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The proper use, further development, testing and deployment of animal genetic resources is essential to enhancement of food security and sustainable intensification of food production. For Red Mangalita conservation, we studied four microsatellite markers (SO228, SW72, SW911 and SW936) in order to genetic characterization of two populations. The results showed that both populations are in genetic imbalance, but also indicate high population variability, without the risk of genetic drift.

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.

Maize is a staple food for many communities with high levels of iron deficiency anemia. Enhancing the iron concentrations and iron bioavailability of maize with traditional breeding practices, especially after cooking and processing, could help alleviate iron deficiency in many of these regions. Previous studies on a small number of maize genotypes and maize flour products indicated that degermination (germ fraction removed with processing) could improve the iron bioavailability of maize. This study expanded upon this research by evaluating the iron bioavailability, mineral concentrations, and phytate concentrations of 52 diverse maize genotypes before (whole kernels) and after degermination. Whole and degerminated maize samples were cooked, dried, and milled to produce corn flour. Iron bioavailability was evaluated with an in vitro digestion Caco2 cell bioassay. In 30 of the maize genotypes, bioavailable iron increased when degerminated, thus indicating a higher fractional iron uptake because the iron concentrations decreased by more than 70% after the germ fraction was removed. The remaining 22 genotypes showed no change or a decrease in iron bioavailability after degermination. These results confirm previous research showing that the germ fraction is a strong inhibitory component for many maize varieties. Phytate concentrations in maize flours were greatly reduced with degermination. However, the relationship between phytate concentrations and the iron bioavailability of processed maize flour is complex, acting as either inhibitor or promoter of iron uptake depending on the color of the maize kernels and processing method used to produce flour. Other factors in the maize endosperm fractions are likely involved in the effects of degermination on iron bioavailability, such as vitreous or floury endosperm compositions and the polyphenol content of the bran. This study demonstrates that iron nutrition from maize can be enhanced by selecting genotypes where the inhibitory effect of the bran color and endosperm fraction are relatively low, especially after processing via degermination.

Sarcocystosis considerably occurs in a wide host range including animals, reptiles, humans, and birds. This study was conducted to determine the prevalence of Sarcocystis spp. using abattoir inspection, genetic characterization, as well as histopathology in water buffaloes in two provinces, Elbehera and Kafrelsheikh, Egypt. Specimens were collected from esophagus, tongue, and masseters of 400 slaughtered buffaloes in Elbehera (n= 215) and Kafrelsheikh (n= 185). Samples were examined macroscopically and histopathologically. Furthermore, genetic characterization of Sarcocystis spp. was performed using the 18SrRNA gene-based PCR. The total prevalence was 71.0% (75.3% and 65.9% in Elbehera and Kafrelsheikh, respectively). Aged buffaloes had a higher prevalence than young ones. Females had a higher prevalence than males. The esophagus was the most infected organ. Molecular analysis revealed that the recovered species was S. fusiformis. This is the first genetic characterization of S. fusiformis in water buffaloes from Elbehera and Kafrelsheikh, Egypt. Higher prevalence proposed the potential role of cats in the transmission of S. fusiformis, which, in turn, requires strict hygienic measures to protect animals and humans from infection.

Enzootic bovine leukosis (EBL) is a chronic viral disease of wide distribution in cattle herds and may take several years for the first manifestation of clinical signs. Most animals do not present clinical signs. However, the economic losses are underestimated due to this disease. Thus, this work aimed to detect and characterize BLV in dairy cattle in the Maranhão state, northeastern Brazil. Blood samples were collected from 176 animals from 8 municipalities in the southeastern state of Maranhão. Bovine blood samples were subjected to DNA extraction and molecular diagnosis using nested PCR assays for BLV, targeting gp51 gene. Positive samples were then sequenced and then subjected to phylogenetic inferences. BLV DNA was detected in 16 cattle (16/176, 9.09%) in 4 municipalities. Phylogenetic analyzes showed that the sequence obtained clustered in a clade containing BLV sequences classified as genotype 6, with a high degree of support. Our data shows BLV occurrence in the Northeast of Brazil and the identification of genotype 6 in this region. These findings contribute to the molecular epidemiology of this agent in Brazil.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a persistent negative impact on both the public health and the global economy. To comprehend the origin, transmission routes and discover the mutations that alter the virus’s transmissibility and pathogenicity, full-length SARS-CoV-2 genomes have to be molecularly characterized. Focusing on a two-year time frame (2020-2021), we provide an in-depth virologic and epidemiological overview of the SARS-CoV-2 pandemic in the Republic of North Macedonia by assessing the frequency and distribution of the circulating SARS-CoV-2 variants. Using genetic characterization and phylogenetic analysis we shed light on the molecular evolution of the virus as well as test for a possible connection between specific SARS-CoV-2 haplotypes and the severity of the clinical symptoms. Our results show that one fifth (21.51%) of the tested respiratory samples for SARS-CoV-2 were positive. A noticeable trend in the incidence and severity of the COVID-19 infections was observed in the 60+ age group between males and females. Of the total number of positive cases, the highest incidence of SARS-CoV-2 was noticed in 60+ males (4,170.4/100,000), with a statistically significant (0,0001) difference between the two sexes. Additionally, a 1.8x increase in male mortality and consequentially significantly higher number of death cases was observed compared to females of the same age group (0.001). A total of 327 samples were sequenced in the period March 2020 - August 2021, showing the temporal distribution of SARS-CoV-2 variants circulating in North Macedonia. The phylogenetic analysis showed that most of the viral genomes were closely related and clustered in four distinctive lineages, B.1, B.1.1.7, B.1.351 and B.1.617.2. A statistically significant difference was observed in the 2C_1 haplotype (p=0.0013), where 10.5% of the patients were hospitalized due to severe clinical condition. By employing genetic sequencing, coupled with epidemiological investigations, we investigated viral distribution patterns, identified emerging variants and detected vaccine breakthrough infections. The present work is the first molecular study giving a comprehensive overview of the genetic landscape of circulating SARS-CoV-2 viruses in North Macedonia in a period of two years.

