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Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, also known as Newcastle disease virus (NDV). Despite vaccination, the frequency of reported outbreaks in Ethiopia has increased. From January to June 2022, an active outbreak investigation was conducted in six commercial chicken farms across areas of central Ethiopia to identify the circulating NDV strains. Thirty pooled tissue specimens were collected from chickens suspected of being infected with NDV. A questionnaire survey of farm owners and veterinarians was also carried out to collect information on the farms and the outbreak status. NDV was isolated using specific-pathogen-free (SPF)-embryonated chicken eggs and detected using haemagglutination and the reverse transcriptase–polymerase chain reaction (RT–PCR). The genotype and virulence of field NDV isolates were determined using phylogenetic analysis of fusion (F) protein gene sequences and the mean death time (MDT) test in SPF-embryonated chicken eggs. The questionnaire results revealed that ND caused morbidity (23.1%), mortality (16.3%), case fatality (70.8%), and significant economic losses. Eleven of thirty tissue specimens tested positive for NDV using haemagglutination and RT–PCR. The MDT testing and sequence analysis revealed the presence of virulent NDV classified as genotype VII of class II velogenic pathotype and distinct from locally used vaccine strains (genotype II). The amino acid sequences of the current virulent NDV fusion protein cleavage site motif revealed 112RRQKR↓F117, unlike the locally used avirulent vaccine strains (112GRQGR↓L117). The epidemiological data, MDT results, cleavage site sequence, and phylogenetic analysis all indicated that the present NDV isolates were virulent. The four NDV sequences were deposited in GenBank with accession numbers F gene (PP726912-15) and M gene (PP726916-19). The genetic difference between avirulent vaccine strains and circulating virulent NDV could explain the low level of protection provided by locally used vaccines. Further studies are needed to better understand the circulating NDV genotypes in different production systems.

Porcine parvovirus 7 (PPV7) was first discovered in swine in 2016, and PPV7 infection has been detected in aborted pig fetuses and in sows that experienced reproductive failure. The objective of this study was to report the prevalence and genetic characterization of PPV7 in Hunan, China. Seventy of the four hundred and twenty-two (16.6%) serum, semen, and tissue samples collected from pigs were positive for PPV7. One complete PPV7 strain and eighteen complete cap gene sequences were obtained; nucleotide and amino acid identity among the nineteen Cap sequences were 88.1–99.4% and 88.1–100%, respectively. They shared identity with previously discovered sequences ranging from 86.6 to 98.9% and 83.7 to 99.8% at the nucleotide- and amino acid-level, respectively. The phylogenetic tree analysis exhibited that PPV7 strains had two major groups based on the presence or absence of five amino acid (181–185) insertions on the Cap protein. Analysis of the Cap protein demonstrated that PPV7 Cap had significant variability, implying that PPV7 evolved at high substitution rates. Substantial variations of that PPV7 Cap may enable the emergence of newly mutated capsid profiles due to its viral adaptation to host responses. Furthermore, antigenic alteration owing to PPV7 Cap protein amino acid mutations at immune epitopes may enable viruses to escape from the host’s immune system. This study determined the prevalence and genetic characteristics of PPV7 circulating in swine in Hunan, China, and provided the impetus and basis to further investigate the pathogenicity and epidemiology of PPV7.

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.

Indigenous goats are important in the livelihoods of rural households in East African countries. This is due to their ability to produce and reproduce in different environments and climatic conditions. Even though these indigenous goats are important, there is little available information on the genetic characterization of these breeds in Africa and at the international level. This paper reviews the status of indigenous goats, highlighting their production systems, phenotypic and genetic characteristics, and genetic diversity, and proposes potential ways for sustainable improvement and conservation in East African countries. Most households use traditional production systems with various uncharacterized goat breeds and ecotypes, which are hence named after the tribe or locality in which they are found. Most of these goats are classified as small East African breeds, with significant variability in morphological features. Some of the challenges to goat production in this region are indiscriminate crossbreeding, lack of pedigree records, parasites and disease incidences, low-quality pastures, and low levels of management. There is a need for a collaborative approach amongst the actors in goat breeding value chains as well as integrating modern genomic tools into breeding programs to enhance selection. This will ensure the resilience and sustainability of these unique indigenous goat populations in East Africa

Leaf samples of 226 cultivated olive trees were collected from traditionally managed olive orchards and genotyped with eleven consensual SSR markers. The proportion of shared allele distance was used for the estimation of distances between olive genotypes. Cluster analyses were performed using a Fitch–Margoliash least-squares algorithm. The number of different genetic subgroups of olive genotypes (K) was investigated using STRUCTURE analysis. The standardization of allele lengths was performed to enable the comparison SSR profiles of Croatian olive genotypes with olive profiles obtained with the same SSR primers in OleaDB and WOGB databases. Overall, 73 SSR profiles of known Croatian varieties and 53 profiles of unknown olive genotypes were differentiated. Synonyms were detected in 18 varieties, and we found intra-varietal differences in 15 varieties. Three genetic subgroups of olive genotypes were determined. Following allele length standardization achieved using nine referral samples, the genetic profiles of 126 cultivated olive genotypes were compared to OleaDB and WOGB databases, out of which 92 genotypes were found to be unique to Croatian olive germplasm. The results revealed the wide genetic diversity of olive germplasm beyond the known, registered varieties. The FAZ_oliveDB database containing the profiles of 126 Croatian olive genotypes was created and made available for public use.

