H. capsulatum hosts in this region to facilitate the implementation of effective disease surveillance., (© 2020 Blackwell Verlag GmbH.)
- Published
- 2021
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29. Influence of genetic polymorphisms in glutathione-S-transferases gene in response to imatinib among Brazilian patients with chronic myeloid leukemia.
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Delmond KA, Delleon H, Goveia RM, Teixeira TM, Abreu DC, Mello-Andrade F, Reis AADS, Silva DME, Barbosa ADP, Tavares RS, Anunciação CE, and Silveira-Lacerda E
- Subjects
- Adult, Aged, Aged, 80 and over, Base Sequence, Brazil, Female, Humans, Kaplan-Meier Estimate, Male, Middle Aged, Young Adult, Genetic Predisposition to Disease, Glutathione S-Transferase pi genetics, Glutathione Transferase genetics, Imatinib Mesylate therapeutic use, Leukemia, Myelogenous, Chronic, BCR-ABL Positive drug therapy, Leukemia, Myelogenous, Chronic, BCR-ABL Positive genetics, Polymorphism, Genetic
- Abstract
Polymorphism in metabolizing enzymes can influence drug response as well as the risk for adverse drug reactions. Nevertheless, there are still few studies analyzing the consequence of polymorphisms for the Glutathione-S-transferases (GST) gene to drug response in chronic myeloid leukemia (CML). This study reports, the influence of GSTP1*B and GSTT1/GSTM1null polymorphisms in response to imatinib in CML patients in a Brazilian population. One hundred thirty-nine CML patients from the Clinical Hospital of Goiânia, Goiás, Brazil, treated with imatinib were enrolled in this study. Genotyping of GSTT1 and GSTM1 genes deletions were performed by qPCR and of GSTP1 gene was performed by RFLP-PCR. The frequency of GSTP1*1B, GSTT1 and GSTM1null polymorphisms were determined for all patients. The influence of each patient's genotypes was analyzed with the patient's response to imatinib treatment. Brazilian CML patients revealed GSTT1 and GSTM1 genes deletions. GSTT1 deletion was found in 19.3% of patients and GSTM1 deletion in 48.7% of patients with CML. GSTT1/GSTM1 deletion was found in 11.7% in Brazilian CML patients. The "G allele" of GSTP1*B, is associated with later cytogenetic response in imatinib therapy. While, the gene presence combined with GG genotype (GSTM1 present/GSTPI-GG) conferred a tend to a later cytogenetic response to patients. GSTP1*B and GSTT1/GSTM1null polymorphisms influence treatment response in CML. Brazilian CML patients presenting GSTP1 AA/AG genotypes alone and in combination with GSTT1 null reach the cytogenetic response faster, while patients presenting GSTP1-GG and GSTMI positive genotypes may take longer to achieve cytogenetic response. As a result, it allows a better prognosis, with the use of an alternative therapy, other than reducing treatment cost.
- Published
- 2021
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30. Development and validation of a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of ZIKV in patient samples from Brazil.
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da Silva SJR, Pardee K, Balasuriya UBR, and Pena L
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- Animals, Base Sequence, Brazil, Cell Line, Chlorocebus aethiops, Culicidae virology, Humans, Point-of-Care Testing, RNA, Viral genetics, Saliva virology, Sensitivity and Specificity, Vero Cells, Molecular Diagnostic Techniques methods, Nucleic Acid Amplification Techniques methods, Real-Time Polymerase Chain Reaction methods, Reverse Transcription genetics, Zika Virus genetics, Zika Virus Infection diagnosis
- Abstract
We have previously developed and validated a one-step assay based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of the Zika virus (ZIKV) from mosquito samples. Patient diagnosis of ZIKV is currently carried out in centralized laboratories using the reverse transcription-quantitative polymerase chain reaction (RT-qPCR), which, while the gold standard molecular method, has several drawbacks for use in remote and low-resource settings, such as high cost and the need of specialized equipment. Point-of-care (POC) diagnostic platforms have the potential to overcome these limitations, especially in low-resource countries where ZIKV is endemic. With this in mind, here we optimized and validated our RT-LAMP assay for rapid detection of ZIKV from patient samples. We found that the assay detected ZIKV from diverse sample types (serum, urine, saliva, and semen) in as little as 20 min, without RNA extraction. The RT-LAMP assay was highly specific and up to 100 times more sensitive than RT-qPCR. We then validated the assay using 100 patient serum samples collected from suspected cases of arbovirus infection in the state of Pernambuco, which was at the epicenter of the last Zika epidemic. Analysis of the results, in comparison to RT-qPCR, found that the ZIKV RT-LAMP assay provided sensitivity of 100%, specificity of 93.75%, and an overall accuracy of 95.00%. Taken together, the RT-LAMP assay provides a straightforward and inexpensive alternative for the diagnosis of ZIKV from patients and has the potential to increase diagnostic capacity in ZIKV-affected areas, particularly in low and middle-income countries.
- Published
- 2021
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31. Mutational spectra induced by flavonoid extracts from pepper tree (Schinus terebinthifolius, Raddi) stem bark.
- Author
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Varela-Barca FNT, Felipe MBMC, and de Medeiros SRB
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- Base Sequence, Brazil, DNA Repair drug effects, Escherichia coli drug effects, Escherichia coli genetics, Mutagens adverse effects, Anacardiaceae adverse effects, Flavonoids adverse effects, Mutation drug effects, Plant Bark adverse effects, Plant Extracts adverse effects, Trees adverse effects
- Abstract
Flavonoids are a diverse family of plant compounds that are involved in pigmentation, protection, and endogenous regulation. Flavonoids also have medicinal applications, suggesting that they may exert chemoprotective effects. However, some studies have shown, that some plant flavonoids have oxidative and toxic effects, including those produced by Schinus terebinthifolius. In Brazil, extracts of this plant are widely used for medical purposes. In this study, we analyzed the mutagenic potential of two flavonoid-enriched fractions from Brazilian pepper tree stem bark using Escherichia coli CC strains deficient and proficient in enzymes involved in the DNA repair of oxidative lesions. The highest mutagenic response was detected in the CC104mutMmutY strain but CC104mutY showed a higher mutation frequency than CC104mutM. The spectrum of mutations induced in plasmid DNA is composed of mutations typically caused by oxidative lesions. However, a new type of lesion must be occurred to explain the cytotoxicity, higher mutation rates in the CC104mutY strain, and the rare A:T → T:A and G:C → C:G transversions found in this work., (© 2020 Wiley Periodicals LLC.)