Background: Vaccine-derived poliovirus (VDPV) is a potential threat to polio eradication because they can reintroduce into the general population and cause paralytic polio outbreaks, a phenomenon that has recently emerged as a prominent public health concern at the end of global polio eradication. This study aimed to describe the epidemiology and genetic characteristics of the first VDPV identified from a patient with acute flaccid paralysis (AFP), with four doses of inactivated polio vaccine immunization in Henan Province, China in 2017. Methods: The patient was diagnosed with type 3 VDPV. Subsequently, a series of epidemiological approaches was implemented, including a retrospective search of AFP cases, rate of vaccination assessment, study of contacts, and supplementary immunization activities. Fecal samples were collected, viral isolation was performed, and the viral isolates were characterized using full-length genomic sequencing and bioinformatic analysis. Results: Phylogenetic analysis showed that the viral isolates from the patient were different from other reported genetic clusters of type 3 VDPV worldwide. They were identified as a Sabin 3/Sabin 1 recombinant VDPV with a crossover site in the P2 region. Nucleotide substitutions, including U → C (472) and C → U (2493), have been identified, both of which are frequently observed as reversion mutations in neurovirulent type 3 poliovirus. A unique aspect of this case is that the patient had been vaccinated with four doses of inactive polio vaccine, and the serum neutralizing antibody for Sabin types 1 and 3 were 1∶16 and 1∶512, respectively. Thus, the patient was speculated to have been infected with type 3 VDPV, and the virus continued to replicate and be excreted for at least 41 d. Conclusions: The existence of this kind of virus in human population is a serious risk and poses a severe challenge in maintaining a polio-free status in China. To the best of our knowledge, this is the first report of VDPV identified in the Henan province of China. Our results highlight the importance of maintaining a high-level vaccination rate and highly sensitive AFP case surveillance system in intercepting VDPV transmission. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The present investigation was aimed to study the sequence, phylogenetic and haplotype analyses of Toxocara cati based on the ITS region, along with the genetic diversity, demographic history and population-genetic structure. The maximum likelihood tree based on Kimura 2-parameter model was constructed using the complete ITS region of all the nucleotide sequences (n = 57) of Toxocara spp. and other related ascarid worms available in the GenBank™. It placed all the sequences of T. cati into four major clades designated as T. cati genotypes 1–4 (TcG1–G4). A total of 66 signature nucleotides were identified in the ITS region between genotypes. The median-joining haplotype network displayed a total of 24 haplotypes, with China exhibiting the highest number of haplotypes (h = 20) followed by India (h = 4), and Japan and Russia (h = 1). It indicated a clear distinction between all the four genotypes. The pairwise FST values between all the genotypes indicated huge genetic differentiation (> 0.25) between different T. cati genotypes. Moreover, the gene flow (Nm) between T. cati genotypes was very low. Results of AMOVA revealed higher genetic variation between genotypes (92.82%) as compared to the variation within genotypes (7.18%). The neutrality indices and mismatch distributions for the G1–G4 genotypes, Indian isolates and the overall dataset of T. cati indicated either a constant population size or a slight population increase. The geographical distribution of all the genotypes of T. cati is also reported. This is the first report of genotyping of T. cati on the basis of the ITS region. [ABSTRACT FROM AUTHOR]

In August 2021, we detected highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses in poultry in southern Benin. The isolates were genetically similar to H5N1 viruses of clade 2.3.4.4b isolated during the same period in Africa and Europe. We also found evidence for 2 separate introductions of these viruses into Benin. [ABSTRACT FROM AUTHOR]

The specimens of Apis mellifera, A. dorsata and A. florea were collected during field surveys during July, 2018 to August, 2020 from selected sites of Punjab, Pakistan. These sites included Bhawalpur, Khaniwal, Kasur, Lahore, Chakwal and Rawalpindi. The captured specimens were identified first on the basis of morphology and then identified using mitochondrial DNA genes. A. mellifera workers, queens and drones were black in color. Apis dorsata workers were yellow, however, queens and drones were brown. Apis florea queens and workers were yellow banded and the drones were black. The phenol chloroform technique was used to extract whole genomic DNA from preserved honey bee tissues. The quality of the DNA was determined using gel electrophoresis, and the quantity was determined using a thermal scientific Nano-drop. COI primers were used for PCR amplification. All of the acquired specimens' DNA sequences revealed reliable and obvious species identification. GenBank was contacted when appropriate amplified DNA samples were uploaded, and accession numbers were acquired (MZ433243.1, MZ433277.1 and MZ433289.1). After removing problematic bases, the Apis mellifera, Apis dorsata, and Apis florea COI gene fragments were 670, 680, and 675, respectively. Closely comparable Apis sequences were collected from NCBI in blast queries and used in phylogenetic studies. Neighbor-Joining tree, Maximum Likelihood tree and Minimum Evolution tree of the genus Apis was constructed based on p-distance using MEGA X. The overall, genetic divergence of genus Apis was 0.098 ± 0.022. It can be concluded that the morphological characteristics provide information as an indicator for estimating genetic variations between honey bee populations. Further work is needed to explore more areas of Pakistan and molecular identification is required to report any new or subspecies from country. [ABSTRACT FROM AUTHOR]

Marek's disease (MD) is a highly contagious lymphoproliferative disease of chickens caused by Gallid alphaherpesvirus 2, commonly known as serotype 1 Marek's disease virus (MDV‐1). Despite widespread vaccination, MD‐related cases have been frequently observed worldwide, including in Thailand. However, no information is available on the genetic characteristics of MDV‐1 field strains circulating in chickens in Thailand. This study investigated the geographic distribution and genetic characteristics of MDV‐1 field strains circulating in chickens in Thailand between 2013 and 2021 by analysing the Meq and pp38 genes. Out of a total of the 286 clinical samples obtained from 70 chicken farms located in major chicken raising areas of Thailand, 138 samples (48.25%) from 46 chicken farms (65.71%) tested positive for MDV‐1 field strains. Results demonstrated that MDV‐1 field strains were extensively distributed in major chicken raising areas. Phylogenetic analyses based on the Meq gene revealed that four clusters of MDV‐1 circulated in chickens in Thailand between 2013 and 2021. Among these clusters, cluster 1 was the predominant cluster circulating in chickens in Thailand. Additionally, our findings based on molecular characteristics of Meq and pp38 gene/protein suggested that most of the Thai MDV‐1 field strains were potentially highly virulent. In conclusion, our data demonstrated the circulation of different clusters of MDV‐1 with virulence characteristics in chickens in Thailand, indicating high genetic diversity of MDV‐1 in Thailand. This study highlights the importance of more effective vaccine development and routine MDV‐1 surveillance for early detection and control of highly virulent MDV‐1. [ABSTRACT FROM AUTHOR]

