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The three programs that make up the Immune Mechanisms of Protection Against Mycobacterium tuberculosis Centers (IMPAc-TB) had to prioritize and select strains to be leveraged for this work. The CASCADE team based at Seattle Children's Research Institute are leveraging M.tb H37Rv, M.tb CDC1551, and M.tb SA161. The HI-IMPACT team based at Harvard T.H. Chan School of Public Health, Boston, have selected M.tb Erdman as well as a novel clinical isolate recently characterized during a longitudinal study in Peru. The PHOENIX team also based at Seattle Children's Research Institute have selected M.tb HN878 and M.tb Erdman as their isolates of choice. Here, we describe original source isolation, genomic references, key virulence characteristics, and relevant tools that make these isolates attractive for use. The global context for M.tb lineage 2 and 4 selection is reviewed including what is known about their relative abundance and acquisition of drug resistance. Host–pathogen interactions seem driven by genomic differences on each side, and these play an important role in pathogenesis and immunity. The few M.tb strains chosen for this work do not reflect the vast genomic diversity within this species. They do, however, provide specific virulence, pathology, and growth kinetics of interest to the consortium. The strains selected should not be considered as "representative" of the growing available array of M.tb isolates, but rather tools that are being used to address key outstanding questions in the field. [ABSTRACT FROM AUTHOR]

Tuberculosis is a global public health concern. Earlier reports suggested the emergence of high rates of drug resistant tuberculosis in Egypt. This study included 102 isolates of Mycobacterium tuberculosis collected from two reference laboratories in Cairo and Alexandria. All clinical isolates were sub-cultured on Löwenstein–Jensen medium and analyzed using both BD BACTEC MGIT 960 SIRE Kit and standard diffusion disk assays to identify the antibiotic sensitivity profile. Extracted genomic DNA was subjected to whole genome sequencing (WGS) using Illumina platform. Isolates that belong to lineage 4 represented > 80%, while lineage 3 represented only 11% of the isolates. The percentage of drug resistance for the streptomycin, isoniazid, rifampicin and ethambutol were 31.0, 17.2, 19.5 and 20.7, respectively. Nearly 47.1% of the isolates were sensitive to the four anti-tuberculous drugs, while only one isolate was resistant to all four drugs. In addition, several new and known mutations were identified by WGS. High rates of drug resistance and new mutations were identified in our isolates. Tuberculosis control measures should focus on the spread of mono (S, I, R, E)- and double (S, E)-drug resistant strains present at higher rates throughout the whole Nile Delta, Egypt. [ABSTRACT FROM AUTHOR]

In early 2024, explosive outbreaks of Oropouche virus (OROV) linked to a novel lineage were documented in the Amazon Region of Brazil. We report the introduction of this lineage into Colombia and its co-circulation with another OROV lineage. Continued surveillance is needed to prevent further spread of OROV in the Americas.

Abstract Tuberculosis is a global public health concern. Earlier reports suggested the emergence of high rates of drug resistant tuberculosis in Egypt. This study included 102 isolates of Mycobacterium tuberculosis collected from two reference laboratories in Cairo and Alexandria. All clinical isolates were sub-cultured on Löwenstein–Jensen medium and analyzed using both BD BACTEC MGIT 960 SIRE Kit and standard diffusion disk assays to identify the antibiotic sensitivity profile. Extracted genomic DNA was subjected to whole genome sequencing (WGS) using Illumina platform. Isolates that belong to lineage 4 represented > 80%, while lineage 3 represented only 11% of the isolates. The percentage of drug resistance for the streptomycin, isoniazid, rifampicin and ethambutol were 31.0, 17.2, 19.5 and 20.7, respectively. Nearly 47.1% of the isolates were sensitive to the four anti-tuberculous drugs, while only one isolate was resistant to all four drugs. In addition, several new and known mutations were identified by WGS. High rates of drug resistance and new mutations were identified in our isolates. Tuberculosis control measures should focus on the spread of mono (S, I, R, E)- and double (S, E)-drug resistant strains present at higher rates throughout the whole Nile Delta, Egypt.

Aedes aegypti is an important mosquito vector of human disease with a wide distribution across the globe. Climatic conditions and ecological pressure drive differences in the biology of several populations of this mosquito species, including blood‐feeding behaviour and vector competence. However, no study has compared activity and/or sleep among different populations/lineages of Ae. aegypti. Having recently established sleep‐like states in three mosquito species with observable differences in timing and amount of sleep among species, we investigated differences in activity and sleep levels among 17 Ae. aegypti lines drawn from both its native range in Africa and its invasive range across the global tropics. Activity monitoring indicates that all the lines show consistent diurnal activity, but significant differences in activity level, sleep amount, number of sleep bouts and bout duration were observed among the lines. The variation in day activity was associated with differences in host preference and ancestry for the lineages collected in Africa. This study provides evidence that the diurnal sleep and activity profiles for Ae. aegypti are consistent, but there are significant population differences for Ae. aegypti sleep and activity levels and interactions with host species may significantly impact mosquito activity. [ABSTRACT FROM AUTHOR]

Background: Human papillomavirus 16 (HPV16) is an oncogenic virus responsible for the majority of invasive cervical cancer cases worldwide. Due to genetic modifications, some variants are more oncogenic than others. We analysed the HPV16 phylogeny in HPV16-positive cervical Desoxyribonucleic Acid (DNA) samples collected from South African and Mozambican women to detect the circulating lineages. Methods: Polymerase chain reaction (PCR) amplification of the long control region (LCR) and 300 nucleotides of the E6 region was performed using HPV16-specific primers on HPV16-positive cervical samples collected in women from South Africa and Mozambique. HPV16 sequences were obtained through Next Generation Sequencing (NGS) methods. Geneious prime and MEGA 11 software were used to align the sequences to 16 HPV16 reference sequences, gathering the A, B, C, and D lineages and generating the phylogenetic tree. Single nucleotide polymorphisms (SNPs) in the LCR and E6 regions were analysed and the phylogenetic tree was generated using Geneious Prime software. Results: Fifty-eight sequences were analysed. Of these sequences, 79% (46/58) were from women who had abnormal cervical cytology. Fifteen SNPs in the LCR and eight in the E6 region were found to be the most common in all sequences. The phylogenetic analysis determined that 45% of the isolates belonged to the A1 sublineage (European variant), 34% belonged to the C1 sublineage (African 1 variant), 16% belonged to the B1 and B2 sublineage (African 2 variant), two isolates belonged to the D1–3 sublineages (Asian-American variant), and one to the North American variant. Conclusions: The African and European HPV16 variants were the most common circulating lineages in South African and Mozambican women. A high-grade squamous intraepithelial lesion (HSIL) was the most common cervical abnormality observed and linked to European and African lineages. These findings may contribute to understanding molecular HPV16 epidemiology in South Africa and Mozambique. [ABSTRACT FROM AUTHOR]