- Published
- 2021
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32. Mosaic genome evolution and phylogenetics of Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) and virulence of seven new isolates from the Brazilian states of Minas Gerais and Mato Grosso.
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Inglis PW, Santos LAVM, Craveiro SR, Ribeiro BM, and Castro MEB
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- Animals, Baculoviridae genetics, Base Sequence, Brazil, Evolution, Molecular, Larva virology, Moths virology, Pest Control, Biological, Phylogeny, Glycine max virology, Genome, Viral genetics, Nucleopolyhedroviruses genetics, Virulence genetics
- Abstract
In a comparative analysis of genome sequences from isolates of the baculovirus Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) from Brazil and Guatemala, we identified a subset of isolates possessing chimeric genomes. We identified six distinct phylogenetically incongruous regions (PIRs) dispersed in the genomes, of between 279 and 3345 bp in length. The individual PIRs possessed high sequence similarity among the affected ChinNPV isolates but varied in coverage in some instances. The donor for four of the PIRs implicated in horizontal gene transfer (HGT) was identified as Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), an alphabaculovirus closely related to ChinNPV, or another unknown but closely related virus. BLAST searches of the other two PIRs returned only ChinNPV sequences, but HGT from an unknown donor baculovirus cannot be excluded. Although Chrysodeixis includens and Trichoplusia ni are frequently co-collected from soybean fields in Brazil, pathogenicity data suggest that natural coinfection of C. includens larvae with ChinNPV and TnSNPV is probably uncommon. Additionally, since the chimeric ChinNPV genomes with tracts of TnSNPV sequence were restricted to a single monophyletic lineage of closely related isolates, a model of progressive restoration of the native DNA sequence by recombination with ChinNPV possessing a fully or partially non-chimeric genome is reasonable. However, multiple independent HGT from TnSNPV to ChinNPV during the evolution of these isolates cannot be excluded. Mortality data suggest that the ChinNPV isolates with chimeric genomes are not significantly different in pathogenicity towards C. includens when compared to most other ChinNPV isolates. Exclusion of the PIRs prior to phylogenetic analysis had a large impact on the topology of part of the maximum-likelihood tree, revealing a homogenous clade of three isolates (IB, IC and ID) from Paraná state in Brazil collected in 2006, together with an isolate from Guatemala collected in 1972 (IA), comprising the lineage uniquely affected by HGT from TnSNPV. The other 10 Brazilian ChinNPV isolates from Paraná, Mato Grosso, and Minas Gerais states showed higher variability, where only three isolates from Paraná state formed a monophyletic group correlating with geographical origin.
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- 2021
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33. A new species of Wallinia Pearse, 1920 (Digenea: Allocreadiidae), in Astyanax bimaculatus (Linnaeus, 1758) (Characidae) in Northeast Brazil, based on morphology and DNA sequences.
- Author
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da Silva BAF, Dias KGA, da Silva RJ, and Yamada FH
- Subjects
- Animals, Base Sequence, Brazil, Costa Rica, DNA, Ribosomal genetics, Intestines parasitology, Mexico, Phylogeny, RNA, Ribosomal, 28S genetics, Rivers parasitology, Trematoda genetics, Venezuela, Characidae parasitology, Fish Diseases parasitology, Trematoda classification, Trematoda isolation & purification, Trematode Infections veterinary
- Abstract
Wallinia caririensis n. sp. is described from the intestine of Astyanax bimaculatus (Linnaeus, 1758) (Characidae) collected in the Batateiras River in the municipality of Crato, Ceará state, Brazil. The description was based on integrative taxonomy approach using DNA sequences from the D1-D3 domains of the 28S rDNA gene. The new species was confirmed through the phylogenetic analysis of the 28S rDNA gene, which showed that Wallinia caririensis n. sp. is a sister taxon of Wallinia brasiliensis (Dias, Müller, Almeida, Silva, Azevedo, Pérez-Ponce de León, and Abdallah, 2018, and Wallinia anindoi Hernández-Mena, Pinacho-Pinacho, García-Varela, Mendonza-Garfias, and Pérez-Ponce de León, 2019), a species which parasitizes Astyanax fasciatus (Cuvier, 1819), A. lacustris (Lucena and Soares, 2016) in Brazil, and A. aeneus (Günther, 1860) in Mexico, with genetic divergences of 2% and 3%, respectively. The new species can be distinguished morphologically from its congeners by possessing large body size (length and width) and tapered extremity in the posterior end of the body, eyespots are present at the pharynx level, and vitelline follicles reach up to the half distance between the posterior testis and the extremity of the body, by having larger testes distributed in coincident zones (i.e., contiguous) and non-operculated eggs (a conspicuous characteristic in W. brasiliensis). To date, species of this genus have already been described in freshwater fishes from Mexico, Costa Rica, Venezuela, and Southeastern Brazil. The species described in this study consists of the second species parasitizing characids in Brazil, and the first record in Northeastern Brazil. This finding fills a gap and expands the biogeographic distribution of the genus Wallinia in South America.
- Published
- 2021
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34. Molecular detection of a Borrelia sp. in nymphs of Amblyomma brasiliense ticks (Acari: Ixodidae) from Iguaçu National Park, Brazil, genetically related to Borrelia from Ethiopia and Côte d'Ivoire.