In this study, the viral genome extraction performance of automatic nucleic acid extractors and manual nucleic acid extraction kits was compared. We showed that compared with manual kits, the automatic extractors showed superior genome extraction performance using bovine viral diarrhea virus (BVDV) genome-positive cattle sera and bovine coronavirus/infectious bovine rhinotracheitis virus-spiked cattle nasal swabs. In addition, the subgenotyping of BVDV strains detected in Tokachi Province in Japan during 2016–2017 was performed. Results showed that most of these BVDV strains belonged to subgenotype 1b, while few strains belonged to subgenotypes 1a and 2a. This study showed the high applicability of automatic nucleic acid extractors in extracting multiple viral genomes and the dominant subgenotype of BVDV in Tokachi. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome (PRRS) is an immunosuppressive disease caused by PRSS virus (PRRSV). PRRSV mainly causes reproductive disorders in pregnant sows and respiratory diseases in piglets. Recently, it has emerged as one of the most important diseases of the pig industry across the globe. In this study, we have collected 231 samples from differently sized pig farms in Eastern China from 2017 to 2022 to investigate the epidemic characteristics of the disease. All samples were screened by RT-PCR and analyzed further using Nsp2 and ORF5 genes. The result showed that the positive rate of PRRSV was 24% (54/231). Phylogenetic analysis (13 positive samples) revealed that all isolates belonged to genotype 2, and they were mainly distributed in four lineages (i.e., lineage 1, 3, 5, and 8). Nsp2 is the most variable protein among all PRRSV NSPs, several isolates from this study had amino acid deletions within Nsp2 compared to that of strain VR-2332. The major structural protein glycoprotein (GP5) protein is encoded by ORF5. Epitope analysis of the 13 isolated strains and additional reference strains revealed that all 13 strains had some mutations on the decoy epitope, the primary neutralizing epitope, T cell epitopes, and B cell epitopes. This study showed that the prevalent PRRSV strain in Eastern China was still HP-PRRSV, while the proportion of NADC30-like and NADC34-like strains have increased. This study further enriches the epidemiological data of PRRS in Eastern China and provides a theoretical basis for vaccine development and prevention and control of the disease across the region. [ABSTRACT FROM AUTHOR]

Balochi sheep is one among the established sheep breeds of Balochistan province in Pakistan. As far as its size is concerned, it is medium sized, having fat tail and inhabits in the Northern regions in Balochistan. Molecular studies are the base of breed characterization. Hence, nearly 25 unrelated (including both male and female) animals of Balochi breed were sampled for DNA extraction. Some specific markers (15 out of available 30 SSR markers) were employed in the present study to highlight genetic polymorphism. The PCR was utilized for amplification of individual DNA samples. All of the 15 SSR markers were amplified. After gel documentation, a total number of 97 alleles were recognized having 1 to 5 polymorphic forms (OARFCB193, OARJMP29, MAF33) to 4 (OARHH47, DYMS1, SRCRSP5). For total loci, number of alleles averaged 2.1162±0.3769. Shannon's Information index (I) 0.6184±0.2447 and the effective number of alleles (Ne) averaged 1.6251±0.4604. Average observed, expected and average heterozygosities were found to be 0.5815±0.1059, 0.4330±0.5811 and 0.4331±0.5811, respectively. It was noted that the F-statistic was ranging from 0.2166 to 0.95182 for the microsatellite markers employed in the study. Expected reduction in heterozygosity was higher than mean value in case of most of the markers with lower standard errors showing the prevalence of homozugous Balochi sheep population. The main cause reason behind prevalence of homozygous population might be inbreeding as only few rams had been used for breeding the flocks. This study would provide basis for breed characterization and lead to breed improvement program. [ABSTRACT FROM AUTHOR]

An inbred strain limits the segregating variance and provides more power and requires fewer experimental animals to produce good reproducibility. This study was undertaken with the aim to assess the impact of sex of offsprings and sex specific microsatellite variants on performance and fitness traits in F4 inbred Swiss albino mice. The phenomics of different performance and fitness traits were estimated on 506 F4 inbred mice population. Two ‘X’ chromosome specific microsatellite loci (DXMit187 and DxMit172) were used for PCR-Microsatellite genotyping of 102 F4 inbred population. PIC estimates showed that both the loci were informative for the population. In the current population, with the increasing level of “F” a declining trend was observed for Body weight at birth (BWB), Body weight at weaning (BWW), Litter size at weaning (LSW) and Litter weight at weaning (LWW). In F4 inbred population, BWW and ABW for males (17.32±0.32g and 30.81±0.31g) were significantly (p

Toxoplasma gondii ( T. gondii ) is an intracellular protozoan that can cause toxoplasmosis in all warm-blooded hosts. This study focused on the prevalence and genetic characterize of T. gondii in ducks from Fujian province, China. Genomic DNA was extracted from duck tissue samples (heart, liver, lung, and muscle). To assess the genetic diversity of the T. gondii isolates, it was determined by using multilocus polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technology. A total of 586 ducks from 5 cities in Fujian province were tested, and 35 (6.0%) of which were found to be positive for the T. gondii B1 gene. Further genotyping of these positive samples at 10 genetic markers (SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico) using PCR-RFLP revealed that one tissue samples (heart samples from Fuzhou ducks) were identified as Type I (ToxoDB#10). This study is the first report on the prevalence and genetic characterization of T. gondii in ducks in Fujian province, and Type I (ToxoDB#10) is found in ducks in China for the first time. The findings document the genetic characterization of T. gondii in free-range ducks from Fujian Province, thereby enriching the understanding of T. gondii genetic diversity in China. Moreover, these results provide essential data support for further prospective studies and underscores the "One Health" concept, emphasizing the integral link among human, animal, and environmental health. [ABSTRACT FROM AUTHOR]

The aim of the present study was to investigate the frequency, genetic variability, and phylogeny of the peste des petits ruminants virus (PPRV) in ovine and caprine fetuses. During 2014 and 2017, a total of 1054 embryos/fetuses were collected in Turkey. A real-time RT-PCR assay was used for the detection of the PPRV RNA. Genetic characterization and phylogenetic analysis of the PPRV field isolates were conducted by sequencing fusion (F) protein and nucleoprotein (N) gene segments. Samples were also collected from ewes (n = 83) and nanny goats (n = 3) that had aborted and whose embryos/fetuses were found to be PPRV positive. PPRV positive embryos/fetuses were also tested for the presence of Listeria monocytogenes , Campylobacter spp., Coxiella burnetii , Chlamydophila abortus , Brucella spp., akabane virus, aino virus, bluetongue virus, border disease virus, bovine viral diarrhea virus, Cache Valley virus, and Schmallenberg virus. PPRV RNA was detected in 123 (11.7 %) of the 1054 embryos/fetuses, 78 of the 83 (94 %) ewes and 3 (100 %) nanny goats. Border disease virus RNA and Chlamydophila abortus DNA were detected in 7 and 12 PPRV positive sheep fetuses, respectively, while other bacterial and viral agents were not detected. Phylogenetically, the field isolates in this study belong to lineage IV, and compared to other strains of lineage IV considered in this study, they showed 1 and 5 new amino acid substitutions in the F and N gene sequences, respectively. The results of the study suggest that PPRV plays an important role in abortion. Therefore, PPRV needs to be taken into consideration in sheep and goats abortions. • PPRV RNA was detected in 123 of the 1054 embryos/aborted fetuses. • PPRV was detected in ewes and nanny goats whose fetuses were found as PPRV positive. • The rate of abortion in PPRV positive flocks ranged between 6.4 % and 37.5 %. • PPRV positivity was significantly higher in fetuses between 1 and 2 months of age. • Other bacterial and viral agents were not detected in PPRV-positive embryos/fetuses. [ABSTRACT FROM AUTHOR]

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.