Rotavirus remains a significant public health threat, especially in low-income countries, where it is the leading cause of severe acute childhood gastroenteritis, contributing to over 128,500 deaths annually. Although the introduction of the Rotarix and RotaTeq vaccines in 2006 marked a milestone in reducing mortality rates, approximately 83,158 preventable deaths persisted, showing ongoing challenges in vaccine accessibility and effectiveness. To address these issues, a novel subcutaneous vaccine formulation targeting multiple rotavirus genotypes has been developed. This vaccine consists of nine VP8* proteins from nine distinct rotavirus genotypes and sub-genotypes (P[4], P[6], P[8]LI, P[8]LIII, P[8]LIV, P[9], P[11], P[14], and P[25]) expressed in E. coli. Two groups of mice were immunized either with a single immunogen, the VP8* from the rotavirus Wa strain (P[8]LI), or with the nonavalent formulation. Preliminary results from mouse immunization studies showed promising outcomes, eliciting antibody responses against six of the nine immunogens. Notably, significantly higher antibody titers against VP8* P[8]LI were observed in the group immunized with the nonavalent vaccine compared to mice specifically immunized against this genotype alone. Overall, the development of parenteral vaccines targeting multiple rotavirus genotypes represents a promising strategy in mitigating the global burden of rotavirus-related morbidity and mortality, offering new avenues for disease prevention and control. [ABSTRACT FROM AUTHOR]

Five phylogenetic lineages were observed by present author in the eleven Tethyan Maastrichtian planktic foraminiferal species of the genus Plummerita. These lineages help to define the major faunal changes from the species throughout of three groups of the Plummerita. The first group (P. haggagae group) belongs to the four-chambered volition (4-ch) with axially pointed spine-like prolongation evolved to another species of five-chambered volition (5-ch) (P. hantkeninoides group), to another species of six-chambered volition (6-ch) (P. reicheli group). The five lineages are: (1) The Plummerita elkefensis (4-ch) to P. hantkeninoides (5-ch), (2) P. haggagae (4-ch) to P. costata (5-ch) to P. spainica (6-ch), (3) P. inflata (5-ch) to P. tunisica (6-ch) (4) P. kellerae (5-ch) to P. caribbeanica (6-ch), (5) P. premolisilvae (5-ch) to P. reicheli (6-ch). Unfortunately, most of these lineage are uncompleted from four to five to six-chamber volution, while only one of them is completed (no. 2). In spite of this uncompleted lineages situation, it seems that we must await further study to complete these lineages by another unknown taxa. [ABSTRACT FROM AUTHOR]

Multiparameter flow cytometry is a routine method in immunological studies incorporated in biomedical, veterinary, agricultural, and wildlife research and routinely used in veterinary clinical laboratories. Its use in the diagnostics of poultry diseases is still limited, but due to the continuous expansion of reagents and cost reductions, this may change in the near future. Although the structure and function of the avian immune system show commonalities with mammals, at the molecular level, there is often low homology across species. The cross-reactivity of mammalian immunological reagents is therefore low, but nevertheless, the list of reagents to study chicken immune cells is increasing. Recent improvement in multicolor antibody panels for chicken cells has resulted in more detailed analysis by flow cytometry and has allowed the discovery of novel leukocyte cell subpopulations. In this article, we present an overview of the reagents and guidance needed to perform multicolor flow cytometry using chicken samples and common pitfalls to avoid. [ABSTRACT FROM AUTHOR]

Background: Since severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) was first reported in Wuhan, China, in December 2019, it has spread rapidly, and many coronavirus disease (COVID‐19) cases have occurred in Gwangju, South Korea. Viral mutations following the COVID‐19 epidemic have increased interest in the characteristics of epidemics in this region, and pathogen genetic analysis is required for infection control and prevention. Methods: In this study, SARS‐CoV‐2 whole‐genome analysis was performed on samples from patients with COVID‐19 in Gwangju from 2020 to 2022 to identify the trends in COVID‐19 prevalence and to analyze the phylogenetic relationships of dominant variants. B.41 and B.1.497 prevailed in 2020, the early stage of the COVID‐19 outbreak; then, B.1.619.1 mainly occurred until June 2021. B.1.617.2, classified as sublineages AY.69 and AY.122, occurred continuously from July to December 2021. Since strict measures to strengthen national quarantine management had been implemented in South Korea until this time, the analysis of mutations was also able to infer the epidemiological relationship between infection transmission routes. Since the first identification of the Omicron variant in late December 2021, the spread of infection has been very rapid, and weekly whole‐genome analysis of specimens has enabled us to monitor new Omicron sublineages occurring in Gwangju. Conclusions: Our study suggests that conducting regional surveillance in addition to nation‐level genomic surveillance will enable more rapid and detailed variant surveillance, which will be helpful in the overall prevention and management of infectious diseases. [ABSTRACT FROM AUTHOR]

Marseilleviruses (MsV) are a group of viruses that compose the Marseilleviridae family within the Nucleocytoviricota phylum. They have been found in different samples, mainly in freshwater. MsV are classically organized into five phylogenetic lineages (A/B/C/D/E), but the current taxonomy does not fully represent all the diversity of the MsV lineages. Here, we describe a novel strain isolated from a Brazilian saltwater sample named Marseillevirus cajuinensis. Based on genomics and phylogenetic analyses, M. cajuinensis exhibits a 380,653-bp genome that encodes 515 open reading frames. Additionally, M. cajuinensis encodes a transfer RNA, a feature that is rarely described for Marseilleviridae. Phylogeny suggests that M. cajuinensis forms a divergent branch within the MsV lineage A. Furthermore, our analysis suggests that the common ancestor for the five classical lineages of MsV diversified into three major groups. The organization of MsV into three main groups is reinforced by a comprehensive analysis of clusters of orthologous groups, sequence identities, and evolutionary distances considering several MsV isolates. Taken together, our results highlight the importance of discovering new viruses to expand the knowledge about known viruses that belong to the same lineages or families. This work proposes a new perspective on the Marseilleviridae lineages organization that could be helpful to a future update in the taxonomy of the Marseilleviridae family. IMPORTANCE Marseilleviridae is a family of viruses whose members were mostly isolated from freshwater samples. In this work, we describe the first Marseillevirus isolated from saltwater samples, which we called Marseillevirus cajuinensis. Most of M. cajuinensis genomic features are comparable to other Marseilleviridae members, such as its high number of unknown proteins. On the other hand, M. cajuinensis encodes a transfer RNA, which is a gene category involved in protein translation that is rarely described in this viral family. Additionally, our phylogenetic analyses suggested the existence of, at least, three major Marseilleviridae groups. These observations provide a new perspective on Marseilleviridae lineages organization, which will be valuable in future updates to the taxonomy of the family since the current official classification does not capture all the Marseilleviridae known diversity. [ABSTRACT FROM AUTHOR]

The three programs that make up the Immune Mechanisms of Protection Against Mycobacterium tuberculosis Centers (IMPAc-TB) had to prioritize and select strains to be leveraged for this work. The CASCADE team based at Seattle Children’s Research Institute are leveraging M.tb H37Rv, M.tb CDC1551, and M.tb SA161. The HI-IMPACT team based at Harvard T.H. Chan School of Public Health, Boston, have selected M.tb Erdman as well as a novel clinical isolate recently characterized during a longitudinal study in Peru. The PHOENIX team also based at Seattle Children’s Research Institute have selected M.tb HN878 and M.tb Erdman as their isolates of choice. Here, we describe original source isolation, genomic references, key virulence characteristics, and relevant tools that make these isolates attractive for use. The global context for M.tb lineage 2 and 4 selection is reviewed including what is known about their relative abundance and acquisition of drug resistance. Host–pathogen interactions seem driven by genomic differences on each side, and these play an important role in pathogenesis and immunity. The few M.tb strains chosen for this work do not reflect the vast genomic diversity within this species. They do, however, provide specific virulence, pathology, and growth kinetics of interest to the consortium. The strains selected should not be considered as “representative” of the growing available array of M.tb isolates, but rather tools that are being used to address key outstanding questions in the field.