- Author
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Santos CAD, Suzin A, Vogliotti A, Nunes PH, Barbieri ARM, Labruna MB, Szabó MPJ, and Yokosawa J
- Subjects
- Amblyomma growth & development, Amino Acid Sequence, Animals, Base Sequence, Borrelia genetics, Brazil, Nymph growth & development, Nymph microbiology, Parks, Recreational, Phylogeny, Sequence Alignment, Amblyomma microbiology, Borrelia classification
- Abstract
Gram-negative spirochetes of the genus Borrelia are transmitted to vertebrate hosts through the tick bite during blood intake. Pathogenic Borrelia species may cause relapsing fever or Lyme borreliosis in humans. Our study aimed to molecularly detect and characterize bacteria of this genus in ticks collected in the Iguaçu National Park, located in southern Brazil. Ticks were collected from the environment (free living) and from hosts from May 2015 to July 2017. In total, 829 ticks were tested, being 741 from the environment and 88 from hosts; 128 ticks were larvae, 523 were nymphs, and 178 were adults (80 males and 98 females). The species identified were: Amblyomma brasiliense (42.9 %), Amblyomma coelebs (16.8 %), Amblyomma sp. (15.0 %), Amblyomma incisum (10.3 %), Amblyomma ovale (8.7 %), Haemaphysalis juxtakochi (5.5 %), Rhipicephalus microplus (0.5 %), Amblyomma longirostre (0.2 %), and Rhipicephalus sanguineus sensu lato (0.1 %). DNA extraction was performed with pools of larvae or nymphs, or individually with adults, for a total of 394 samples. The PCR technique used to detect Borrelia DNA was performed with two rounds of amplification reactions targeting a segment of the flagellin B gene (flaB). Amplification occurred in only one DNA sample, which was obtained from nymphs of A. brasiliense collected from the vegetation of a trail. The nucleotide sequence analysis revealed 90.8 % identity to a sequence of Borrelia sp. from Côte d'Ivoire, and 89.1 % identity to a sequence from Ethiopia. Phylogenetic analysis revealed that the Borrelia sequence from A. brasiliense was distinct from the Borrelia species of the groups belonging to Lyme borreliosis, relapsing fever and the one associated with reptile and echidna as hosts. The sequence is likely from a putative new species of Borrelia and was detected for the first time in A. brasiliense ticks., (Copyright © 2020 Elsevier GmbH. All rights reserved.)
- Published
- 2020
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35. Costus stripe mosaic virus, a tentative new member of the genus Potyvirus.
- Author
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Alexandre MAV, Duarte LML, Ramos-González PL, Chaves ALR, Harakava R, Rodrigues LK, Chabi-Jesus C, and Kitajima EW
- Subjects
- Amino Acid Sequence, Base Sequence, Brazil, Cysteine Endopeptidases genetics, Open Reading Frames, RNA, Viral genetics, Sequence Analysis, DNA, Viral Proteins genetics, Costus virology, Genome, Viral, Mosaic Viruses classification, Phylogeny
- Abstract
Morphological, biological, serological, and molecular tests underpin the description of costus stripe mosaic virus (CoSMV) as a new member of the genus Potyvirus, family Potyviridae. Found affecting the native ornamental Costus spiralis in Brazil, the pathogen showed a severely restricted natural and experimental host range. Excluding the poly(A) tail, the CoSMV genome contains a large open reading frame (ORF) of 9,446 nucleotides that encodes a polyprotein with 3,046 amino acids, which is potentially cleaved into ten products, and a small ORF (77 amino acids) knows as PIPO. Genome analysis demonstrated the highest CoSMV nucleotide sequence identity to onion yellow dwarf virus (51.79%). No evidence of recombination was detected in the CoSMV genome, and phylogenetic analysis revealed its basal position in a group formed by members of the genus Potyvirus, along with Cyrtanthus elatus virus A (Vallota speciosa virus) and canna yellow streak virus. CoSMV was not transmitted by aphids of the species Aphis solanella, Myzus persicae or Uroleucon sonchi, which could be due to mutations in the HC-Pro motifs required for aphid transmission. A divergence in the P1 protein cleavage site was found when compared to other members of the family Potyviridae. Based on its unique biological and molecular characteristics and the current species demarcation criteria, we propose CoSMV to be a new tentative member of the genus Potyvirus.
- Published
- 2020
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36. Canine parvovirus 2b in fecal samples of asymptomatic free-living South American coatis (Nasua nasua, Linnaeus, 1766).
- Author
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Spera CG, Lorenzetti E, Lavorente FLP, de Calasans Marques G, Bisca JM, Teixeira CR, Alfieri AA, and Alfieri AF
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Brazil, Dogs, Feces virology, Female, Male, Parvoviridae Infections virology, Parvovirus, Canine classification, Parvovirus, Canine genetics, Phylogeny, Parvoviridae Infections veterinary, Parvovirus, Canine isolation & purification, Procyonidae virology
- Abstract
Canine parvovirus type 2 (CPV-2) is classified into three subtypes (CPV-2a, CPV-2b, and CPV-2c) and is the main cause of enteritis and myocarditis in young domestic and wild animals. This study aimed to evaluate the presence of CPV-2 in the feces of asymptomatic free-living coatis from Garden Forest Reserve, Palmital city, SP, Brazil. Fecal samples from 21 coatis (both sexes, different ages, and different aspects of feces) were collected in August 2014 and March 2015. The nucleic acid extracted was submitted to a polymerase chain reaction (PCR) assay to amplify a fragment of the VP2 gene of CPV-2. Eight (38%) fecal samples were positive in the PCR assay and were confirmed by sequencing. The 7 nucleotide (nt) sequences analyzed showed 100% nt identity with the prototype strain of CPV-2b (CPV-39 strain). The analysis of the deduced amino acid (aa) sequence revealed the presence of the GAT codon (aa D-Asp) at position 426 of the VP2 viral protein (subtype 2b). This study describes for the first time the identification of CPV-2b in asymptomatic free-living coatis (Nasua nasua) and suggests that coatis are susceptible to Carnivore protoparvovirus 1 infection and are important as a reservoir and an asymptomatic carrier to other wild and domestic animal species.