Ganges River sprat, Corica soborna Hamilton, is an indigenous fish species and an excellent source of animal protein with medicinal values in Bangladesh. Samples from two populations of this fish species were collected from Kaptai Lake and Kirtankhola River in Bangladesh to elucidate their genetic diversity based on Random Amplified Polymorphic DNA (RAPD) analysis. Ten primers were selected for this analysis: OPA-04; OPAL-04; OPA-03; OPF-01; OPG-05; OPG-04; OPA-09; OPAK-04; OPAW-09; OPA-02. A total of sixty-eight bands were found of which thirty-two were polymorphic and indicated a moderate level as 51.07% polymorphisms between these two fish populations. The size of the bands ranged between 200 to 1300 bp in their analysis. Based on the specific primer banding patterns, a maximum polymorphism of 100% was found for primer OPF-01; however, the lowest of 14.29% polymorphism was found for primer OPG-04 for these two populations. The genetic distance and genetic identity of 0.8210 and 0.4400, respectively, also indicated that these two populations were moderately distant from each other. A dendrogram based on Nei’s (1972) genetic distance was constructed using the Unweighted Pair Group Method of Arithmetic Means (UPGMA), and it segregated these two populations into one major cluster C1. Therefore, the present study revealed that these two Ganges River sprat populations are moderately genetically diversified. An effective management program and policy should be undertaken to conserve and manage these indigenous fish species in Bangladesh.

The family Parvoviridae comprises many major viral pathogens that can infect humans and multiple other species, causing severe diseases. However, knowledge of parvoviruses that infect equids is limited. In the present study, we found that three equine parvoviruses (EqPVs), namely, equine parvovirus-hepatitis (EqPV-H), equine parvovirus-cerebrospinal fluid (EqPV-CSF) and equine copivirus (EqCoPV) cocirculated among horses in China. We examined the prevalence of these three EqPVs in 225 horse serum samples in China and found EqPV-H, EqPV-CSF and EqCoPV viremia in 7.6% (17/225), 2.7% (6/225) and 2.2% of samples (5/225), respectively. We also obtained the complete genomes of one EqPV-H strain, six EqPV-CSF strains and one EqCoPV strain. After phylogenetic analysis of the EqPVs, we found that EqPV-CSF and EqCoPV may have evolved from the same ancestor. The EqPV-CSF strains (E111 and A27) and EqCoPV strain (F124) were genetically similar to foreign strains, but the EqPV-CSF strains (B48, E96, C61 and F146) comprised unique clades. This study determined the prevalence of three EqPVs in Chinese horses and analyzed the genetic characteristics of EqPVs prevalent strains in Chinese horse herds. Our data provide a theoretical basis for follow-up research on the prevention and control of EqPVs.

ABSTRACT: Non-typhoidal Salmonella (NTS) poses a global threat to public health. Poultry, one of the main reservoirs of NTS, is usually not clinically affected by most NTS, yet the economic losses to the poultry industry due to control and mitigation efforts, and due to negative publicity can be tremendous.NTS strains are routinely characterized into serotypes in a time-consuming, labor-intensive multistep process that requires skilled personnel. Moreover, the discriminatory power of serotyping is limited compared to other subtyping methods. Whole-genome sequence data enable the identification of genetic variation within serotypes. However, sequencing is often limited by available resources, and analyzing and interpreting the genetic data may be time-consuming. Source tracing during epidemiological outbreak investigations requires rapid and efficient characterization of strains to control pathogen spread. Here we designed a multiplex polymerase chain reaction (PCR) assay for the detection of genetic variants of Salmonella Muenchen, a serotype that has emerged in Israel in the last 3 yr in both clinical human cases and different hosts. Test sensitivity of 99.21% and specificity of 94 to 100% were determined using in-silico PCR with a dataset of 18,282 NTS assemblies from 37 NTS serotypes. Similarly, test sensitivity of 100% and specificity of 96.2 to 100% were determined in-vitro with 120 NTS isolates of 52 serotypes. Moreover, the test enabled differentiation between the common sequence types of serotype Muenchen using both approaches. As opposed to traditional serotyping and other subtyping methods, the designed test allows for rapid and cost-efficient detection of the emerging S. Muenchen serotype and its variants in a single step. Future development of similar assays for other dominant serotypes may help reduce the time and cost required for detection and initial characterization of dominant NTS strains. Overall, these tests will be beneficial to both public health and for reducing of the economic losses to the poultry industry due to NTS infections.

Canine parvovirus type 2 (CPV-2) and feline panleukopenia virus (FPV) cause severe disease in young animals, pups, and kittens. CPV-2 evolved from FPV by altering the species-specific binding of the viral capsid to the host receptor, i.e., the transferrin receptor (TfR), and CPV-2 genetic variants have been identified by specific VP2 amino acid residues (297, 426). Early studies focused on the main capsid protein VP2; however, there have been limited studies on the non-structural protein NS1. In this study, we identified the genetic variants of clinical samples in dogs and cats in northern China during 2019–2020. The genetic characterization and phylogenetic analyses of VP2 and NS1 gene were also conducted. The results revealed that the CPV-2c was identified as the major genetic variant. One new CPV-2b and two CPV-2c strains were collected from cats. Four mutation sites (60, 630, 443, and 545 amino acid residues) were located in the functional domains of the NS1 protein. The phylogenetic analysis of VP2 and NS1 genes showed that they were clustered by geographical regions and genotypes. The gene mutation rate of CPV-2 was increasing in recent years, resulting in a complex pattern of gene evolution in terms of host preference, geographical selection, and new genetic variants. This study emphasizes that continuous molecular epidemiological surveillance is required to understand the genetic diversity of FPV and CPV-2 strains.