ABSTRACT The objective was to verify the existence of lineages in the Mangalarga Marchador breed using microsatellites and to phenotypically characterize the lineages found using linear morphometric measurements taken at the time the animals were registered to be used as a tool for selecting individuals according to each breeder’s selection objective. The genotyping database contained 255,257 Mangalarga Marchador horses born between 2005 and 2021. In addition, a database was used with pedigree information on 622,299 animals born between 1952 and 2020 and a database of phenotypes assessed at the time of definitive registration of these animals, containing 303,248 animals born between 1950 and 2018. The databases used came from the Associação Brasileira dos Criadores do Cavalo Mangalarga Marchador. To verify the existence of genetic differences according to the lineages of the breed, a discriminant analysis of principal components (DAPC) and the Kruskall Wallis test were carried out to perform phenotypic characterization to compare the means of the morphometric measurements, both using the R software. The DAPC analysis showed the genetic differentiation of the Angaí and Herdade lineages in relation to the others. The Herdade lineage showed greater phenotypic differentiation when compared with the three separate genetic groups in this study, demonstrating that the animals of this lineage are smaller and more gathered and have higher scores for gait and morphology. When compared to the historically described Mangalarga Marchador lineages, the breed does not have so many genetic groups, separating it into just three groups (Angaí, Herdade, and General), and when compared to phenotypic characteristics, only the Herdade lineage stood out.

The etiological agent of coronavirus disease (COVID-19) that emerged at the end of year 2019 was first reported in Wuhan, China and was found to be SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2). The massive COVID-19 waves were due to various variants. As per the reports of other study it was also found that Omicron variant spread faster than various other variant such as delta variant. Omicron has been reported from various countries and now from many states of India too. Therefore, keeping this in mind, this study was undertaken to study all the lineages of SARS-CoV-2 Omicron variant of disease COVID-19 that are circulating in the population of Uttarakhand with objective to study next generation sequencing of all the RT-PCR positive of SARS-CoV-2 and to find out all the lineages of the Omicron variant of SARS-CoV-2. This was a retrospective study conducted from 1st January 2022 to 30th September 2022. Next generation sequencing was performed on all the samples that were tested for COVID-19 by using Ion AmpliSeq kit on Ion Chef instrument. A total of 2149 samples were tested in which majority of samples belong to age group of 21-40 years. Males were affected more than females. BA.2 was found to be the predominant lineage of total of 46 lineages that were identified. Their mutations were also studied. We conclude that different variants of clade 21L, 22B, 22D and Omicron subvariant BA.2, BA.2.38 and BA.2.75 were the ones that were circulating amongst the population of Uttarakhand. The characteristic mutation that was found were T19I and V213G in NTD, S373P, S375F, T376A, and D405N in RBD.

ObjectiveTo interrogate the circulating SARS-CoV-2 lin-eages and recombinant variants in persons living in migrant shelters and persons who inject drugs (PWID).Materials and methodsWe combined data from two studies with marginalized populations (migrants in shelters and persons who inject drugs) in Tijuana, Mexico. SARS-CoV-2 variants were identified on nasal swabs specimens and compared to publicly available genomes sampled in Mexico and California.ResultsAll but 2 of the 10 lineages identified were predomi-nantly detected in North and Central America. Discrepan-cies between migrants and PWID can be explained by the temporal emergence and short time span of most of these lineages in the region.ConclusionThe results illustrate the temporo-spatial structure for SARS-CoV-2 lineage dispersal and the potential co-circulation of multiple lineages in high-risk populations with close social contacts. These conditions create the potential for recombination to take place in the California-Baja California border.

The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions. [ABSTRACT FROM AUTHOR]

The etiological agent of coronavirus disease (COVID-19) that emerged at the end of year 2019 was first reported in Wuhan, China and was found to be SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2). The massive COVID-19 waves were due to various variants. As per the reports of other study it was also found that Omicron variant spread faster than various other variant such as delta variant. Omicron has been reported from various countries and now from many states of India too. Therefore, keeping this in mind, this study was undertaken to study all the lineages of SARS-CoV-2 Omicron variant of disease COVID-19 that are circulating in the population of Uttarakhand with objective to study next generation sequencing of all the RT-PCR positive of SARS-CoV-2 and to find out all the lineages of the Omicron variant of SARS-CoV-2. This was a retrospective study conducted from 1st January 2022 to 30th September 2022. Next generation sequencing was performed on all the samples that were tested for COVID-19 by using Ion AmpliSeq kit on Ion Chef instrument. A total of 2149 samples were tested in which majority of samples belong to age group of 21-40 years. Males were affected more than females. BA.2 was found to be the predominant lineage of total of 46 lineages that were identified. Their mutations were also studied. We conclude that different variants of clade 21L, 22B, 22D and Omicron subvariant BA.2, BA.2.38 and BA.2.75 were the ones that were circulating amongst the population of Uttarakhand. The characteristic mutation that was found were T19I and V213G in NTD, S373P, S375F, T376A, and D405N in RBD. [ABSTRACT FROM AUTHOR]

Disease management and epidemiological investigations of porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2) often rely on grouping together highly related sequences. In the USA, the last five years have seen a major shift within the swine industry when classifying PRRSV-2, beginning to move away from RFLP (restriction fragment length polymorphisms)-typing and adopting the use of phylogenetic lineage-based classification. However, lineages and sub-lineages are large and genetically diverse, making them insufficient for identifying new and emerging variants. Thus, within the lineage system, a dynamic fine-scale classification scheme is needed to provide better resolution on the relatedness of PRRSV-2 viruses to inform disease management and monitoring efforts and facilitate research and communication surrounding circulating PRRSV viruses. Here, we compare fine-scale systems for classifying PRRSV-2 variants (i.e., genetic clusters of closely related ORF5 sequences at finer scales than sub-lineage) using a database of 28,730 sequences from 2010 to 2021, representing >55% of the U.S. pig population. In total, we compared 140 approaches that differed in their tree-building method, criteria, and thresholds for defining variants within phylogenetic trees. Three approaches resulted in variant classifications that were reproducible and robust even when the input data or input phylogenies were changed. For these approaches, the average genetic distance among sequences belonging to the same variant was 2.1–2.5%, and the genetic divergence between variants was 2.5–2.7%. Machine learning classification algorithms were trained to assign new sequences to an existing variant with >95% accuracy, which shows that newly generated sequences can be assigned to a variant without repeating the phylogenetic and clustering analyses. Finally, we identified 73 sequence-clusters (dated

The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. A total of 7540 complete nucleotide genomes from 51 African nations were obtained and analysed using the National Center for Biotechnology Information and Global Initiative on Sharing Influenza Data databases to examine the genetic diversity and spread dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Using various clade and lineage nomenclature schemes, we examined their diversity and used maximum parsimony inference methods to reconstruct the evolutionary hypotheses about the spread of the virus in Africa. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa three years after the COVID-19 pandemic, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya and Nigeria as key sources of viral transmission among sub-Saharan African nations. These findings provide insights into the viral strains that circulate in Africa and their evolutionary patterns.