- Published
- 2020
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37. Genome constellations of rotavirus a isolated from avian species in Brazil, 2008-2015.
- Author
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Beserra LAR, Barbosa CM, Berg M, Brandão PE, Soares RM, and Gregori F
- Subjects
- Animals, Base Sequence, Brazil, Chickens, Genetic Variation, Genotype, Phylogeny, RNA, Viral genetics, Rotavirus classification, Rotavirus isolation & purification, Rotavirus Infections virology, Bird Diseases virology, Genome, Viral, Poultry Diseases virology, Rotavirus genetics, Rotavirus Infections veterinary
- Abstract
Rotaviruses are members of the family Reoviridae and are a common cause of acute diarrhea in many mammalian and avian species. They are non-enveloped icosahedral particles and their genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). Genotypes are defined based upon the diversity found in these genes and viral characterization plays a central role on epidemiological studies and prevention. Here we investigate the distribution of Brazilian RVAs genotypes in 8 chicken samples collected between 2008 and 2015 from different regions by RT-PCR, partial (Sanger) nucleotide sequencing and phylogenetic analysis from all rotavirus genes. Although the identified genotypes were typical from avian host species, when analyzed together, they form novel genetic constellations: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. This study highlights that avian rotaviruses are widespread among commercial farms in Brazil, and the co-circulation of at least two different genomic constellations indicates that may present a way bigger genetic variability, that can be increased by the possible transmission events from other birds, lack of specific preventive measures, as well as the different viral evolution mechanisms.
- Published
- 2020
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38. Genomic information on Stenotrophomonas maltophilia ST264 isolated from a cystic fibrosis pediatric patient in Brazil.
- Author
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Braga FS, D'Allincourt Carvalho Assef AP, Leão RS, Albano RM, and Marques EA
- Subjects
- Anti-Bacterial Agents pharmacology, Base Sequence, Brazil, Humans, Microbial Sensitivity Tests, Multilocus Sequence Typing, Stenotrophomonas maltophilia drug effects, Stenotrophomonas maltophilia isolation & purification, Cystic Fibrosis microbiology, Genome, Bacterial, Gram-Negative Bacterial Infections microbiology, Stenotrophomonas maltophilia genetics
- Abstract
Stenotrophomonas maltophilia is one of the Gram-negative bacilli most frequently found in the airways of cystic fibrosis patients. This opportunistic pathogen is intrinsically multidrug-resistant, and therefore, its treatment presents a challenge. The genetic characterization of S. maltophilia is largely unknown, especially from those strains that colonize/infect the airways of cystic fibrosis patients. This work reports the draft genome sequences of three S. maltophilia isolates recovered from the sputum of a cystic fibrosis pediatric patient in Southeast Brazil. Several resistance- and virulence-related genes were detected. Furthermore, one intact phage and one incomplete prophage region were also identified in all strains. Multilocus sequence typing showed that all strains belonged to a new sequence type (ST264). Interestingly, all S. maltophilia strains were genetically identical, showing persistence for at least 16 months. To our knowledge, this is the first report of S. maltophilia draft genome sequences obtained from a cystic fibrosis pediatric patient in Brazil.
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- 2020
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39. Identification of ACKR1 variants associated with altered Duffy phenotype expression in blood donors from southern Brazil.
- Author
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Höher G, Rodrigues MMO, Waskow G, Agnes G, Von Burg PV, Onsten T, Fiegenbaum M, and Almeida S
- Subjects
- Base Sequence, Brazil, Humans, Phenotype, Duffy Blood-Group System metabolism, Receptors, Cell Surface metabolism
- Abstract
The atypical chemokine receptor 1 gene (ACKR1) is responsible for the clinically significant Duffy blood group. The main antigens of this system, Fya and Fyb, can be related to a null or weak expression of the DARC protein. In the present work, we aimed to identify ACKR1 gene variants in blood donors from southern Brazil based on discrepancies between their serological and molecular typing results. Then, we analyzed the association of these variants with the expression of the Duffy phenotype. The Fy antigen types were determined via hemagglutination and real-time PCR (c.125 G > A, c.265C > T and c.-67T > C SNPs) tests in a sample composed of 382 regular repetitive voluntary blood donors to the Blood Bank of Hospital de Clínicas de Porto Alegre. An inconclusive correlation between phenotype-genotype analyses was found in 11 (2.88 %) donors, and the entire ACKR1 gene was sequenced in these samples. Our investigation found 11 genetic variants, four of which (c.-541C > T, c.21 + 150C > T, c.22-58A > G, and c.298 G > A SNPs) seem to have putative functional effects on the structure and expression of DARC undertaken for in silico analysis (SIFT, PolyPhen-2 and RegulomeDB). Molecular events can result in apparent discrepancies between red cell genotypes and phenotypes. Our findings provided insight into the molecular background of FY antigens to improve technical approaches for red cell genotyping., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020 Elsevier Ltd. All rights reserved.)
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- 2020
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40. Ehrlichia spp. and Anaplasma spp. in Xenarthra mammals from Brazil, with evidence of novel 'Candidatus Anaplasma spp.'