Pigeon Newcastle disease (ND) is a serious infectious illness caused by the pigeon Newcastle disease virus (NDV) or Paramyxovirus type 1 (PPMV-1). Genotype VI NDV is a primary factor in ND among Columbiformes (such as pigeons and doves). In a recent study, eight pigeon NDV strains were discovered in various provinces in China. These viruses exhibited mesogenic characteristics based on their MDT and ICPI values. The complete genome sequences of these eight strains showed a 90.40% to 99.19% identity match with reference strains of genotype VI, and a 77.86% to 80.45% identity match with the genotype II vaccine strain. Additionally, analysis of the F gene sequence revealed that these NDV strains were closely associated with sub-genotypes VI.2.2.2, VI.2.1.1.2.1, and VI.2.1.1.2.2. The amino acid sequence at the cleavage site of the F protein indicated virulent characteristics, with the sequences 112KRQKRF117 and 112RRQKRF117 observed. Pigeons infected with these sub-genotype strains had a low survival rate of only 20% to 30%, along with lesions in multiple tissues, highlighting the strong spread and high pathogenicity of these pigeon NDV strains. Molecular epidemiology data from the GenBank database revealed that sub-genotype VI.2.1.1.2.2 strains have been prevalent since 2011. In summary, the findings demonstrate that the prevalence of genotype VI NDV is due to strains from diverse sub-genotypes, with the sub-genotype VI.2.1.1.2.2 strain emerging as the current epidemic strain, highlighting the significance of monitoring pigeon NDV in China.

Small ruminant lentiviruses are a group of viruses infecting goat and sheep worldwide. These viruses exhibit an extraordinary degree of genetic and antigenic variability that severely influence in vivo and in vitro features, as well as diagnostic test results. Small ruminant farming is the most important animal farming business in Greece, with a high impact on the Greek primary economy. Although SRLV infection and its impact on animal production are well established in the country, little is known about the circulating SRLV strains and their prevalence. The aim of this study was to characterize SRLVs circulating in Greece with a combined serological and molecular approach, using the bulk milk matrix collected from 60 farms in different municipalities. This study allowed us to estimate a seroprevalence of around 52% at the herd level. The B1, B2 and A3 subtypes and a novel A viral cluster were identified. Moreover, the amplicon sequencing method allowed us to identify more than one viral subtype in a sample. These results again confirm the high variability of these viruses and highlight the importance of the constant monitoring of viral evolution, in particular in antigens of diagnostic interest.

The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a FST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area.

The high genetic heterogeneity of small ruminant lentiviruses (SRLV) renders the genetic characterization of the circulating strains crucial for the epidemiological investigation and the designation of effective diagnostic tools. In Greece, research data regarding the genetic diversity of the circulating SRLV strains is scarce, hindering the implementation of efficient surveillance and control programs. The objective of the study was to genetically characterize SRLV strains isolated from intensive dairy sheep farms in Greece and evaluate the variability of the immunodominant regions of the capsid protein. For this reason, a total of 12 SRLV-infected animals from four intensive dairy sheep farms with purebred Chios and Lacaune ewes were used for the amplification and sequencing of an 800 bp gag-pol fragment. The phylogenetic analyses revealed a breed-related circulation of strains; Chios ewes were infected with strains belonging exclusively to a separate group of genotype A, whereas strains belonging to subtype B2 were isolated from Lacaune ewes. Immunodominant epitopes of capsid protein were quite conserved among the strains of the same genotype, except for the Major Homology Region which showed some unique mutations with potential effects on viral evolution. The present study contributes to the extension of the current knowledge regarding the genetic diversity of SRLV strains circulating in sheep in Greece. However, broader genetic characterization studies are warranted for the exploration of possible recombinant events and the more comprehensive classification of the circulating strains.

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.

Fowl adenovirus-induced hepatitis–pericardial effusion syndrome outbreaks have been increasingly reported in China since 2015, resulting in substantial economic losses to the poultry industry. The genetic diversity of indigenous chicken results in different immune traits, affecting the evolution of these viruses. Although the molecular epidemiology of fowl adenovirus serotype 4 (FAdV-4) has been well studied in commercial broiler and layer chickens, the prevalence and genetic characteristics of FAdV-4 in indigenous chickens remain largely unknown. In this study, samples were collected from six indigenous chicken breeds in Yunnan province, China. FAdV-positive samples were identified in five of the six indigenous chicken populations via PCR and 10 isolates were obtained. All FAdVs belonged to serotype FAdV-4 and species FAdV-C. The hexon, fiber, and penton gene sequence comparison analysis demonstrated that the prevalence of FAdV-4 isolates in these chickens might have originated from other provinces that exported chicks and poultry products to Yunnan province. Moreover, several distinct amino acid mutations were firstly identified in the major structural proteins. Our findings highlighted the need to decrease inter-regional movements of live poultry to protect indigenous chicken genetic resources and that the immune traits of these indigenous chickens might result in new mutations of FAdV-4 strains.