Background: The genetic diversity of Mycobacterium tuberculosis complex (MTBC) strains was characterized among isolates from individuals with pulmonary tuberculosis (PTB) symptoms attended holy water sites (HWSs) in the Amhara region, Ethiopia. Methods: A cross-sectional study was done from June 2019 to March 2020 to describe the genetic diversity and drug-resistance profiles of MTBC isolates. Sputum specimens were collected and cultured in the Löwenstein-Jensen culture medium. Line Probe Assay, MTBDRplus VER 2.0, and MTBDRsl VER 2.0 were used to detect first-and second-line anti-TB drug-resistance patterns. A spoligotyping technique was utilized to characterize the genetic diversity. Statistical analysis was performed using STATA 15. Results: Of 560 PTB-symptomatic participants, 122 (21.8%) were culture-positive cases. Spoligotyping of 116 isolates revealed diverse MTBC sublineages, with four major lineages: Euro-American (EA) (Lineage 4), East-African-Indian (EAI) (Lineage 3), Ethiopian (ETH) (Lineage 7), East Asian (EA) (Lineage 2). The majority (96.6%) of the isolates were EA (lineage 4) and EAI, with proportions of 54.3% and 42.2%, respectively. A total of 31 spoligotype patterns were identified, 26 of which were documented in the SITVIT2 database. Of these, there were 15 unique spoligotypes, while eleven were grouped with 2-17 isolates. SIT149/T3-ETH (n = 17), SIT26/CAS1-DELHI (n = 16), SIT25/CAS1-DELHI (n = 12), and SIT52/T2 (n = 11) spoligotypes were predominant. A rare spoligotype pattern: SIT41/Turkey and SIT1/Beijing, has also been identified in North Shewa. The overall clustering rate of sub-lineages with known SIT was 76.4%.Of the 122 culture-positive isolates tested, 16.4% were resistant to rifampicin (RIF) and/or isoniazid (INH). Multidrug-resistant TB (MDR-TB) was detected in 12.3% of isolates, five of which were fluoroquinolones (FLQs) resistant. SIT149/T3-ETH and SIT21/CAS1-KILI sublineages showed a higher proportion of drug resistance. Conclusions: Diverse MTBC spoligotypes were identified, with the T and CAS families and EA (lineage 4) predominating. A high prevalence of drug-resistant TB, with SIT149/T3-ETH and CAS1-KILI sublineages comprising a greater share, was observed. A study with large sample size and a sequencing method with stronger discriminatory power is warranted to understand better the genetic diversity of circulating MTBC in this cohort of study, which would help to adopt targeted interventions.

The discovery of the fungal pathogen Ophidiomyces ophidiicola (Oo), the aetiologic agent of Snake Fungal Disease (SFD), has raised a growing interest in the North American and European scientific communities, in particular toward conservation. This pathogen is known or suspected to be associated with the declines of some snake populations in North America and was detected later in Europe. Its ecology, distribution and phylogeography still remain largely unknown. In this study, we collected skin swabs from 271 free-ranging snakes in Switzerland across 8 different species and 13 sites. The overall pathogen prevalence was at least 28% with sequences consistent with both the European and the North American lineages (respectively Clade I and II) of Oo. Semi-aquatic snakes were more likely to be infected by Oo , and high human disturbance (human frequentation and direct impact on snakes) was associated with a higher Oo prevalence, whereas season, body condition and snake species introduction was not. This study suggests that Switzerland might represent a region characterised by high genetic variability in Oo , and where long-term monitoring might be particularly important to follow the evolution of the disease in free-ranging snakes. [ABSTRACT FROM AUTHOR]

Background: The tuberculosis (TB) epidemic remains a major global health problem, particularly in Eswatini. Our study aimed to investigate the circulating genotypes in Eswatini and to determine genotype changes of susceptible Mycobacterium tuberculosis (M. tb) genotypes when they develop into multidrug-resistant tuberculosis (MDR-TB) genotypes during treatment. Methods: Participants (n = 390) were prospectively enrolled from referral clinics and patients who met the inclusion criteria were included in the study. A total of 206 M. tb strains were detected at baseline and follow-up (at six months or the last positive sample from a treated patient) by GeneXpert® MTB/RIF assay (Cepheid, USA) and microscopy, respectively. The decontaminated specimens were processed on the BACTEC™ Mycobacteria Growth Indicator Tube (MGIT™) 960 Mycobacteria Culture System (Becton Dickinson, USA) for culture drug sensitivity testing (DST) at both baseline and follow-up. Spoligotyping was performed on both baseline and follow-up strains. The study results were analysed using the Statistical Package for the Social Sciences (SPSS) version 25 software and STATA. Results: A total of 82.5% (170/206) of genotypes had valid spoligotyping patterns, with 4 lineages and 20 genotypes. The distribution of the lineages varied among the different regions in Eswatini. A high proportion of the Beijing genotype at 24.27% (50/206) and the S genotype at 16.50% (34/206) were detected. Furthermore, the Beijing genotype strain was predominantly found in followup genotypes from the Manzini region with 48.9% (23/47), which was significant. A significant proportion of follow-up specimens developed MDR-TB (p = 0.001), with the Beijing genotype being the major genotype in most follow-up specimens (p < 0.000). Conclusion: In Eswatini, the Beijing genotype is associated with MDR-TB in follow-up specimens, which indicates community-wide transmission. [ABSTRACT FROM AUTHOR]

The diverse climate types and geographical structures across Anatolia result in a high level of species diversity. Among these, the lizard species Lacerta diplochondrodes exhibits several distinct populations, with some of them recognized as subspecies. The primary objective of our study was to investigate whether populations from Thrace and the Western Black Sea region of Türkiye differ from other documented populations. For this purpose, we conducted a comprehensive analysis of genetic and morphometric parameters. For the genetic analysis, we utilized the COI and cyt-b gene regions as molecular markers. Principal Component Analysis (PCA) and Canonical Discriminant Analysis (CDA) were used for the morphometric analyses to differentiate populations. Our findings indicate that a population found in the Bolu region in Western Black Sea region of Turkey differs from the other populations both in morphometric and genetic traits. The L. d. diplochondrodes and L. d. cariensis populations represent sister lineages, and they are both genetically and morphologically only weakly differentiated. These two lineages are therefore referred to as L. d. diplochondrodes. Overall, four different lineages can be distinguished in Türkiye, out of which the lineage of the Western Black Sea region (Bolu lineage) is described for the first time. [ABSTRACT FROM AUTHOR]

Multiparameter flow cytometry is a routine method in immunological studies incorporated in biomedical, veterinary, agricultural, and wildlife research and routinely used in veterinary clinical laboratories. Its use in the diagnostics of poultry diseases is still limited, but due to the continuous expansion of reagents and cost reductions, this may change in the near future. Although the structure and function of the avian immune system show commonalities with mammals, at the molecular level, there is often low homology across species. The cross-reactivity of mammalian immunological reagents is therefore low, but nevertheless, the list of reagents to study chicken immune cells is increasing. Recent improvement in multicolor antibody panels for chicken cells has resulted in more detailed analysis by flow cytometry and has allowed the discovery of novel leukocyte cell subpopulations. In this article, we present an overview of the reagents and guidance needed to perform multicolor flow cytometry using chicken samples and common pitfalls to avoid.