- Author
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Calchi AC, Vultão JG, Alves MH, Yogui DR, Desbiez ALJ, De Santi M, Santana MS, da Silva TMV, Werther K, Teixeira MMG, Machado RZ, and André MR
- Subjects
- Anaplasma genetics, Animals, Base Sequence, Bayes Theorem, Brazil, DNA, Intergenic genetics, Ehrlichia genetics, Geography, Hydrolysis, Likelihood Functions, Phylogeny, Polymorphism, Genetic, Temperature, Anaplasma isolation & purification, Ehrlichia isolation & purification, Xenarthra microbiology
- Abstract
Anaplasmataceae agents are obligatory intracellular Gram-negative α-proteobacteria that are transmitted mostly by arthropod vectors. Although mammals of the Superorder Xenarthra (sloths, anteaters, and armadillos) have been implicated as reservoirs for several zoonotic agents, only few studies have sought to detect Anaplasmataceae agents in this group of mammals. This study aimed to investigate the occurrence and genetic diversity of Anaplasma spp. and Ehrlichia spp. in blood and spleen samples of free-living Xenarthra from four different states in Brazil (São Paulo, Mato Grosso do Sul, Rondônia, and Pará). Nested and conventional PCR screening assays were performed to detect the rrs and dsb genes of Anaplasma spp. and Ehrlichia spp., respectively. The assays were positive in 27.57% (91/330) of the Anaplasma spp. and 24.54% (81/330) of the Ehrlichia spp. Of the 91 positive Anaplasma spp. samples, 56.04% were positive in a conventional PCR assay targeting the 23S-5S intergenic region. Phylogenetic and distance analyses based on the rrs gene allocated Anaplasma sequences from sloths captured in Rondônia and Pará states in a single clade, which was closely related to the A. marginale, A. ovis, and A. capra clades. The sequences detected in southern anteaters from São Paulo were allocated in a clade closely related to sequences of Anaplasma spp. detected in Nasua nasua, Leopardus pardalis, and Cerdocyon thous in Brazil. These sequences were positioned close to A. odocoilei sequences. Genotype analysis corroborated previous findings and demonstrated the circulation of two distinct Anaplasma genotypes in animals from north and southeast Brazil. The first genotype was new. The second was previously detected in N. nasua in Mato Grosso do Sul state. The intergenic region analyses also demonstrated two distinct genotypes of Anaplasma. The sequences detected in Xenarthra from Pará and Rondônia states were closely related to those in A. marginale, A. ovis, and A. capra. Anaplasma spp. sequences detected in Xenarthra from São Paulo and were allocated close to those in A. phagocytophilum. The analyses based on the dsb gene grouped the Ehrlichia spp. sequences with sequences of E. canis (São Paulo, Mato Grosso do Sul, and Pará) and E. minasensis (Rondônia and Pará). The data indicate the occurrence of E. canis and E. minasensis and two possible new Candidatus species of Anaplasma spp. in free-living mammals of the Superorder Xenarthra in Brazil.
- Published
- 2020
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41. The grass squid Pickfordiateuthis pulchella is a paedomorphic loliginid.
- Author
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Anderson FE and Marian JEAR
- Subjects
- Animals, Base Sequence, Bayes Theorem, Brazil, Computer Simulation, Decapodiformes classification, Phylogeny
- Abstract
The wide disparity in adult body size observed both within and among animal taxa has long attracted widespread interest, with several general rules having been proposed to explain trends in body size evolution. Adult body size disparity among the cephalopod mollusks is remarkable, with adult body sizes ranging from a few centimeters to several meters. Some of the smallest cephalopods are found within Pickfordiateuthis, a group comprising three described species of squid found in the western Atlantic and tropical eastern Pacific. Pickfordiateuthis pulchella, the type species of the genus, was initially proposed to be closely related to the loliginid squids (Loliginidae), with subsequent descriptions of additional species supporting a placement within Loliginidae. Pickfordiateuthis is remarkable in that all species reach sexual maturity at about one-fifth to one-tenth the size seen in most loliginid species. To date, no phylogenetic analyses have included representatives of Pickfordiateuthis. To infer the phylogenetic position of Pickfordiateuthis and explore its implications for body size evolution, we collected specimens of Pickfordiateuthis pulchella from Brazilian waters and sequenced regions of two loci-the mitochondrial large ribosomal subunit (rrnL a.k.a. 16S) gene and the nuclear gene rhodopsin. Maximum likelihood and Bayesian analyses of these sequences support a placement of Pickfordiateuthis pulchella as sister to a clade comprising the Western Hemisphere loliginid genera Doryteuthis and Lolliguncula. Analyses of body size evolution within Loliginidae suggest that a shift to a smaller body size optimum occurred along the lineage leading to P. pulchella, with some evidence of shifts toward larger sizes in the ancestors of Loligo and Sepioteuthis; these inferences seem to be robust to phylogenetic uncertainty and incomplete taxon sampling. The small size and juvenile-like morphological traits seen in adult Pickfordiateuthis (e.g., sepiolid-like fins and biserial sucker arrangement in the tentacles) may be due to paedomorphosis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)
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- 2020
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42. Sequence analysis of nucleoprotein gene reveals the co-circulation of lineages and sublineages of rabies virus in herbivorous in Rio Grande do Sul state, Brazil.