Aspergillus niger is a major cell factory for citric acid production, and the process of citrate export from mitochondria to cytoplasm is predicted to be one of rate-limiting steps in citric acid accumulation. Currently, the mitochondrial citrate transporters (Ctps) in A. niger are not fully characterized. Here, six putative Ctp encoding genes (ctpA to ctpF) were identified based on their homology with a mitochondrial citrate transporter ScCtp1 from Saccharomyces cerevisiae. Disruption of individual ctpA to ctpF caused varying degrees of decline in citric acid accumulation at different fermentation stages, whereas a mutant strain S1696 with disruption of all six ctps showed complete loss of citiric acid production. S1696 also exhibited delayed growth, reduced conidia formation, and decreased pigmentogenesis. Exogenous addition of citrate partially restored the conidia formation and pigmentogenesis in S1696 mutant. Reintroduction of individual ctps (ctpA to ctpF) into S1696 at the amyA locus showed that ctpA, ctpB, and ctpD restored the citric acid titers to 88.5, 93.8, and 94.6% of the parent strain, respectively. Additionally, the formation of conidia and pigment production was partially restored after reintroduction of ctpA, ctpB, or ctpD. Overexpression of respective ctpA, ctpB, and ctpD in the parent strain resulted in increases in citric acid accumulation by 32.8, 19.3, and 24.2%, respectively. These results demonstrate that CtpA, CtpB, and CtpD play important roles in citric acid transport across the mitochondrial membrane and function in a redundant manner. Enhancement of citric acid transport process can serve as a target for boosting citric acid accumulation in A. niger. [ABSTRACT FROM AUTHOR]

Purpose: Porcine cysticercosis is a neglected zoonotic disease of significant veterinary and medical importance owing to its economic impact and public health significance. The present study aimed at genetic characterization of Taenia solium metacestodes in slaughtered pigs of Haryana (North India). Methods: A total of 213 (160 and 53 from Chandigarh and Hisar, respectively) slaughtered pigs intended for human consumption were screened for the presence of T. solium metacestodes. The retrieved metacestodes were confirmed molecularly based on the partial amplification of mitochondrial cytochrome c oxidase subunit 1 (CO1) gene. Evolutionary divergence, haplotype and nucleotide diversities and neutrality indices of the retrieved isolates were also assessed. Results: Out of the 213 pigs, 2 (0.94%) revealed the presence of metacestodes involving 1 pig each from Chandigarh (0.62%) and Hisar (1.9%). The sequences obtained after custom sequencing were submitted to GenBank under the accession numbers LC661682-83. The present study haplotype clustered with haplotypes of Asian origin and showed variation from other haplotypes by 1–23 mutational steps. However, the present study isolates also showed nucleotide polymorphisms (A198T, A199G, A201T, G204A, T206A, C210T, T212G, T213A, T216G/A, T217C, T221C, C524T, G994A) at different positions, which indicated the presence of sub-lineages. Low nucleotide diversity (π = 0.020) and negative value of Tajima's D (− 1.304) observed for the haplotypes under consideration was indicative of purifying selection and recent population expansion. Conclusions: Our study confirms the circulation of T. solium Asian genotype (with distinct sub-lineages) in study area and recommends strict control measures to contain the zoonotic disease. [ABSTRACT FROM AUTHOR]

Sabanejewia romanica was recorded for the first time on the territory of Serbia in three direct tributaries of the Danube River (Rečka River, Slatinska River and Zamna River). This is the first record of the species outside Romania, the westernmost point of its occurrence and the first verified record of the species from the right tributaries of the Danube River. Genetic characterisation of the Serbian specimens showed that they are the most related to the Romanian S. romanica, with a high recorded net evolutionary divergence between them. Further studies with included populations from the whole geographical range of S. romanica should provide an accurate picture of genetic diversity and phylogenetic relations within the species. [ABSTRACT FROM AUTHOR]

A total of 1007 samples (910 fecal droplets and 97 cloacal swabs) were collected from 14 species of migratory wild birds in most wetlands during 3 successive migration seasons from September to March (2015–2018) in Southern Egypt. The samples were propagated in embryonated chicken eggs and positive allantoic fluids by hemagglutination test were tested for Newcastle disease virus (NDV) and avian influenza virus (AIV) prevalence using RT-PCR and specific primers targeting the NDV fusion (F) and AIV matrix genes. Further subtyping of the AIV hemagglutinin (HA) and neuraminidase (NA) was conducted, and representative isolates were selected and sequenced for full F gene of NDVs and HA and NA genes of the AIV. Overall isolation rate of hemagglutinating viruses was 5.56% (56/1007), from them 5.36% (3/56) AIV, 85.71% (48/56) NDV and 8.93% (5/56) co-infection of NDV and AIV was detected. The sequences analysis of full F genes of 10 NDV isolates revealed that they have multi-basic amino acid motifs 111E/GRRQKR/F117 as velogenic strains with nucleotides and amino acids similarities of 96–100%. In addition, they phylogenetically clustered into groups and subgroups within genotype VII.1.1 and sub-genotype VIIj with a close relation to NDVs isolated from chickens in Egypt. The AIV H5N8 subtype was in clade 2.3.4.4b with a highly pathogenic nature and close relation to Egyptian domesticated H5N8 viruses rather than those from wild birds. The current data showed the contribution of migratory birds to the continuous circulation of virulent NDV and AIV H5N8 among domesticated chickens in Southern Egypt. [ABSTRACT FROM AUTHOR]

Simple Summary: Prairie dogs are native to the United States, Canada, and Mexico. They have been brought to Thailand and become popular as exotic pets and providing humans with exotic pets in close-contact environments. Prairie dogs have been known to carry several waterborne protozoan pathogens. One of those pathogens is known as Giardia, a flagellate protozoan parasite which can cause gastrointestinal illness in humans and other animals. This study has identified the Giardia parasite in the feces of prairie dogs. There were 13% of prairie dogs pets in Bangkok, Thailand that carried the Giardia parasite. We also found that the parasite was categorized as a human parasite. Therefore, there was potential risk that prairie dogs could contract a Giardia infection from humans as a source, and that humans could receive the parasite from their exotic pets via the fecal-oral route in shared environments. We suggest that exotic pet owners should pay more attention to effective sanitation and provide clean food and water for their exotic pets. Owners should bring their exotic pets for veterinary services and screening of zoonotic pathogens using fecal examination regularly. Treatment can successfully cure the infected pets as well as prevent the spreading of pathogen to the environment. 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. [ABSTRACT FROM AUTHOR]