Background: Human papillomavirus 16 (HPV16) is an oncogenic virus responsible for the majority of invasive cervical cancer cases worldwide. Due to genetic modifications, some variants are more oncogenic than others. We analysed the HPV16 phylogeny in HPV16-positive cervical Desoxyribonucleic Acid (DNA) samples collected from South African and Mozambican women to detect the circulating lineages. Methods: Polymerase chain reaction (PCR) amplification of the long control region (LCR) and 300 nucleotides of the E6 region was performed using HPV16-specific primers on HPV16-positive cervical samples collected in women from South Africa and Mozambique. HPV16 sequences were obtained through Next Generation Sequencing (NGS) methods. Geneious prime and MEGA 11 software were used to align the sequences to 16 HPV16 reference sequences, gathering the A, B, C, and D lineages and generating the phylogenetic tree. Single nucleotide polymorphisms (SNPs) in the LCR and E6 regions were analysed and the phylogenetic tree was generated using Geneious Prime software. Results: Fifty-eight sequences were analysed. Of these sequences, 79% (46/58) were from women who had abnormal cervical cytology. Fifteen SNPs in the LCR and eight in the E6 region were found to be the most common in all sequences. The phylogenetic analysis determined that 45% of the isolates belonged to the A1 sublineage (European variant), 34% belonged to the C1 sublineage (African 1 variant), 16% belonged to the B1 and B2 sublineage (African 2 variant), two isolates belonged to the D1–3 sublineages (Asian-American variant), and one to the North American variant. Conclusions: The African and European HPV16 variants were the most common circulating lineages in South African and Mozambican women. A high-grade squamous intraepithelial lesion (HSIL) was the most common cervical abnormality observed and linked to European and African lineages. These findings may contribute to understanding molecular HPV16 epidemiology in South Africa and Mozambique.

Rotavirus remains a significant public health threat, especially in low-income countries, where it is the leading cause of severe acute childhood gastroenteritis, contributing to over 128,500 deaths annually. Although the introduction of the Rotarix and RotaTeq vaccines in 2006 marked a milestone in reducing mortality rates, approximately 83,158 preventable deaths persisted, showing ongoing challenges in vaccine accessibility and effectiveness. To address these issues, a novel subcutaneous vaccine formulation targeting multiple rotavirus genotypes has been developed. This vaccine consists of nine VP8* proteins from nine distinct rotavirus genotypes and sub-genotypes (P[4], P[6], P[8]LI, P[8]LIII, P[8]LIV, P[9], P[11], P[14], and P[25]) expressed in E. coli. Two groups of mice were immunized either with a single immunogen, the VP8* from the rotavirus Wa strain (P[8]LI), or with the nonavalent formulation. Preliminary results from mouse immunization studies showed promising outcomes, eliciting antibody responses against six of the nine immunogens. Notably, significantly higher antibody titers against VP8* P[8]LI were observed in the group immunized with the nonavalent vaccine compared to mice specifically immunized against this genotype alone. Overall, the development of parenteral vaccines targeting multiple rotavirus genotypes represents a promising strategy in mitigating the global burden of rotavirus-related morbidity and mortality, offering new avenues for disease prevention and control.

Abstract Background The tuberculosis (TB) epidemic remains a major global health problem and Eswatini is not excluded. Our study investigated the circulating genotypes in Eswatini and compared them at baseline (start of treatment) and follow-up during TB treatment. Methods Three hundred and ninety (n = 390) participants were prospectively enrolled from referral clinics and patients who met the inclusion criteria, were included in the study. A total of 103 participants provided specimens at baseline and follow-up within six months. Mycobacterium tuberculosis (M.tb) strains were detected by GeneXpert® MTB/RIF assay (Cephied, USA) and Ziehl -Neelsen (ZN) microscopy respectively at baseline and follow-up time-points respectively. The 206 collected specimens were decontaminated and cultured on BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA). Drug sensitivity testing was performed at both baseline and follow-up time points. Spoligotyping was performed on both baseline and follow-up strains after DNA extraction. Results Resistance to at least one first line drug was detected higher at baseline compared to follow-up specimens with most of them developing into multidrug-resistant (MDR)-TB. A total of four lineages and twenty genotypes were detected. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 46.12% (95/206) followed by the East Asian with 24.27% (50/206); Indo-Oceanic at 9.71% (20/206) and Central Asian at 1.94% (4/206). Furthermore, a high proportion of the Beijing genotype at 24.27% (50/206) and S genotype at 16.50% (34/206) were detected. The Beijing genotype was predominant in follow-up specimens collected from the Manzini region with 48.9% (23/47) (p = 0.001). A significant proportion of follow-up specimens developed MDR-TB (p = 0.001) with Beijing being the major genotype in most follow-up specimens (p

Abstract Background Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. Results Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. Conclusion Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh.

Assisted reproductive technologies are key to maintain genetic stocks of endangered wild species, such as the Iberian ibex (Capra pyrenaica). Due to the low availability of ibex ovaries, heterologous in vitro fertilization (IVF) with domestic goat (Capra hircus) oocytes constitutes an excellent alternative to determine the fertilization capacity of ibex sperm doses. The aim of this study was to optimize heterologous ibex-goat IVF procedures by testing two different IVF media (TALP and SOF) and to determine whether estrous sheep serum (ESS) is required for fertilization. We found that TALP medium provides optimal conditions to conduct heterologous ibex-goat IVF, yielding blastocyst rates above 50%, and that supplementation with ESS is not required. No differences were found in embryo quality between embryos fertilized in TALP, SOF alone, or SOF supplemented with 2 or 20% ESS, based on the analysis of cell lineages development at day (D) 8 and D10 of development. Optimized heterologous ibex-goat IVF, together with embryo quality assessment through lineages development analysis, constitute an excellent system to assess fertilization capacity of ibex sperm doses, and opens the possibility of performing homologous in vitro embryo production in this species.

IntroductionRecombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants.MethodWhole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points.ResultsMutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis.ConclusionTogether, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.

The objectives of the present study were to isolate and identify Listeria monocytogenes in salad vegetables and milk products sold in different markets of Mymensingh district in Bangladesh, and to characterize this organism (serogroups, virulence genes) along with antibiogram study. A total of 85 samples of salad vegetables (tomato, carrot and cucumber) were collected from six different markets of five upazilas of Mymensingh district, and 83 milk products such as cheese, yogurt and icecream of two available brands were collected from Mymensingh sadar upazila. Isolation and identification of Listeria monocytogenes was done by cultural, biochemical, PCR and MALDI-TOF assays. The presence of serogroups (lineage I, lineage II, lineage III) and virulence-associated genes (inlA, actA, prfA, and hlyA) were determined by multiplex PCR. The antimicrobial susceptibility test of the isolates was done with 22 antimicrobial agents using disk diffusion assay. The overall prevalence of L. monocytogenes was 7.1%. Among salad vegetables, contamination of cucumber was highest (19.2%), and among milk products, the highest contamination was in icecream (7.1%). Five isolates (41.7%) belonged to Lineage II and seven isolates (58.3%) to Lineage III. Only two isolates (16.67%) harbored one or more virulence-associated genes. The highest resistance was observed to oxacillin and nalidixic acid followed by erythromycin and meropenem. Findings of the present study would be useful to evaluate the risk posed by salad vegetables and milk products, and to the concerned authorities for eventual future food regulations.