While there is a rich collection of maize germplasm from Italy, it lacks genetic resources from the Aosta Valley, an isolated mountain region where landraces have been preserved in the absence of modern germplasm introductions. These local materials, which are still cultivated mainly at household level, can have high importance from a genetic and historical point of view. In the present study, five landraces named, after the collecting sites, Arnad, Arnad-Crest, Châtillon, Entrebin and Perloz, were sampled in Aosta Valley and subjected to historic, morphologic and genetic characterization. This study provided evidence for the landraces’ long presence in Aosta Valley, a significant genetic variability and differentiation among the investigated landraces. Globally, 67 different alleles were detected ranging from 4 for markers phi127 and p-bnlg176 to 10 for phi031, with a mean of 6.7 alleles per locus. Observed heterozygosity levels were comprised from 0.16 to 0.51 and are generalkly lower than expected heterozigosity supporting fixation at some loci. STRUCTURE analysis revealed clear separation between accessions revealing the presence of four ancestral populations. This may be explained by the long reproductive isolation experienced by these materials. Finally, morphological observations confirm the high diversity between landraces revealing that they generally have flint kernels, variable color from yellow to dark red (Châtillon) while Perloz showed kernels with an apical beak. The present work confirms the importance of mountain areas in conserving biodiversity and increases the rich Italian maize germplasm with materials well adapted to marginal areas. Such new genetic variability may be used to breed new materials for more resilient agriculture.

Chrysanthemums represent the second most important cut flower after rose on the global commercial market. The phenomenal importance and global popularity of chrysanthemums have attracted breeders’ attention, resulting in the release of vast numbers of cultivars. Identifying these cultivars is crucial to protecting breeders’ intellectual property rights and improving the efficiency of breeding. Distinguishing chrysanthemum genotypes based on their morphological characteristics is challenging as they vary highly within this group, hence requiring the use of efficient molecular markers. In this study, we evaluated the genetic diversity of 57 spray-type chrysanthemum cultivars bearing white, ivory, and cream-colored flowers. A total of six loci were evaluated regarding their polymorphism efficiency across the tested cultivars. Allele numbers ranged from 2 to 6, with a mean of 3.5 alleles per locus. The average polymorphism information content (PIC) was 0.53 for six SSR markers. Cluster analysis of genetic relationships using the UPGMA method showed a genetic distance of 0.31 to 1.00, and the 57 white variants of chrysanthemum cultivars were characterized using the tested SSR markers. However, two sets of cultivars, namely, Pure Angel–Neba and Ladost–White wing, exhibited total genetic similarity and hence could not be discriminated. These results provide efficient SSR markers that can be used to identify chrysanthemum cultivars (and assess their genetic relationships) that cannot be discriminated based on phenotype.

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis , an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca . However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The bla NDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.

(1) Background: Integrative taxonomy has been important in the comprehension of relationships among nematode parasites. Philometridae is a highly diverse family of these organisms, but poorly-known regarding genetic characterization and evolution. An integrative taxonomic analysis was performed to improve the knowledge of the evolutionary history of Philometridae. (2) Methods: Phylogenies were reconstructed based on genetic sequences alone and integrated with morphological/life history traits, which were phylogenetically mapped. The host–parasite cophylogeny was evaluated. (3) Results: Previously unpublished 28S rDNA sequences are given for some species. The phylogeny from this marker, although limited by data scarcity, showed similar patterns as that from 18S rDNA. Clades shared common features related to the structure of the esophagus and of the tail in males (especially the gubernaculum), site of infection, habitat, host taxa and geographic origin; most of these features were phylogenetically informative. The integrative phylogeny was better resolved. A cophylogenetic signal was present mainly in clades of freshwater species. (4) Conclusions: The speciation process in Philometridae is not unique or uniform; host capture, host–parasite co-evolution and allopatric (especially in freshwater) events may be occurring simultaneously in different lineages, places and times. Cases of plesiomorphy retention probably occur. Evolutionary convergence of poorly-informative characters is suggested, even though they are important for species diagnosis.

In the framework of the sustainable management of the genetic diversity (morphometric and molecular) of the “Tergui” camel population represented by the phenotypes (Abahou, Amelal, Alemlagh, Atelagh, and Azerghaf), surveys in the Hoggar area of 87 individuals from 11 localities were conducted in order to estimate the variability of the inter-intra-population. The morphological results provide full information about the structure of this population and demonstrate an important polymorphism. The results of the genotyping of the DNA with 20 microsatellite markers made it possible to demonstrate inter- and intra-population genetic variability characterized by a high rate of heterozygosity (Hnb) and effective alleles. The rate of heterozygosity in our phenotypes varied from 0.56 to 0.63, which is higher than that observed in foreign populations ranging from 0.537 to 0.629. A total of 169 alleles of 20 microsatellite loci were detected. The mean number of alleles per locus was 7.15, 6.15, 3.10, 4.45, and 3.25 for Abahou, Amelal, Alemlagh, Atelagh, and Azerghaf, respectively. The loci evaluation showed higher PIC values greater than 0.5, which are considered very instructive. The heterozygous values observed for all the loci analyzed were lower than expected, which could be attributed to inbreeding in the population or subdivision of the studied population into distinct breeds and phenotypes. On the other hand, the number of observed alleles is higher and has shown a frequency that exceeds 7.3%. The genetic differentiation values between the phenotypes analyzed were much lower and the level of differences accounted for 1.1% of the total genetic variation. All loci contributed to this differentiation with FST values being moderately low and similar but very significant (p < 0.001). The overall FST value was similar but slightly higher than that of 0.9%. The genetic similarity between the phenotypes and the classification methods (AFC and DACP) gave results similar to the phenotypic characteristics, and showed that they appear to be genetically very similar, thereby supporting the decision to consider them only mildly differentiated.