Background and Objectives: Blocking the attachment of diphtheria toxins to host cells through the intact receptor binding site (tox B) was the initial mechanism of action of the diphtheria vaccine. Diphtheria outbreaks in populations with good vaccination coverage can be caused by mutations or changes in the genetic structure of the tox B protein. The aim of this study was to characterize the Tox B protein produced by Corynebacterium diphtheriae isolated from 2018 to 2019 in patients in Jakarta who had already received the diphtheria vaccine. Materials and Methods: Of the 89 throat swab specimens of patients with a clinical diagnosis of diphtheria, 10 were positive for diphtheria and toxin. PCR was used to amplify the tox B DNA fragment in the 10 positive isolates. DNA sequencing was conducted with overlapping primers and the DNA sequences were analysed by using SeqScape V2.7. Results: Of the 10 isolates, nine isolate showed a DNA mutation (G30A), but the mutation did not change the amino acid encoding arginin (silent mutation). Our findings indicate that the efficacy of the diphtheria vaccine used in Indonesia has not decreased because of mutations in the tox B genes not change the amino acid. Conclusion: Overall, there are no amino acid changes in the tox B protein, indicating that the outbreaks are not affected by mutation in tox B. Another possible mechanism -- overexpression of the toxin -- is likely responsible for causing diphtheria in patients who have a complete history of immunization in Indonesia. [ABSTRACT FROM AUTHOR]

Taenia solium cysticercosis is a potentially eradicable neglected zoonotic disease with public health importance. The genetic lineages of T. solium in Asia and Africa/America are distinct and the genetic composition of the parasite was found to influence the clinical symptoms in patients with cysticercosis. In the present study, the Cysticerci collected from pigs of two southern states of India (Karnataka and Andhra Pradesh) were genetically characterized based on mitochondrial (COX 1 and Cyt b) and ribosomal (ITS‐1 and TBR) DNA markers. The study confirms the existence of two mitochondrial lineages of the parasite as Asian and African/American. Cytochrome oxidase 1 (COX 1) based analysis revealed the existence of two sub‐lineages of the parasite within the Asian lineage based on the polymorphism at 994 position as 994A/G. In India, both the sub‐lineages were identified and genetic divergence among different Indian isolates was evident. Further, the sequence analysis of Cytochrome B (Cyt b) revealed the existence of six sub‐lineages of T. solium in India as 69T/69G, 97A/97G as well as 264T/264C. The analysis of nucleotide sequence of large subunit ribosomal DNA (TBR) revealed the existence of two sub‐lineages in India based on the deletion of a nucleotide at 624th position. The cysts collected in the present study were more closely related to those of China and Indonesia than with other Indian isolates. Further, the sequence analysis did not indicate the presence of Taenia asiatica in the examined pigs and African/American lineages of T. solium. The results of the present study help to better understand the genetic diversity of T. solium in India. [ABSTRACT FROM AUTHOR]

Infectious bursal disease (IBD) is a highly contagious immunosuppressive disease of poultry. To better understand the epidemiology of IBD virus (IBDV) in the country, a total of 39 field IBDVs from commercial broiler flocks in seven regions of the Philippines were analyzed. Clinical signs observed were uniformity problems, inappetence, lethargy, stunted growth, poor average daily gain, irregular size of bursa of Fabricius, and mortality rates ranging from four to 19%. Phylogenetic analysis highlighted the following: three (7.69%) field strains were from G1 classic genotype; 16 (41.03%) were G1 vaccine IBDVs; 17 (43.59%) were G2 variants; two (5.12%) were G3 vvIBDVs; and one (2.56%) was a G7 vaccine IBDV. Regional distribution showed that G1 IBDVs were detected in regions 2, 3, 4, 5, 6, 7, and 11, G2 IBDVs were observed in Regions 3 and 4, G3 IBDVs in Regions 6 and 7, and G7 IBDV in Region 3. It was demonstrated that G2 IBDVs were closely related (95-96%) to variant strains from the USA, whereas the G1 and G3 IBDVs were closely related (96.00-100%) to IBDVs from several countries in Southeast and Far East Asia. This study is so far the first to comprehensively document the molecular as well as the epidemiological characteristics of IBDVs in the Philippines. [ABSTRACT FROM AUTHOR]

Introduction. After two seasons of absence and low circulation, influenza activity increased significantly in the winter of 2022-2023. This study aims to characterize virological and epidemiological aspects of influenza infection in Bulgaria during the 2022-2023 season and perform a phylogenetic/molecular analysis of the hemagglutinin ( HA ) and neuraminidase ( NA ) sequences of representative influenza strains. Hypothesis/Gap Statement. Influenza A and B viruses generate new genetic groups/clades each season, replacing previously circulating variants. This results in increased antigenic distances from current vaccine strains. Strengthening existing influenza surveillance is essential to meet the challenges posed by the co-circulation of influenza and SARS-CoV-2. Methodology. We tested 2713 clinical samples from patients with acute respiratory illnesses using a multiplex real-time RT-PCR kit (FluSC2) to detect influenza A/B and Severe acute respiratory syndrome coronavirus-2(SARS-CoV-2) simultaneously. Representative Bulgarian influenza strains were sequenced at the WHO Collaborating Centres in London, UK, and Atlanta, USA. Results. Influenza virus was detected in 694 (25.6 %) patients. Of these, 364 (52.4 %), 213 (30.7 %) and 117 (16.9 %) were positive for influenza A(H1N1)pdm09, A(H3N2) and B/Victoria lineage virus, respectively. HA genes of the 47 influenza A(H1N1)pdm09 viruses fell into clades 5a.2. and 5a.2a.1 within the 6B.5A.1A.5a.2 group. Twenty-seven A(H3N2) viruses belonging to subclades 2b, 2a.1, 2a.1b and 2a.3a.1 within the 3C.2a1b.2a.2 group were analysed. All 23 sequenced B/Victoria lineage viruses were classified into the V1A.3a.2 group. We identified amino acid substitutions in HA and NA compared with the vaccine strains, including several substitutions in the HA antigenic sites. Conclusion. The study's findings showed genetic diversity among the influenza A viruses and, to a lesser extent, among B viruses, circulating in the first season after the lifting of anti-COVID-19 measures.

Background and Objectives: Blocking the attachment of diphtheria toxins to host cells through the intact receptor binding site (tox B) was the initial mechanism of action of the diphtheria vaccine. Diphtheria outbreaks in populations with good vaccination coverage can be caused by mutations or changes in the genetic structure of the tox B protein. The aim of this study was to characterize the Tox B protein produced by Corynebacterium diphtheriae isolated from 2018 to 2019 in patients in Jakarta who had already received the diphtheria vaccine. Materials and Methods: Of the 89 throat swab specimens of patients with a clinical diagnosis of diphtheria, 10 were positive for diphtheria and toxin. PCR was used to amplify the tox B DNA fragment in the 10 positive isolates. DNA sequencing was conducted with overlapping primers and the DNA sequences were analysed by using SeqScape V2.7. Results: Of the 10 isolates, nine isolate showed a DNA mutation (G30A), but the mutation did not change the amino acid encoding arginin (silent mutation). Our findings indicate that the efficacy of the diphtheria vaccine used in Indonesia has not decreased because of mutations in the tox B genes not change the amino acid. Conclusion: Overall, there are no amino acid changes in the tox B protein, indicating that the outbreaks are not affected by mutation in tox B. Another possible mechanism – overexpression of the toxin – is likely responsible for causing diphtheria in patients who have a complete history of immunization in Indonesia.