Recently, the concept of "cultural governance" has gained analytical traction in research on Chinese urban development. This is mostly diagnosed as a top-down process of defining and imposing cultural forms in government-led projects, such as in tourism. We argue that the case of Shenzhen manifests important differences, and is highly significant, considering the national and international status of this mega-city. Based on detailed field studies, supplemented with information about other cases, we show that in Shenzhen local cultural forms show resilience and increasing public presence, while also being shaped by inclusive cultural policies that are informed by the national drive towards reinstating traditional Chinese values as part and parcel of national identity. One manifestation is the enactment of the traditional ritual space of the village in urban architecture, such as the duality of ancestral hall and village temple, often at so-called "cultural squares," and the expression of territorial ambitions of lineages in competitive projects of redevelopment. We suggest enhancing the concept of cultural governance by the concept of governmentality to grasp these phenomena analytically. [ABSTRACT FROM AUTHOR]

Background: Human Papillomavirus (HPV) causes various types of cancer in both men and women. Woman with HPV infection has a risk of developing invasive cervical cancer. Globally, HPV 16 and 18 were predominant. This study aims to find the distribution of various HPV types in South Andaman. Methods: A cross-sectional study was conducted among women in South Andaman, where cervical scrapes were collected after collecting written informed consent. Detection of HPV genotypes was carried out by using a PCR assay. Further, sequencing analysis was performed using MEGA11 to identify various genotypes in this territory. Result: Of these 1000 samples, 32 were positive for HR-HPV 16, and four were positive for HR-HPV 18. Fifteen HPV genotypes were detected using molecular evolutionary analysis. Six cases were identified with multiple genotypes. The most prevalent genotype is HPV 16 which belongs to Lineage-A and sub-lineage A2. HPV 18 identified in South Andaman belonged to the lineage A1 to A5. Discussion: Various HPV types were identified among women in South Andaman. Global burden of cervical cancer associated with various HPV sub-lineages. HPV-16 A1 sub-lineage was globally widespread, whereas sub-lineages A1, A2 and D1 prevailed in South Andaman. Conclusions: HR-HPV identified in this study enlightens the importance of HPV vaccination among women in remote places. These findings will help to strengthen public health awareness programs and prevention strategies for women in remote areas. [ABSTRACT FROM AUTHOR]

A vaccine breakthrough infection and a rebound infection cases of COVID-19 are studied and analyzed for the ten U.S. Department of Health and Human Services (HHS) regions and the United States as a nation in this work. An innovative multi-strain susceptible-vaccinated- exposed-asymptomatic-symptomatic-recovered (SVEAIR) epidemic model is developed for this purpose for a population assumed to be susceptible to n-different variants of the disease, and those who are vaccinated and recovered from a specific strain k(k ≤ n) of the disease are immune to present strain and its predecessors j x 1, 2, ..., k, but can still be infected by newer emerging strains j x k þ 1, k þ 2, ..., n. The model is used to estimate epidemiological parameters, namely, the latent and infectious periods, the transmission rates, vaccination rates, recovery rates for each of the Delta B.1.617.2, Omicron B.1.1.529, and lineages BA.2, BA.2.12.1, BA.4, BA.5, BA.1.1, BA.4.6, and BA.5.2.6 for the United States and for each of the ten HHS regions. The transmission rate is estimated for both the asymptomatic and symptomatic cases. The effect of vaccines on each strain is analyzed. Condition that guarantees existence of an endemic with certain number of strains is derived and used to describe the endemic state of the population. [ABSTRACT FROM AUTHOR]

While resistance mutations are often implicated in the failure of cancer therapy, lack of response also occurs without such mutants. In bladder cancer mouse xenografts, repeated chemotherapy cycles have resulted in cancer stem cell (CSC) enrichment, and consequent loss of therapy response due to the reduced susceptibility of CSCs to drugs. A particular feedback loop present in the xenografts has been shown to promote CSC enrichment in this system. Yet, many other regulatory loops might also be operational and might promote CSC enrichment. Their identification is central to improving therapy response. Here, we perform a comprehensive mathematical analysis to define what types of regulatory feedback loops can and cannot contribute to CSC enrichment, providing guidance to the experimental identification of feedback molecules. We derive a formula that reveals whether or not the cell population experiences CSC enrichment over time, based on the properties of the feedback. We find that negative feedback on the CSC division rate or positive feedback on differentiated cell death rate can lead to CSC enrichment. Further, the feedback mediators that achieve CSC enrichment can be secreted by either CSCs or by more differentiated cells. The extent of enrichment is determined by the CSC death rate, the CSC self-renewal probability, and by feedback strength. Defining these general characteristics of feedback loops can guide the experimental screening for and identification of feedback mediators that can promote CSC enrichment in bladder cancer and potentially other tumors. This can help understand and overcome the phenomenon of CSC-based therapy resistance.

The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.

Vibrio vulnificus is a multi-host pathogenic species currently subdivided into five phylogenetic lineages (L) plus one pathovar with the ability to infect fish due to a transmissible virulence plasmid. This plasmid (or a fragment of it) has been transmitted between lineages within the species, contributing to the evolution of V. vulnificus. This study aimed to provide an experimental approximation to the V. vulnificus mutation rate by determining spontaneous mutation rates from bacterial cultures of representants of the different lineages by whole-genome sequencing. To this purpose, synonymous SNP differences, i.e., spontaneous mutation not subjected to the evolutive forces, between initial and final culture after serial growth were evaluated and used for mutation rate calculation. [ABSTRACT FROM AUTHOR]

Background: The tuberculosis (TB) epidemic remains a major global health problem and Eswatini is not excluded. Our study investigated the circulating genotypes in Eswatini and compared them at baseline (start of treatment) and follow-up during TB treatment. Methods: Three hundred and ninety (n = 390) participants were prospectively enrolled from referral clinics and patients who met the inclusion criteria, were included in the study. A total of 103 participants provided specimens at baseline and follow-up within six months. Mycobacterium tuberculosis (M.tb) strains were detected by GeneXpert® MTB/RIF assay (Cephied, USA) and Ziehl -Neelsen (ZN) microscopy respectively at baseline and follow-up time-points respectively. The 206 collected specimens were decontaminated and cultured on BACTEC™ MGIT™ 960 Mycobacteria Culture System (Becton Dickinson, USA). Drug sensitivity testing was performed at both baseline and follow-up time points. Spoligotyping was performed on both baseline and follow-up strains after DNA extraction. Results: Resistance to at least one first line drug was detected higher at baseline compared to follow-up specimens with most of them developing into multidrug-resistant (MDR)-TB. A total of four lineages and twenty genotypes were detected. The distribution of the lineages varied among the different regions in Eswatini. The Euro-American lineage was the most prevalent with 46.12% (95/206) followed by the East Asian with 24.27% (50/206); Indo-Oceanic at 9.71% (20/206) and Central Asian at 1.94% (4/206). Furthermore, a high proportion of the Beijing genotype at 24.27% (50/206) and S genotype at 16.50% (34/206) were detected. The Beijing genotype was predominant in follow-up specimens collected from the Manzini region with 48.9% (23/47) (p = 0.001). A significant proportion of follow-up specimens developed MDR-TB (p = 0.001) with Beijing being the major genotype in most follow-up specimens (p < 0.000). Conclusion: Eswatini has a high M.tb genotypic diversity. A significant proportion of the TB infected participants had the Beijing genotype associated with MDR-TB in follow-up specimens and thus indicate community wide transmission. [ABSTRACT FROM AUTHOR]