In Andalusia (Spain), there are different wine regions that have a great recognized tradition. In these regions, the cultivation of the vine is ancient and there are still vineyards planted with local varieties of Vitis vinifera L. that have not yet been identified. The aim of this research study was to identify 49 accessions of grapevine collected in the districts of four provinces in Andalusia (Spain). All samples were genotyped with 20 microsatellite markers in order to ascertain the identity and analyze the genetic diversity of the collected material. In total, 30 different genotypes were obtained, 22 of them which were identified with named, known varieties by comparison to the Spanish or European microsatellite databases, and eight which are referred to as new genotypes. All loci were polymorphic, and a total of 159 alleles were detected, ranging from 4 to 12 alleles per locus, with an average allele number of 7.95. The overall observed heterozygosity was 0.763 and was slightly higher than expected (0.715), while the gene diversity per locus varied between 0.167 (VVIN73) and 0.967 (VVMD5). A dendrogram representing the genetic similarities among cultivars was depicted using the UPGMA method to investigate their relationships. The eight new genotypes identified in this research work could represent ancient local varieties in danger of extinction. These new cultivars may be used to determine original wines.

In South Korea, a total of 21 African swine fever (ASF) infected farms were confirmed during 2019–2021. ASF viruses (ASFVs) were isolated from the blood and spleen samples of the 21 affected farms and their genetic characteristics were analyzed. Phylogenetic analysis indicated that the 21 Korean ASFV strains belonged to p72 genotype II and serogroup 8. All isolates were of the intergenic region (IGR) II variant with 10 tandem repeat sequences between I73R and I329L and the central variable region (CVR) 1 variant of the B602L gene. There were no IGR variations between the A179L and A137R and between the MGF 505 9R and10R nor mutations in the O174L, K145R, MGF 505-5R, CP204L, and Bt/Sj regions. The genes of the 21 ASFV strains were identical to those of Georgia 2007/1 and Chinese and Vietnamese strains (Pig/HLJ/2018, China/2018/AnhuiXCGQ, and ASFV_NgheAn_2019); however, X69R of the J268L region of the 18th isolate (Korea/Pig/Goseong/2021) had three nucleotide (CTA) insertions at the 209th position, which led to the addition of one tyrosine (Y) at the C-terminal. This suggests that there are variations among ASFVs circulating in South Korea and the 18th ASFV-infected farm was due to a variant different from those of the other 20 pig farms.

The growing interest in maize landraces over the past two decades has led to the need to characterize the Italian maize germplasm. In Italy, hundreds of maize landraces have been developed, but only a few of them have been genetically characterized, and even fewer are currently employed in agriculture or for breeding purposes. In the present study, 13 maize landraces of the west Emilia-Romagna region were morphologically and genetically characterized. These accessions were sampled in 1954 from three provinces, Modena, Parma, and Piacenza, during the characterization project of Italian maize landraces. The morphological characterization of these 13 accessions was performed according to the UPOV protocol CPVO/TP2/3, examining 34 phenotypic traits. A total of 820 individuals were genotyped with 10 SSR markers. The genetic characterization revealed 74 different alleles, a F ST mean value of 0.13, and a Nm mean of 1.73 over all loci. Moreover, AMOVA analysis disclosed a low degree of differentiation among accessions, with only 13% of genetic variability found between populations, supporting PCoA analysis results, where the first two coordinates explained only 16% of variability. Structure analysis, supported by PCoA, showed that only four accessions were clearly distinguished for both K = 4 and 6. Italian landraces can be useful resources to be employed in maize breeding programs for the development of new varieties, adapted to different environmental conditions, in order to increase crop resilience and expand the maize cultivation area.

Pigeon Newcastle disease (ND) is a serious infectious illness caused by the pigeon Newcastle disease virus (NDV) or Paramyxovirus type 1 (PPMV-1). Genotype VI NDV is a primary factor in ND among Columbiformes (such as pigeons and doves). In a recent study, eight pigeon NDV strains were discovered in various provinces in China. These viruses exhibited mesogenic characteristics based on their MDT and ICPI values. The complete genome sequences of these eight strains showed a 90.40% to 99.19% identity match with reference strains of genotype VI, and a 77.86% to 80.45% identity match with the genotype II vaccine strain. Additionally, analysis of the F gene sequence revealed that these NDV strains were closely associated with sub-genotypes VI.2.2.2, VI.2.1.1.2.1, and VI.2.1.1.2.2. The amino acid sequence at the cleavage site of the F protein indicated virulent characteristics, with the sequences 112 KRQKRF 117 and 112 RRQKRF 117 observed. Pigeons infected with these sub-genotype strains had a low survival rate of only 20% to 30%, along with lesions in multiple tissues, highlighting the strong spread and high pathogenicity of these pigeon NDV strains. Molecular epidemiology data from the GenBank database revealed that sub-genotype VI.2.1.1.2.2 strains have been prevalent since 2011. In summary, the findings demonstrate that the prevalence of genotype VI NDV is due to strains from diverse sub-genotypes, with the sub-genotype VI.2.1.1.2.2 strain emerging as the current epidemic strain, highlighting the significance of monitoring pigeon NDV in China., Competing Interests: The authors declare no conflicts of interest.