The white-tailed eagle, Haliaeetus albicilla, has been involved in the life cycle of several Sarcocystis species as the intermediate and definitive host. To date, it has been supposed that the eagle might play the role as the definitive host for S. Lutrae, and, herein, we tried to elucidate it based on morphometric and molecular analyses. One out of two eagles harbored oocysts (17.0−17.4 × 11.3–11.9 μm) and sporocysts (11.3–12.3 × 8.3–9.3 μm) in the intestinal mucosa, whose sequences at 18S rRNA, 28S rRNA, ITS1, and cox1 showed similar identity (97.64–100%) to published sequences of S. lutrae from other hosts. The presence of sporulated oocysts in the lamina propria of villi confirms that S. lutrae truly infects the white-tailed eagle. The white-tailed eagle is confirmed as the definitive host of S. lutrae in the Czech Republic.

(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.

Simple Summary: Wild boars and feral pigs are underinvestigated hosts for influenza A viruses (IAVs). This study confirmed and evaluated viral circulation in the Emilia-Romagna wild boar population between 2017 and 2022. Samples were collected at post mortems and screened for IAVs; 0.37% of the tested animals provided positive results. Positive samples were subtyped, isolated, and genotyped via full-genome sequencing. The results highlight the co-circulation of the same viral genotypes in overlapping years in both pigs and wild boars in the same geographical area. Considering the role of domestic and wild Sus scrofa species in the IAVs' ecology, surveillance against these viruses in the wild boar population needs to be implemented. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: There are many causes of mortality in free-living songbirds, and, usually, the general public is not particularly interested in these issues. Only when large numbers of dead birds are observed within small geographic areas and within a short period of time is some public attention focused on these phenomena. In this study, we investigated episodes of mass mortality of songbirds, especially in greenfinches all over Austria, which occurred between 2012 and 2020. We noticed that all of these losses were caused by a particular protozoal parasite (Trichomonas (T.) gallinae) which induced severe inflammation of the upper digestive tract and subsequently death due to starvation. We were able to establish clear links with almost identical disease outbreaks in other countries and thus trace the path of the pathogen through Europe. It could be shown that T. gallinae has spread over the whole of Austria in recent years and occurred in many different songbird species, with a preference for greenfinches, leading to a significant decline in the population of this bird species. Since most birds are presumably infected at feeding sites, hygiene conditions and the correct selection of feeders play an important role in the prevention of disease. 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. [ABSTRACT FROM AUTHOR]

Simple Summary: Cryptosporidium is a widespread pathogen that infects a broad range of vertebrates, including humans, in which it is one of the main causes of diarrhea worldwide. Marine fishes also harbor Cryptosporidium species, including zoonotic ones. The goal of this study is to evaluate the presence of Cryptosporidium species in edible marine fishes using molecular tools. The area of study, located in the Western Mediterranean, is an important area for marine fish production and capture. The following three groups were studied: cultivated fish, wild fish that aggregate in the surroundings of marine fish farms and wild fish from extractive fisheries. Results show that the most affected group is the group of wild fish from the vicinity of fish farms. Two species were mainly identified, C. molnari (fish specific) and zoonotic C. ubiquitum. The presence of zoonotic C. ubiquitum in two European sea bass (Dicentrarchus labrax) highlights a potential risk for fish consumers. 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Carob (Ceratonia siliqua L.) with limited widespread in Turkey is considered as secondary forest tree. In this study, molecular characterizations were made for 508 genotypes of seven different carob populations colelcted from Eagean, Western and Eastern Mediterranean regions of Turkey with the aid of sequence-related amplified polymorphism (SRAP) technique. Identification of wild carob genotypes, relativity levels and genetic variations among them were performed. Genetic similarities among 508 wild carob genotypes collected from Eagean, Western and Eastern Mediterranean regions of Turkey varied between 0.20-1.00 and there was a large variation among the genotypes. The genetic similarities among 250 wild carob genotypes collected from Aegean region varied between 0.36-1.00. The genetic similarities among 154 wild carob genotypes collected from Western Mediterranean region varied between 0.23-1.00. The genetic similarities among 102 wild carob genotypes collected from Eastern Mediterranean region varied between 0.21-1.00. Through the molecular analyses conducted with SRAP primers, besides the large variations among the entire genotypes, large variations were also observed between the genotypes of different regions. With this study, genetic variations were put forth among the wild carob genotypes naturally growing in different regions of Turkey. It was concluded based on present findings that marker system could reliably be used to put forth genetic variations among wild carob genotypes. [ABSTRACT FROM AUTHOR]

Previous studies revealed that the small ruminant lentivirus (SRLV) population in Poland is highly heterogeneous. All SRLVs detected from Polish sheep and goats so far have belonged to subtypes B1, B2, A1, A5, A12, A13, A16, A17, A18, A23 and A24. However, all characterized strains originated from asymptomatic animals. This is the first study that characterizes the molecular properties of SRLVs isolated from different organs of six arthritic goats. Segments from three genomic regions (gag, LTR and env) were analyzed. In addition, we quantified the SRLV proviral load in the blood and different organs and examined its association with different degrees of histopathological lesions. All sequences obtained from the goats involved in this study were homogeneous, showing an average degree of variability of 4.8%, 3.7% and 8.8% for gag, LTR and env, respectively. Phylogenetic analysis revealed that the sequences from the analyzed goats were clustered within SRLVs group A and formed a new subtype within this group, tentatively named A27. The histopathological examination of the lung, mammary gland, synovial membranes of joints and brain of the analyzed goats revealed evidence of inflammatory processes associated with SRLV infection, which was confirmed by positive immunohistochemistry assays. No significant correlation was observed between histological features and alterations in the sequences from different tissues. No tissue-specific signature pattern was identified. It was shown that animals with a higher proviral load showed more lesion severity in various SRLV-affected tissues, indicating a positive association between these two parameters. Our results also revealed differences in the SRLV load between animals even though the sequences derived from all of the goats were closely related, suggesting that host factors may restrict and control viral replication. This study provides new information about SRLV variants isolated from arthritic goats; however, more studies, including the isolation and characterization of biological properties of these viruses, should be performed to evaluate their pathogenic potential. [ABSTRACT FROM AUTHOR]