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de Almeida GL, Cargnelutti JF, Ries AS, Ferreira JC, Rosa JCA, Batista HBCR, Flores EF, and Weiblen R
- Subjects
- Animals, Base Sequence, Brain virology, Brazil epidemiology, Cattle virology, Herbivory, Phylogeny, RNA, Viral genetics, Rabies epidemiology, Rabies virology, Rabies virus classification, Sequence Analysis, Sheep virology, Nucleocapsid Proteins genetics, Rabies veterinary, Rabies virus genetics
- Abstract
An unprecedented outbreak of rabies occurred in Rio Grande do Sul state (RS) from 2012 onward, resulting in thousands of bovine deaths, important economic losses, and posing risk to human health. This article describes a genetic analysis of 145 rabies viruses (RABV) recovered from herbivorous from RS between 2012 and 2017, based on partial sequence analysis of the nucleoprotein (N) gene. High nucleotide (nt) identity (95.5 to 100%) and amino acid (aa) similarity (96.7 to 100%) were observed among the analyzed sequences. These sequences displayed a high sequence nt identity/aa similarity with bovine RABV sequences (96.4-97.9%; 98.1-100%, respectively) and vampire bat RABV sequences (96.3-97.5%; 97.8-99.5%). Phylogenetic analyzes based on the N sequence allowed for the segregation of viruses into two distinct clusters. Cluster 1 comprised RABV sequences covering the whole studied period, whereas cluster 2 grouped a lower number of viruses from 2013, 2014, 2015, to 2017. In some cases, viruses obtained from the same region within a short period of time grouped to distinct clusters or sub-clusters, indicating the co-circulation of distinct virus lineages in these outbreaks. The segregation into sub-clusters was also observed for viral sequences obtained from the same region at different times, indicating the involvement of distinct viruses. In summary, partial sequence analyses revealed a high conservation of N protein and the circulation of two lineages and different sublineages of RABV in the region. In addition, our results confirm the suitability of N gene to study the genetic relationships among RABV isolates.
- Published
- 2020
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43. Detection and characterization of Ilheus and Iguape virus genomes in historical mosquito samples from Southern Brazil.
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Cunha MS, Luchs A, da Costa AC, Ribeiro GO, Dos Santos FCP, Nogueira JS, Komninakis SV, Marinho RDSS, Witkin SS, Villanova F, Deng X, Sabino EC, Delwart E, Leal É, Nogueira ML, and Maiorka PC
- Subjects
- Animals, Base Sequence, Brazil epidemiology, Flaviviridae Infections epidemiology, Flaviviridae Infections virology, Mice, Mosquito Vectors virology, Phylogeny, RNA, Viral genetics, Culicidae virology, Flavivirus genetics, Flavivirus isolation & purification, Genome, Viral
- Abstract
In Brazil, flaviviruses have caused massive outbreaks. Surveillance programs designed to monitor virus activity in vectors provides a system for mapping disease distribution and for identifying specific vector species for targeted control. The present study aimed to describe the detection, whole genome characterization and phylogenetic analysis of Ilheus virus (ILHV) and Iguape virus (IGUV) strains obtained from historical mosquito's samples. Twelve isolates of pooled mosquito specimens (inoculated in neonate mouse brain) collected in the state of São Paulo, Brazil, in 1993, 1994 and 1997 were investigated. Viral RNA was extracted and analyzed by qRT-PCR using Flavivirus genus-specific primers. Positive samples were sequenced and underwent phylogenetic analyses. Flavivirus was detected in 50% of the specimens. Positive samples were successfully Sanger sequenced. Three Anopholes cruzii pools collected in 1994 were positive for IGUV. One Culex sp. pool, one Anopheles triannulatus pool, and one Coquillettidia juxtamansonia pool, collected in 1994, were positive for ILHV. Metagenomic sequencing successfully characterize one ILHV and four IGUV full genomes, and revealed a high degree of homology between the Brazilian ILHV and IGUV strains and isolates available in GenBank. Phylogenetic analysis of partial ILHV NS5 gene revealed three distinct lineages (clades), an indication of genetic heterogeneity in strains circulating in Brazil. Nucleotide insertions and a high-level of nucleotide diversity were observed in the NS1 protein and capsid region of IGUV strains, respectively. Detection of ILHV and IGUV in mosquitoes from Southeastern Brazil confirms the historical circulation of these viruses in this area. Furthermore, this first evidence of ILHV in Anopheles triannulatus suggests the potential importance of Anopheles mosquitoes in the IGUV transmission cycle. Genomic and phylogenetic analysis of these viruses provided insights into their diversity and evolution, which are important for the emergence patterns of flaviviruses and their evolutionary trends in Brazil, an endemic country for several arbovirus. in In-depth studies of ILHV and IGUV including vector competence and molecular studies are needed to shed light on their epidemiology and potential risk of future emergence., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020. Published by Elsevier B.V.)
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- 2020
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44. Clinical, Molecular, Functional, and Structural Characterization of CYP17A1 Mutations in Brazilian Patients with 17-Hydroxylase Deficiency.
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Coeli-Lacchini FB, Mermejo LM, Bodoni AF, Elias LLK, Silva WA Jr, Antonini SR, Moreira AC, and de Castro M
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- Adolescent, Adrenal Hyperplasia, Congenital blood, Adrenal Hyperplasia, Congenital genetics, Adult, Amino Acid Sequence, Base Sequence, Brazil, Exons, Female, Hormones blood, Humans, Male, Mutation, Steroid 17-alpha-Hydroxylase chemistry, Steroid 17-alpha-Hydroxylase metabolism, Young Adult, Adrenal Hyperplasia, Congenital enzymology, Steroid 17-alpha-Hydroxylase genetics
- Abstract
17-Hydroxylase-deficiency (17OHD) is a rare form of congenital adrenal hyperplasia. The aim of the work was to study clinical, biochemical, and the follow up of 17OHD patients and evaluate the function and structure of CYP17A1 mutations. Brazilian patients (three 46, XX and four 46, XY; 17±1.9 years) with combined 17-hydroxylase/17,20-lyase deficiency were evaluated. CYP17A1 gene was sequenced. Functional analysis was performed transfecting COS7 cells, which were exposed to progesterone or 17α-hydroxypregnolone substrates. Hormones were determined by RIA or LC-MS/MS. Three-dimensional structural modeling was performed by Modeller software. All patients presented prepubertal female external genitalia, primary amenorrhea, hypergonadotrophic hypogonadism, hypokalemic hypertension, decreased cortisol, and increased ACTH and corticosterone levels. Five patients presented previously described mutations: p.W406R/p.W406R, IVS2-2A>C/p.P428L, and p.P428L/p.P428L. Two patients presented the compound heterozygous p.G478S/p.I223Nfs*10 mutations, whose CYP17A1 activity and the three dimensional structural modeling are originally studied in this paper. CYP17A1 activity of p.G478S was 13 and 58% against progesterone and 17-hydroxypregnenolone, respectively. The p.I223Nfs*10 caused a truncated inactive protein. Three-dimensional p.G478S structural modeling showed different internal hydrophobic interaction with W313 and created an additional chain side contact with L476 residue. Due to the rarity of 17OHD, the long term follow up (15.3±3.1 years) of our patients will help endocrinologists on the management of patients with 17OHD. The mutation p.G478S/pI223Nfs*10 led to severe 17OHD and impaired CYP17A1 structure and function. The integration of in silico and in vitro analysis showed how the amino acid changes affected the CYP17A1 activity and contributed to clarify the molecular interactions of CYP17A1., Competing Interests: The authors declare that they have no conflict of interest., (© Georg Thieme Verlag KG Stuttgart · New York.)