Giardia is a flagellate protozoa that can be transmitted via direct contact and by consuming contaminated water. It is pathogenic in humans and various other animals, including exotic pets. Pet prairie dogs are popular in Thailand, but they have not been investigated regarding giardiasis. Giardia infection was measured, and genetic characterization was performed to investigate the zoonotic potential of Giardia carried by pet prairie dogs. In total, 79 fecal samples were examined from prairie dogs visiting the Kasetsart University Veterinary Teaching Hospital during 2017–2021. Simple floatation was conducted. Two Giardia-positive samples were submitted for DNA extraction, PCR targeting the Giardiassu rRNA, tpi and gdh genes was performed, and genetic characterization using sequencing analysis was conducted. Risk factors associated with Giardia infection were analyzed. Giardia infection was found in 11 out of the 79 pet prairie dogs (13.9%). Giardia infection was significantly higher in male prairie dogs (p = 0.0345). Coccidia cysts (12.7%), the eggs of nematodes (6.3%), and amoeba cysts (2.5%) were also detected. Genetic characterization of the two Giardia-positive samples revealed that they were G. duodenalis assemblage A, sub-genotypes AI and assemblage B, and sub-genotype BIV, the zoonotic assemblages. This was the first report of Giardia infection in pet prairie dogs in Bangkok, Thailand. The results revealed that these pet prairie dogs in Thailand were infected with zoonotic assemblages of G. duodenalis sub-genotype AI, which might have been derived from animal contaminants, whereas sub-genotype BIV might have been derived from human contaminants. Owners of prairie dogs might be at risk of giardiasis or be the source of infection to their exotic pets.

A systematic surveillance against influenza A viruses (IAVs) in the Suidae population is essential, considering their role as IAV mixing vessels. However, the viral circulation in wild Sus scrofa species is poorly investigated in comparison to the knowledge of IAV infection dynamics in domestic pigs. This study investigated the circulation and the genetic diversity of wild boars’ IAVs detected in the Emilia-Romagna region (2017–2022). A total of 4605 lung samples were screened via an M gene real-time RT-PCR for SwIAV; positive samples were subtyped by multiplex RT-PCR, and viral isolation was attempted. Isolated strains (3 out of the 17 positives) were fully sequenced to evaluate viral genotypic diversity. H1N1 was the most frequently detected subtype, with identification of H1pdm09N1 and H1avN1. Whole-genome phylogenetic analysis revealed SwIAVs belonging to different genotypes, with different genetic combinations, and highlighted the simultaneous circulation of the same genotypes in both pigs and wild boars, supporting the hypothesis of SwIAV spillover events at the wildlife–livestock interface. This study represents an update on the wild boar SwIAV Italian situation, and the strains’ complete genome analysis showed an evolving and interesting situation that deserves further investigation.

Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.

In the early summer of 2012, sudden mass mortality among songbirds, particularly in greenfinches (Chloris chloris, syn: Carduelis chloris) was observed in Austria, which was caused by the protozoan parasite Trichomonas gallinae. This pathogen induced fibrinonecrotic ingluvitis and/or esophagitis, leading to impairment of food intake and ultimately death due to starvation. The pathogen was successfully detected within the lesions by polymerase chain reaction (PCR) and chromogenic in situ hybridization. The epizootic resulted in a significant decline in the Austrian greenfinch population. Continuing passive surveillance in the subsequent years (2013–2020) revealed that the condition occurred each year and was present in the entire country. Genetic characterization of the pathogen showed the presence of an identical strain irrespective of geographical location, bird species, and year.

Fish not only harbor host-specific species/genotypes of Cryptosporidium, but also species like zoonotic C. parvum or anthroponotic C. hominis, which can pose a risk for fish consumers. This study aims to investigate fish cryptosporidiosis in an important aquaculture and fishery area of the Western Mediterranean (Comunidad Valenciana, Spain). We analyzed 404 specimens belonging to the following three groups: cultivated fish (N = 147), wild synanthropic fish (N = 147) and wild fish from extractive fisheries (N = 110). Nested PCR targeting the 18S rRNA gene, followed by sequencing and phylogenetic analysis, were performed. Positive isolates were also amplified at the actin gene locus. An overall prevalence of 4.2% was detected, with the highest prevalence in the synanthropic group (6.1%). C. molnari was identified in thirteen specimens from seven different host species. Zoonotic C. ubiquitum was detected in two European sea bass (Dicentrarchus labrax). One isolate similar to C. scophthalmi was detected in a cultivated meagre (Argyrosomus regius), and one isolate, highly divergent from all the Cryptosporidium species/genotypes described, was identified from a synanthropic round sardinella (Sardinella aurita). This study contributes to increasing the molecular data on fish cryptosporidiosis, expanding the range of known hosts for C. molnari and identifying, for the first time, zoonotic C. ubiquitum in edible marine fishes, pointing out a potential health risk.