Background: Wastewater-based epidemiological surveillance has been considered a powerful tool for early detection and monitoring of the dynamics of SARS-CoV-2 and its lineages circulating in a community. This study is aimed to investigate the complexity of SARS-CoV-2 infection dynamics in Dhaka city by examining its genetic variants in wastewater. Also, the study seeks to determine a connection between the SARS-CoV-2 variations detected in clinical testing and those found in wastewater samples. Results: Out of 504 samples tested in RT-qPCR, 185 (36.7%) tested positive for SARS-CoV-2 viral RNA. The median log10 concentration of SARS-CoV-2 N gene copies/Liter of wastewater (gc/L) was 5.2, and the median log10 concentration of ORF1ab was 4.9. To further reveal the genetic diversity of SARS-CoV-2, ten samples with ORF1ab real-time RT-PCR cycle threshold (Ct) values ranging from 28.78 to 32.13 were subjected to whole genome sequencing using nanopore technology. According to clade classification, sequences from wastewater samples were grouped into 4 clades: 20A, 20B, 21A, 21J, and the Pango lineage, B.1, B.1.1, B.1.1.25, and B.1.617.2, with coverage ranging from 94.2 to 99.8%. Of them, 70% belonged to clade 20B, followed by 10% to clade 20A, 21A, and 21J. Lineage B.1.1.25 was predominant in Bangladesh and phylogenetically related to the sequences from India, the USA, Canada, the UK, and Italy. The Delta variant (B.1.617.2) was first identified in clinical samples at the beginning of May 2021. In contrast, we found that it was circulating in the community and was detected in wastewater in September 2020. Conclusion: Environmental surveillance is useful for monitoring temporal and spatial trends of existing and emerging infectious diseases and supports evidence-based public health measures. The findings of this study supported the use of wastewater-based epidemiology and provided the baseline data for the dynamics of SARS-CoV-2 variants in the wastewater environment in Dhaka, Bangladesh. [ABSTRACT FROM AUTHOR]

The avian infectious bronchitis virus (IBV) is a coronavirus that mutates frequently, leading to a contagious and acute disease that results in economic losses to the global poultry industry. Due to its genetic and serological diversity, IBV poses a challenge in preventing and controlling the pathogen. The full-length S1 sequence analysis identifies seven main genotypes (GI–GVII) comprising 35 viral lineages. In addition to the previously described lineage, a new GI lineage (GI-30) and two lineages from novel genotypes (GVIII-1 and GIX-1) have been described in Mexico. To prevent the spread of IBV outbreaks in a specific geographic location and select the suitable vaccine, it is helpful to genetically identify the circulating IBV types. Moreover, sequencing genomes can provide essential insights into virus evolution and significantly enhance our understanding of IBV variability. However, only genomes of previously described lineages (GI-1, GI-9, GI-13, and GI-17) have been reported for Mexican strains. Here, we sequenced new genomes from Mexican lineages, including the indigenous GI-30, GVIII-1, and GIX-1 lineages. Comparative genomics reveals that Mexico has relatively homogenous lineages (i.e., GI-13), some with greater variability (i.e., GI-1 and GI-9), and others extremely divergent (GI-30, GVIII-1, and GIX-1). The circulating lineages and intra-lineage variability support the unique diversity and dynamic of Mexican IBV. [ABSTRACT FROM AUTHOR]

The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed sometimes in Latin American countries in the circulation of the different lineages of the Omicron VOC. Once the sub-lineages were introduced in the country, community transmission was responsible for generating a characteristic distribution of them, with a predominance of sub-lineages not necessarily similar to the one observed in travelers or neighboring countries. [ABSTRACT FROM AUTHOR]

The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. We retrieved and analyzed spike protein sequences from Pakistan and compared them with reference sequences reported worldwide. Our analysis revealed the clustering of Pakistan-origin isolates in nine different clades representing different regions worldwide, suggesting the transmission of multiple lineages within the country. We found 96 PANGO lineages of SARS-CoV-2 in Pakistan, and 64 of these corresponded to 4 WHO-designated variants: Alpha, Beta, Delta, and Omicron. The most dominant variants in Pakistan were Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2, AY.108), and Omicron (BA.2.75, BA.5.2), and the N-terminal domain and receptor binding regions were the most hypervariable regions of the spike gene. Compared to the reference strain, characteristic substitutions were found in dominant variants. Our findings emphasize the importance of continuously monitoring and assessing nucleotide and residue substitutions over time to understand virus evolutionary trends better and devise effective disease control interventions. [ABSTRACT FROM AUTHOR]

The representation and integration of internal and external cues is crucial for any organism to execute appropriate behaviors. In insects, a highly conserved region of the brain, the central complex (CX), functions in the representation of spatial information and behavioral states, as well as the transformation of this information into desired navigational commands. How does this relatively invariant structure enable the incorporation of information from the diversity of anatomical, behavioral, and ecological niches occupied by insects? Here, we examine the input channels to the CX in the context of their development and evolution. Insect brains develop from ~ 100 neuroblasts per hemisphere that divide systematically to form "lineages" of sister neurons, that project to their target neuropils along anatomically characteristic tracts. Overlaying this developmental tract information onto the recently generated Drosophila "hemibrain" connectome and integrating this information with the anatomical and physiological recording of neurons in other species, we observe neuropil and lineage-specific innervation, connectivity, and activity profiles in CX input channels. We posit that the proliferative potential of neuroblasts and the lineage-based architecture of information channels enable the modification of neural networks across existing, novel, and deprecated modalities in a species-specific manner, thus forming the substrate for the evolution and diversification of insect navigational circuits. [ABSTRACT FROM AUTHOR]