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- 2020
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45. Altered in vitro muscle differentiation in X-linked myopathy with excessive autophagy.
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Fernandes SA, Almeida CF, Souza LS, Lazar M, Onofre-Oliveira P, Yamamoto GL, Nogueira L, Tasaki LY, Cardoso RR, Pavanello RCM, Silva HCA, Ferrari MFR, Bigot A, Mouly V, and Vainzof M
- Subjects
- Autophagy, Base Sequence, Biopsy, Brazil, Cell Proliferation, Child, Preschool, Female, Gene Expression Regulation, Genetic Diseases, X-Linked genetics, Humans, Infant, Newborn, Lysosomes metabolism, Male, Membrane Fusion, Muscle Development genetics, Muscle Fibers, Skeletal metabolism, Muscle Fibers, Skeletal pathology, Muscular Diseases genetics, Myoblasts metabolism, Myoblasts pathology, Pedigree, RNA, Messenger genetics, RNA, Messenger metabolism, Vacuolar Proton-Translocating ATPases genetics, Vacuolar Proton-Translocating ATPases metabolism, Vacuoles pathology, Vacuoles ultrastructure, Cell Differentiation, Genetic Diseases, X-Linked pathology, Muscle, Skeletal pathology, Muscular Diseases pathology
- Abstract
X-linked myopathy with excessive autophagy (XMEA) is a genetic disease associated with weakness of the proximal muscles. It is caused by mutations in the VMA21 gene, coding for a chaperone that functions in the vacuolar ATPase (v-ATPase) assembly. Mutations associated with lower content of assembled v-ATPases lead to an increase in lysosomal pH, culminating in partial blockage of macroautophagy, with accumulation of vacuoles of undigested content. Here, we studied a 5-year-old boy affected by XMEA, caused by a small indel in the VMA21 gene. Detection of sarcoplasmic Lc3 (also known as MAP1LC3B)-positive vacuoles in his muscle biopsy confirmed an autophagy defect. To understand how autophagy is regulated in XMEA myogenesis, we used patient-derived muscle cells to evaluate autophagy during in vitro muscle differentiation. An increase in lysosomal pH was observed in the patient's cells, compatible with predicted functional defect of his mutation. Additionally, there was an increase in autophagic flux in XMEA myotubes. Interestingly, we observed that differentiation of XMEA myoblasts was altered, with increased myotube formation observed through a higher fusion index, which was not dependent on lysosomal acidification. Moreover, no variation in the expression of myogenic factors nor the presence of regenerating fibers in the patient's muscle were observed. Myoblast fusion is a tightly regulated process; therefore, the uncontrolled fusion of XMEA myoblasts might generate cells that are not as functional as normal muscle cells. Our data provide new evidence on the reason for predominant muscle involvement in the context of the XMEA phenotype.This article has an associated First Person interview with the first author of the paper., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)
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- 2020
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46. Paracoccidioides brasiliensis habitat: far beyond armadillo burrows?
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de Macedo PM, Scramignon-Costa BS, Almeida-Paes R, Trilles L, de Oliveira LSC, Zancopé-Oliveira RM, do Valle ACF, and Wanke B
- Subjects
- Animals, Base Sequence, Brazil, Ecosystem, Paracoccidioides genetics, Paracoccidioides growth & development, Sequence Analysis, DNA, Soil Microbiology, Armadillos, DNA, Fungal genetics, Paracoccidioides isolation & purification, Paracoccidioidomycosis microbiology
- Abstract
Paracoccidioides spp. isolation from environmental samples is rare and hardly reproducible. Molecular techniques have facilitated the fungal detection. However, it can be still difficult. Some strategies to enhance the capacity of DNA detection have been adopted, including the analysis of soil samples belonging to the habitat of animals from which Paracoccidioides spp. have already been isolated, notably armadillo burrows. To date, the detection of Paracoccidioides spp. has not yet been reported from outbreak hotspots. Clusters and outbreaks of acute paracoccidioidomycosis (PCM), usually a more severe clinical form, have currently occurred in urban areas being associated to climate changes, deforestation, and great constructions. These occurrences potentially signalise the fungus' environmental niche, a riddle not yet solved. The authors performed an environmental investigation in a deeply disturbed area, after a highway construction in Rio de Janeiro, Brazil, where a recent outbreak of acute PCM occurred. Specific DNA sequences of Paracoccidioides brasiliensis were detected in shallow soil samples around the highway, reinforcing the association between the road construction and this PCM outbreak.
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- 2020
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47. DNA barcoding identifies three species of croakers (Pisces, Sciaenidae) in the ichthyoplankton of the High Paraná River.