Tick-borne encephalitis virus (TBEV) is the causative agent of tick-borne encephalitis (TBE), a severe zoonosis occurring in the Palearctic region mainly transmitted through Ixodes ticks. In Italy, TBEV is restricted to the north-eastern part of the country. This report describes for the first time a case of clinical TBE in a roe deer (Capreolus capreolus L.). The case occurred in the Belluno province, Veneto region, an area endemic for TBEV. The affected roe deer showed ataxia, staggering movements, muscle tremors, wide-base stance of the front limbs, repetitive movements of the head, persistent teeth grinding, hypersalivation and prolonged recumbency. An autopsy revealed no significant lesions to explain the neurological signs. TBEV RNA was detected in the brain by real-time RT-PCR, and the nearly complete viral genome (10,897 nucleotides) was sequenced. Phylogenetic analysis of the gene encoding the envelope protein revealed a close relationship to TBEV of the European subtype, and 100% similarity with a partial sequence (520 nucleotides) of a TBEV found in ticks in the bordering Trento province. The histological examination of the midbrain revealed lymphohistiocytic encephalitis, satellitosis and microgliosis, consistent with a viral etiology. Other viral etiologies were ruled out by metagenomic analysis of the brain. This report underlines, for the first time, the occurrence of clinical encephalitic manifestations due to TBEV in a roe deer, suggesting that this pathogen should be included in the frame of differential diagnoses in roe deer with neurologic disease.

Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels. Swine (sw) IAVs of H1N1 (including H1N1pdm09), H3N2, and H1N2 subtypes are enzootic in pigs globally, with different geographic distributions. This study investigated the genetic diversity of swIAVs detected during passive surveillance of pig farms in Northern Italy between 2017 and 2020. A total of 672 samples, IAV-positive according to RT-PCR, were subtyped by multiplex RT-PCR. A selection of strains was fully sequenced. High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern. The hemagglutinin of the H1Nx swIAVs belonged to HA-1A, HA-1B, and HA-1C lineages. Increasing variability was found in HA-1C strains with the circulation of HA-1C.2, HA-1C.2.1 and HA-1C.2.2 sublineages. Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed. HA-1B strains were mostly represented by the Δ146-147 Italian lineage HA-1B.1.2.2, in combination with the 1990s human-derived NA gene. One antigenic variant cluster in HA-1A strains was identified in 2020. SwIAV circulation in pigs must be monitored continuously since the IAVs’ evolution could generate strains with zoonotic potential.

The deliberate or accidental introduction of invasive alien species (IAS) causes negative ecological and economic impacts altering ecosystem processes, imperiling native species and causing damage to human endeavors. A monthly monitoring program was performed in Lake Trasimeno (Central Italy) from July 2018 to July 2019 in order to provide an upgrade of the population ecology of Procambarus clarkii and to assess the genetic diversity by analyzing the relationships among mitochondrial DNA diversity. Our results confirmed that P. clarkii is well acclimatized in the lake, revealing a stable population structure favored by the resources and conditions typical of this ecosystem, which seem to be optimal for the maintenance of the species. Four distinct mitochondrial haplotypes were detected, but one of them was clearly overrepresented (76%), suggesting that a single predominant introduction event may have occurred in this area, likely followed by secondary events. The identification of the typical genetic variants provides a better understanding of the evolutionary scenarios of P. clarkii in this biotope and it can be helpful in management plans concerning the expanding populations of this invasive alien species.

The first detection of a Highly Pathogenic Avian Influenza (HPAI) H5N8 virus in Bulgaria dates back to December 2016. Since then, many outbreaks caused by HPAI H5 viruses from clade 2.3.4.4B have been reported in both domestic and wild birds in different regions of the country. In this study, we characterized the complete genome of sixteen H5 viruses collected in Bulgaria between 2019 and 2021. Phylogenetic analyses revealed a persistent circulation of the H5N8 strain for four consecutive years (December 2016–June 2020) and the emergence in 2020 of a novel reassortant H5N2 subtype, likely in a duck farm. Estimation of the time to the most recent common ancestor indicates that this reassortment event may have occurred between May 2019 and January 2020. At the beginning of 2021, Bulgaria experienced a new virus introduction in the poultry sector, namely a HPAI H5N8 that had been circulating in Europe since October 2020. The periodical identification in domestic birds of H5 viruses related to the 2016 epidemic as well as a reassortant strain might indicate undetected circulation of the virus in resident wild birds or in the poultry sector. To avoid the concealed circulation and evolution of viruses, and the risk of emergence of strains with pandemic potential, the implementation of control measures is of utmost importance, particularly in duck farms where birds display no clinical signs.