Algal biogeography in Hawai'i has not been studied in detail for many species. The islands are home to swift-current deep-water channels separating suitable habitats. The ability of these channels to act as barriers to dispersal has been studied in several animal lineages and is assessed here using the widespread red alga Amansia glomerata C.Agardh. A variety of analytical techniques based on 129 mitochondrial COI barcoding sequences collected across c. 2500 km were used to assess the genetic diversity of A. glomerata in Hawai'i. Haplotype network analyses demonstrated that the species is split into four main lineages which overlap in large parts of their range, yet there is insufficient support to recognize the lineages as separate species. Measures of haplotype diversity, nucleotide diversity, and neutrality tests suggest that at least three of these lineages have undergone recent population expansion. Biogeographic barriers were found to largely match those of marine animal groups in the archipelago. No evidence was found for distinct haplotypes or lineages between shallow and mesophotic reefs. A number of potential collection locations are suggested for the 1822 lectotype of the species, which was included in the molecular analyses. Potential scenarios leading to observed diversity patterns in the archipelago are presented. Amansia glomerata exhibits a high degree of haplotypic variation in Hawai'i, suggesting it may exhibit vast molecular divergences across its broader range, which extends from Hawai'i to southeastern Africa. Phylogéographie d'Amansia glomerata C.Agardh (Ceramiales, Rhodomelaceae) à Hawai'i: une seule espèce à forte divergence. La biogéographie des algues à Hawai'i n'a pas été étudiée en détail pour de nombreuses espèces. Les îles abritent des chenaux rapides d'eau profonde séparant les habitats appropriés. La capacité de ces chenaux à agir comme des barrières à la dispersion a été étudiée dans plusieurs lignées animales et est évaluée ici à l'aide de l'algue très répandue Amansia glomerata C.Agardh. Une variété de techniques analytiques basées sur 129 séquences de code-barres COI mitochondriales collectées sur environ 2500 km ont été utilisées pour évaluer la diversité génétique d'A. glomerata à Hawai'i. Les analyses du réseau d'haplotypes ont démontré que l'espèce est divisée en quatre lignées principales qui se chevauchent dans de grandes parties de leur aire de répartition, mais il n'y a pas suffisamment de soutien pour reconnaître les lignées comme plusieurs espèces. Les mesures de la diversité des haplotypes, de la diversité des nucléotides et des tests de neutralité suggèrent qu'au moins trois de ces lignées ont subi des expansions démographiques récentes. Les barrières biogéographiques correspondent largement à celles des groupes d'animaux marins de l'archipel. Aucune preuve n'a été trouvée pour des haplotypes ou des lignées distincts entre les récifs peu profonds et mésophotiques. Un certain nombre de lieux de collecte potentiels sont suggérés pour le lectotype de l'espèce de 1822, qui a été inclus dans les analyses moléculaires. Des scénarios potentiels conduisant à des modèles de diversité observés dans l'archipel sont présentés. Amansia glomerata présente un degré élevé de variation haplotypique à Hawai'i, ce qui suggère qu'il peut présenter de vastes divergences moléculaires sur son aire de répartition plus large, qui s'étend d'Hawai'i au sud-est de l'Afrique. [ABSTRACT FROM AUTHOR]

Background: HSPCs are targets for benzene-induced hematotoxicity and leukemogenesis. However, benzene toxicity targeting microRNAs (miRNAs) and transcription factors (TF) that are involve in regulating self-renewing and differentiation of HSPCs comprising of different hematopoietic lineages remains poorly understood. In this study, the effect of a benzene metabolite, 1,4-benzoquinone (1,4-BQ) exposure, in HSPCs focusing on the self-renewing (miRNAs: miR-196b and miR-29a; TF: HoxB4, Bmi-1) and differentiation (miRNAs: miR-181a, TF: GATA3) pathways were investigated. Methods: Freshly isolated mouse BM cells were initially exposed to 1,4-BQ at 1.25 to 5 µM for 24 h, followed by miRNAs and TF studies in BM cells. Then, the miRNAs expression was further evaluated in HSPCs of different lineages comprised of myeloid, erythroid and pre-B lymphoid progenitors following 7-14 days of colony forming unit (CFU) assay. Results: Exposure to 1,4-BQ in BM cells significantly (p < 0.05) reduced the miR-196b (2.5 and 5 µM), miR-181a (1.25, 2.5 and 5 µM) and miR-29a (1.25 µM) along with upregulation of miR-29a at 2.5 µM. Meanwhile, 1,4-BQ exposure in HSPCs significantly increased the miR-196b expression level (p < 0.05) only in myeloid and pre-B lymphoid progenitors at 2.5 and 5 µM. Significant (p < 0.05) reduction in expression of miR-181a in myeloid (1.25 µM), erythroid (5 µM) progenitors along with miR-29a in myeloid (1.25 µM) and pre-B lymphoid (5 µM) progenitors were noted following exposure to 1,4-BQ. Meanwhile, increased expression of miR-181a was observed in pre-B lymphoid progenitor upon exposure to 1,4-BQ, but only at 5 µM. As for TF studies, expression of HoxB4 protein was significantly increased (p < 0.05) at all 1,4-BQ concentrations as compared to Bmi-1 and GATA3, which were significantly (p < 0.05) elevated starting at 2.5 µM of 1,4-BQ. Conclusion: 1,4-BQ induces aberration of miRNAs and transcription factors protein expression that are involved in regulating self-renewing and differentiation pathways of HSPCs. Moreover, epigenetic toxicity as evidenced from the miRNAs expression was found to be mediated by a lineage-driven mechanism. The role of cell lineage in governing the toxicity of 1,4-BQ in HSPCs lineages deserves further investigation. [ABSTRACT FROM AUTHOR]

West Nile virus is a re-emerging arbovirus whose impact on public health is increasingly important as more and more epidemics and epizootics occur, particularly in America and Europe, with evidence of active circulation in Africa. Because birds constitute the main reservoirs, migratory movements allow the diffusion of various lineages in the world. It is therefore crucial to properly control the dispersion of these lineages, especially because some have a greater health impact on public health than others. This work describes the development and validation of a novel whole-genome amplicon-based sequencing approach to West Nile virus. This study was carried out on different strains from lineage 1 and 2 from Senegal and Italy. The presented protocol/approach showed good coverage using samples derived from several vertebrate hosts and may be valuable for West Nile genomic surveillance. [ABSTRACT FROM AUTHOR]

Objective. To interrogate the circulating SARS-CoV-2 lin­eages and recombinant variants in persons living in migrant shelters and persons who inject drugs (PWID). Materials and methods. We combined data from two studies with marginalized populations (migrants in shelters and persons who inject drugs) in Tijuana, Mexico. SARS-CoV-2 variants were identified on nasal swabs specimens and compared to publicly available genomes sampled in Mexico and California. Results. All but 2 of the 10 lineages identified were predomi­nantly detected in North and Central America. Discrepan­cies between migrants and PWID can be explained by the temporal emergence and short time span of most of these lineages in the region. Conclusion. The results illustrate the temporo-spatial structure for SARS-CoV-2 lineage dispersal and the potential co-circulation of multiple lineages in high-risk populations with close social contacts. These conditions create the potential for recombination to take place in the California-Baja California border.

Abstract Background Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. Results Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. Conclusion This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.

This work is focused on the members of the Late Cretaceous-Early Paleogene (K-Pg) diagnostic benthic foraminiferal genus Orthokarstenia which is regionally important in paleontology and stratigraphic correlations. The large number of tests available and the rapid morphologic changes, offer an opportunity to study evolutionary changes in these foraminiferal taxa over a time span of about 25 m. y. (75-50 Ma). Six species of the genus Orthokarstenia are presented: O. applinae, O. eleganta, O. esnehensis, O. higazyi, O. nakkadyi and O. oveyi, which were recorded in eight localities in the Southern Tethys: Nigeria, Tunisia, Egypt (central and north Africa), Jordan, Saudi Arabia, UAE, Iran and Pakistan (southwest Asia). Evolutionary changes of them are indicated by such criteria, such as changes in the test-size, chambers arrangement, type of sutures, periphery or surface ornamentation. These changes help to define the major faunal change of the Campanian/Maastrichtian (C/M) boundary, K/Pg boundary, and can used in biostratigraphic subdivisions and correlations based on benthic foraminifera, beside planktic foraminiferal zonation.