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Briñoccoli YF, Garrido GG, and Alvarez A
- Subjects
- Animals, Argentina, Base Sequence, Biodiversity, Brazil, Paraguay, Phylogeny, Polymerase Chain Reaction, Rivers, DNA Barcoding, Taxonomic, Perciformes classification, Perciformes genetics
- Abstract
In the province of Misiones (Argentina), the filling of the Yacyretá Reservoir (Argentina-Paraguay) to its final dimensions in 2011 formed new aquatic ecosystem, e.g., Garupá Stream was converted into a subreservoir. Reports have been made in this stream of adult individuals and spawning of the Family Sciaenidae, excellent colonizers of modified environments. The larvae of this family are morphologically similar, particularly among Pachyurus and Plagioscion species, making taxonomic differentiation difficult. In the present work, sciaenidae larvae were characterized molecularly at the cytochrome c oxidase subunit I gene in order to determine which species use this environment for reproduction. Additionally, genetic distances, Barcode Index Number (BIN) and Automatic Barcode Gap Discovery method (ABGD) were estimated and phylogenetic trees were reconstructed. The results indicated the presence of Plagioscion ternetzi and Pachyurus bonariensis larvae, and for the first time in tributaries of the region, Plagioscion squamosissimus. The incorporation of P. bonariensis and P. squamosissimus to the faunistic assemblage of ichthyoplankton in the Garupá Stream supports better characterization of the species richness of this secondary watercourse modified by the Yacyretá Reservoir, and advancement in our understanding of use of this area for reproduction.
- Published
- 2020
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48. Newly sequenced genomes of four Bacillus Calmette Guerin vaccines.
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Sisco MC, Silva MG, Lopez B, Arguelles C, Mendonça-Lima L, de Waard JH, Duarte RS, and Suffys PN
- Subjects
- Argentina, Base Sequence, Brazil, Humans, Molecular Sequence Data, Polymorphism, Single Nucleotide, Venezuela, BCG Vaccine genetics, Chromosome Mapping, Mycobacterium bovis genetics
- Abstract
Bacillus Calmette Guerin (BCG) vaccines comprise a family of related strains. Whole genome sequencing has allowed the better characterisation of the differences between many of the BCG vaccines. As sequencing technologies improve, updating of publicly available sequence data becomes common practice. We hereby announce the draft genome of four commonly used BCG vaccines in Brazil, Argentina and Venezuela.
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- 2020
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49. First Record of a B Chromosome in Polybia fastidiosuscula Saussure (Vespidae) and Investigation of Chromatin Composition Through Microsatellite Mapping.
- Author
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Marchioro P, Campos LAO, and Lopes DM
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- Animals, Base Pairing, Base Sequence, Brazil, Chromosome Banding, Female, RNA, Ribosomal, 18S genetics, Wasps classification, Chromatin genetics, Chromosomes, Insect genetics, Karyotype, Microsatellite Repeats genetics, Wasps genetics
- Abstract
The characterization of karyotypes is an important aspect in understanding the structure and evolution of genomes. Polybia is a genus of social wasps of the family Vespidae. This genus has 58 species, but for only 8 of these chromosome number and morphology have been reported in the literature. The aim of this study was to describe and characterize the Polybia fastidiosuscula Saussure karyotype, presenting the first case of a B chromosome in Vespidae. In addition, we investigated the chromatin composition of this species through C-banding, base-specific fluorochrome staining, and physical mapping of 7 microsatellites and 18S rDNA. Four colonies of P. fastidiosuscula from Minas Gerais and Paraná states, Brazil, were analyzed. The chromosome number identified was 2n = 34, and 2 colonies presented a B chromosome. We characterized the chromatin composition of this species, analyzing the existence of different microsatellite-rich heterochromatic regions which are also enriched with AT or GC base pairs. We suggest an intraspecific origin of the B chromosome based on the homology of the heterochromatic composition with A chromosomes and also verify that the TTAGG and TCAGG sequences are not telomeric, but only microsatellites that occur in the centromeres of most chromosomes, as well as GAG and CGG., (© 2021 S. Karger AG, Basel.)
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- 2020
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50. Multidrug-resistant CTX-M-15-positive Klebsiella pneumoniae ST307 causing urinary tract infection in a dog in Brazil.
- Author
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Sartori L, Sellera FP, Moura Q, Cardoso B, Cerdeira L, and Lincopan N
- Subjects
- Animals, Anti-Bacterial Agents pharmacology, Bacterial Proteins genetics, Base Sequence, Brazil, Dogs, Drug Resistance, Multiple, Bacterial drug effects, Drug Resistance, Multiple, Bacterial genetics, Genome Size, Genome, Bacterial, Klebsiella pneumoniae isolation & purification, Microbial Sensitivity Tests, Multilocus Sequence Typing, Virulence Factors genetics, Whole Genome Sequencing, Dog Diseases microbiology, Klebsiella Infections microbiology, Klebsiella pneumoniae enzymology, Klebsiella pneumoniae genetics, Urinary Tract Infections microbiology, beta-Lactamases genetics, beta-Lactamases metabolism
- Abstract
Objectives: Klebsiella pneumoniae sequence type 307 (ST307) has emerged as a new high-risk clone worldwide. The aim of this study was to report the draft genome sequence of a multidrug-resistant CTX-M-15-positive K. pneumoniae strain causing urinary tract infection in a companion animal in Brazil., Methods: Whole-genome sequencing was performed on an Illumina NextSeq platform and the genome was de novo assembled using SPAdes. Data analysis was performed using online tools from the Center for Genomic Epidemiology., Results: The genome size of K. pneumoniae strain PRETA was calculated at 5 450 575 bp, containing a total of 5355 protein-coding sequences. The strain was assigned to the high-risk ST307 and carried the clinically relevant bla
CTX-M-15 gene, besides other genes conferring resistance to aminoglycosides, tetracyclines, quinolones, trimethoprim and fosfomycin., Conclusion: These data offer novel information for comparative genomic analyses in order to track the transmission dynamics and epidemiology of the newly emerging high-risk clone ST307., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)- Published
- 2019
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