Fowl adenovirus-induced hepatitis-pericardial effusion syndrome outbreaks have been increasingly reported in China since 2015, resulting in substantial economic losses to the poultry industry. The genetic diversity of indigenous chicken results in different immune traits, affecting the evolution of these viruses. Although the molecular epidemiology of fowl adenovirus serotype 4 (FAdV-4) has been well studied in commercial broiler and layer chickens, the prevalence and genetic characteristics of FAdV-4 in indigenous chickens remain largely unknown. In this study, samples were collected from six indigenous chicken breeds in Yunnan province, China. FAdV-positive samples were identified in five of the six indigenous chicken populations via PCR and 10 isolates were obtained. All FAdVs belonged to serotype FAdV-4 and species FAdV-C. The hexon, fiber, and penton gene sequence comparison analysis demonstrated that the prevalence of FAdV-4 isolates in these chickens might have originated from other provinces that exported chicks and poultry products to Yunnan province. Moreover, several distinct amino acid mutations were firstly identified in the major structural proteins. Our findings highlighted the need to decrease inter-regional movements of live poultry to protect indigenous chicken genetic resources and that the immune traits of these indigenous chickens might result in new mutations of FAdV-4 strains.

Current knowledge of Cryptosporidium species/genotypes in marine fish is limited. Following phylogenetic analysis at the 18S rDNA locus, a recent study identified six new genotypes of Cryptosporidium colonizing edible fish found in European seas. Of these, five grouped in a clade together (#Cryptofish 1–5) and one grouped separately (#Cryptofish 7). In the present study, after phylogenetic analyses of #Cryptofish1, #Cryptofish2, #Cryptofish4, #Cryptofish5 and #Cryptofish7 at the actin locus, the presence of two major clades was confirmed. In addition, when possible, longer 18S amplicons were generated. In conclusion, the small genetic distances between these genotypes designated as a novel marine genotype I (#Cryptofish 1-5) suggest that they may be genetic variants of the same species, while the designated novel marine genotype 2 (#Cryptofish 7) is clearly representative of a separate species.

On 17 September 2019, the first outbreak of African swine fever in a pig farm was confirmed in South Korea. By 9 October, 14 outbreaks of ASF in domestic pigs had been diagnosed in 4 cities/counties. We isolated viruses from all infected farms and performed genetic characterization. The phylogenetic analysis showed that all of fourteen ASFV isolates in South Korea belong to genotype II and serogroup 8. Additionally, all isolates had an intergenic region (IGR) II variant with additional tandem repeat sequences (TRSs) between the I73R and I329L genes and showed characteristics of central variable region (CVR) 1 of the B602L gene and IGR 1 of MGF 505 9R/10R genes. These are identical to the genetic characteristics of some European isolates and Chinese isolates.

Border Disease (BD) is a worldwide distributed pathology accountable for significant losses in the sheep and goat farming industry. The etiological agent is a Pestivirus within the family Flaviviridae called border disease virus (BDV). Despite the Sardinian ovine population being by far larger than any other Italian region, the prevalence and distribution of BD on the island are unknown. Here, we aim to determine the distribution of BDV in sheep flocks and to genetically characterize the circulating strains in Sardinia. The geographical distribution, antibody positivity, and viral genome presence have been analysed for 1286 sheep flocks distributed all over the island from bulk tank milk sampled between May 2014 and 2015. Of the flocks tested, 11.28% (95% CI 9.66–13.12) resulted positive for the presence of anti-pestivirus antibodies with an uneven distribution between Sardinian provinces. In addition, using RT-PCR, nine BDV genomes were amplified from milk pellets of the seropositive samples. Phylogenetic analysis revealed that all the viruses amplified clustered in the same group classified as BDV-7. This represents the first study on the distribution of pestivirus infection and genetic characterization of BDV strains circulating in the Sardinian sheep population. Future studies are needed to clarify the origin, the evolution, and the epidemiology of BDV-7 in Sardinia.

Feline coronavirus (FCoV) is a complex viral agent that causes a variety of clinical manifestations in cats, commonly known as feline infectious peritonitis (FIP). It is recognized that FCoV can occur in two different serotypes. However, differences in the S protein are much more than serological or antigenic variants, resulting in the effective presence of two distinct viruses. Here, we review the distinct differences in the S proteins of these viruses, which are likely to translate into distinct biological outcomes. We introduce a new concept related to the non-taxonomical classification and differentiation among FCoVs by analyzing and comparing the genetic, structural, and functional characteristics of FCoV and the FCoV S protein among the two serotypes and FCoV biotypes. Based on our analysis, we suggest that our understanding of FIP needs to consider whether the presence of these two distinct viruses has implications in clinical settings.

This study aimed to identify bovine breeds through trichological morphology and morphometry and to validate this technique by comparing it with genetic characterization. Animals from Caracu, Curraleiro Pé-Duro, Nelore, and Bovino Pantaneiro breeds were studied. Morphological and morphometric analyses of the guard hairs were performed. The cuticular pattern was observed on the shaft and the medulla pattern on the shield of the samples. The cattle genetic characterization was accomplished using microsatellite markers. Statistical analyses were performed using R version 3.2.4 software. Pearson’s correlation test showed a high positive and significant correlation between the matrices generated by trichological and genetic analyses (r = 0,996 and p < 0.001). Trichological analysis is a useful method for cattle breed identification. Its potential for identifying other species of interest for animal production should be studied since it is a simple, low-cost, and non-invasive method.

While there is a rich collection of maize germplasm from Italy, it lacks genetic resources from the Aosta Valley, an isolated mountain region where landraces have been preserved in the absence of modern germplasm introductions. These local materials, which are still cultivated mainly at household level, can have high importance from a genetic and historical point of view. In the present study, five landraces named, after the collecting sites, Arnad, Arnad-Crest, Châtillon, Entrebin and Perloz, were sampled in Aosta Valley and subjected to historic, morphologic and genetic characterization. This study provided evidence for the landraces' long presence in Aosta Valley, a significant genetic variability and differentiation among the investigated landraces. Globally, 67 different alleles were detected ranging from 4 for markers phi127 and p-bnlg176 to 10 for phi031 , with a mean of 6.7 alleles per locus. Observed heterozygosity levels were comprised from 0.16 to 0.51 and are generalkly lower than expected heterozigosity supporting fixation at some loci. STRUCTURE analysis revealed clear separation between accessions revealing the presence of four ancestral populations. This may be explained by the long reproductive isolation experienced by these materials. Finally, morphological observations confirm the high diversity between landraces revealing that they generally have flint kernels, variable color from yellow to dark red (Châtillon) while Perloz showed kernels with an apical beak. The present work confirms the importance of mountain areas in conserving biodiversity and increases the rich Italian maize germplasm with materials well adapted to marginal areas. Such new genetic variability may be used to breed new materials for more resilient agriculture.

Chikungunya virus (CHIKV) is a mosquito-borne virus belonging to the genus Alphavirus. The virus is transmitted to humans by the bite of infected female Aedes mosquitoes, primarily Aedes aegypti. CHIKV infection is spreading worldwide, and it periodically sparks new outbreaks. There are no specific drugs or effective vaccines against CHIKV. The interruption of pathogen transmission by mosquito control provides the only effective approach to the control of CHIKV infection. Many studies have shown that CHIKV can be transmitted among the Ae. aegypti through vertical transmission. The previous chikungunya fever outbreaks in Thailand during 2008−2009 were caused by CHIKV, the East/Central/South African (ECSA) genotype. Recently, there have been 3794 chikungunya cases in 27 provinces reported by the Bureau of Epidemiology of Health Ministry, Thailand during 1 January−16 June 2019; however, the cause of the re-emergence of CHIKV outbreaks is uncertain. Therefore, the aims of this study were to detect and analyze the genetic diversity of CHIKV infection in field-caught mosquitoes. Both female and male Ae. aegypti were collected from endemic areas of Thailand, and CHIKV detection was done by using E1-nested RT-PCR and sequencing analysis. A total of 1646 Ae. aegypti samples (900 females and 746 males) were tested. CHIKV was detected in 54 (3.28%) and 14 samples (0.85%) in female and male mosquitoes, respectively. Seventeen samples of female Ae. aegypti collected from the Ubon Ratchathani, Chiang Rai, Chiang Mai, Nakhon Sawan, and Songkhla provinces found mutation at E1: A226V. Interestingly, E1: K211E mutation was observed in 50 samples collected from Nong Khai, Bangkok, Prachuap Khiri Khan, and Krabi. In addition, the phylogenetic tree indicated that CHIKV in Ae. aegypti samples were from the Indian Ocean Clade and East/South African Clade. Both clades belong to the ECSA genotype. The information obtained from this study could be used for prediction, epidemiological study, prevention, and effective vector control of CHIKV. For instance, a novel CHIKV strain found in new areas has the potential to lead to a new outbreak. Health authorities could plan and apply control strategies more effectively given the tools provided by this research.

Small Ruminant Lentiviruses (SRLVs) are widespread in many countries and cause economically relevant, slow, and persistent diseases in sheep and goats. Monitoring the genetic diversity of SRLVs is useful to improve the diagnostic tools used in the eradication programs. In this study, SRLVs detected in Spanish Assaf sheep with different grades of lymphoproliferative mastitis were sequenced. Genetic characterization showed that most samples belonged to type A and were closer to Spanish SRLV isolates previously classified as A2/A3. Four samples belonged to subtype B2 and showed higher homology with Italian B2 strains than with Spanish B2 isolates. Amino acid sequences of immuno-dominant epitopes in the gag region were very conserved while more alterations were found in the LTR sequences. No significant correlations were found between grades of mastitis and alterations in the sequences although samples with similar histological features were phylogenetically closer to each other. Broader genetic characterization surveys in samples with different grades of SRLV-lesions are required for evaluating potential correlations between SRLV sequences and the severity of diseases.

To determine the presence and the prevalence of four different honeybee viruses (acute bee paralysis virus-ABPV, black queen cell virus-BQCV, chronic bee paralysis virus-CBPV, deformed wing virus-DWV) in wild bumblebees, pooled randomly selected bumblebee samples were collected from twenty-seven different locations in the territory of Croatia. All samples were prepared and examined using the RT-PCR methods for quantification of mentioned honeybee viruses. Determined prevalence (%) of identified positive viruses were in the following decreasing order: BQCV > DWV > ABPV, CBPV. Additionally, direct sequencing of samples positive for BQCV ( n = 24) and DWV ( n = 2) was performed, as well as a test of molecular phylogeny comparison with those available in GenBank. Selected positive field viruses' strains showed 95.7 to 100% (BQCV) and 98.09% (DWV) nucleotide identity with previously detected and deposited honeybee virus strains in the geographic areas in Croatia and neighboring Slovenia. In this article, the first detection of four honeybee viruses with genetic characterization of high diversity strains circulating in wild bumblebees in Croatia is presented.