Background and Aim: The Marek's disease virus (MDV) is a neoplastic disease causing serious economic losses in poultry production. This study aimed to investigate MDV occurrence in poultry flocks in the Lower Egypt during the 2020 breakout and genetically characterized Meq, gL, and ICP4 genes in field strains of MDV. Materials and Methods: Forty samples were collected from different breeds from eight Egyptian governorates in 2020. All flocks had received a bivalent vaccine (herpesvirus of turkey FC-126 + Rispens CVI988). However, weight loss, emaciation, reduced egg production, paralysis, and rough/raised feather follicles occurred. Samples were collected from feather follicles, liver, spleen, and nerve tissue for diagnosis by polymerase chain reaction. MDV genetic characterization was then performed by sequencing the Meq, gL, and ICP4 genes of five positive samples representing different governorates and breeds. Results: A total of 28 samples were positive for MDV field strains, while two were related to MDV vaccinal strains. All samples tested negative for ALV (A, B, C, D, and J) and REV. Phylogenetic analysis of the Meq gene of sequenced samples revealed that all MDVs were related to the highly virulent European viruses (Gallid herpesvirus 2 ATE and PC12/30) with high amino acid (A.A.) identity 99.2-100%. Alternatively, there was low A.A. identity with the vaccine strains CVI988 and 3004 (up to 82.5%). These results indicate that further investigation of the efficacy of current Egyptian vaccines is required. The Egyptian strains also harbor a specific mutation, allowing clustering into two subgroups (A and B). By mutation analysis of the Meq gene, the Egyptian viruses in our study had R101K, P217A, and E263D mutations present in all Egyptian viruses. Furthermore, R176A and T180A mutations specific to our strains contributed to the high virulence of highly virulent strains. There were no mutations of the gL or ICP4 genes. Conclusion: Further studies should evaluate the protection contributed by current vaccines used in Egypt.

Background and objective: Giardia lamblia is the intestinal flagellated protozoan parasite that infects vertebrates, including humans. Giardiasis is the major diarrheal disease found worldwide. It can be symptomatic or may be an asymptomatic carrier that led to chronic disease. This study aimed to determine the proportion of giardiasis among food handlers and evaluate the correlation between two laboratory methods for identifying the Giardia lamblia. Methods: A total of 308 stool samples were collected from food handlers that annually attend the central laboratory in Erbil City. Wetmount microscopic examination was performed for the diagnosis of cysts and trophozoites of the Giardia parasite. Molecular analysis done for positive samples, DNA extraction performed using the QIAamp Fast DNA Stool Mini Kit (Qiagen Company, Germany). Nested PCR analysis was done targeting the Glutamate dehydrogenase gene using two sets of primers for amplification of 734bp fragment. Gel electrophoresis was performed for visualizing the amplified DNA by Ultraviolet light. Results: The mean age of food handler participants was 29 years. Most (93.8%) of the food handlers were males, and the majority (98.6%) of the participants did not have any signs and symptoms. Four (7.4%) microscopy positive sample participants were highly educated. There was no association between educational level and positive rate by microscopy (P = 0.066). The majority of participants did not receive treatments, particularly most of the microscopic positive samples. The food handlers did not take any antiparasitic treatments 9 (3.4%) (P = 0.676). From 11 (3.6%) microscopically positive samples, 10 (90.9%) Giardia lamblia gdh gene 734 bp fragments were amplified by nested PCR. Conclusion: Amplification of 734bp of gdh gene by the nested PCR is the most specific and sensitive method for identifying Giardia lamblia. Food handlers were important people to care about sanitation and preparing food, particularly for avoiding diseases transmitted by food.

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. [ABSTRACT FROM AUTHOR]

Vigna radiata (mung bean) is a most cultivated legume crop having high nutritive and clinical value. A survey was accompanied to isolate leaf spot pathogen from mung bean plants. Infected leaf samples were collected and a novel pathogen, Alternaria arborescens was isolated and identified on morphological and molecular basis. Molecular identification was done using nucleotide sequence analysis of rDNA internal spacer sequence (ITS), partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and elongation factor (EF) regions. Morphological characters demonstrated grayish-black, woolly, concentric rings on Malt Extract Agar (MEA) plates. The conidiophores were well defined; septate with terminal and sub-terminal branches having tan to brown, short ovoid or ellipsoid, and 7-11 µm sized conidia with transverse septation. In molecular characterization, BLAST analysis of the rDNA-ITS region of the pathogen, A. arborescens exhibited maximum (99%) homology with other A. arborescens GenBank strains. Similarly, 100% homology was found with partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and translation elongation factor. Afterward, Koch's pathogenicity aptitude of the identified pathogen was confirmed by the occurrence of the same disease symptomology and re-isolation of identical organisms from artificially inoculated leaves in the in vitro and in vivo trials. The study signifies the novel documentation of A. arborescens as a leaf spot pathogen of mung bean in Pakistan. The manifestation of this pathogen could result in a serious economic impact on mung bean or might be a possible pathogen of other pulse crops if not managed in time. [ABSTRACT FROM AUTHOR]

Bats stand as one of the most diverse groups in the animal kingdom and are key players in the global transmission of emerging pathogens. However, their role in transmitting Enterocytozoon bieneusi and Cryptosporidium spp. remains unclear. This study aimed to evaluate the occurrence and genetic diversity of the two pathogens in fruit bats (Rousettus leschenaultii) in Hainan, China. Ten fresh fecal specimens of fruit bats were collected from Wanlvyuan Gardens, Haikou, China. The fecal samples were tested for E. bieneusi and Cryptosporidium spp. using Polymerase Chain Reaction (PCR) analysis and sequencing the internal transcribed spacer (ITS) region and partial small subunit of ribosomal RNA (SSU rRNA) gene, respectively. Genetic heterogeneity across Cryptosporidium spp. isolates was assessed by sequencing 4 microsatellite/minisatellite loci (MS1, MS2, MS3, and MS16). The findings showed that out of the ten specimens analyzed, 2 (20 %) and seven (70.0 %) were tested positive for E. bieneusi and Cryptosporidium spp., respectively. DNA sequence analysis revealed the presence of two novel Cryptosporidium genotypes with 94.4 to 98.6 % sequence similarity to C. andersoni , named as Cryptosporidium bat-genotype-XXI and bat-genotype-XXII. Three novel sequences of MS1, MS2 and MS16 loci identified here had 95.4 to 96.9 % similarity to the known sequences, which were deposited in the GenBank. Two genotypes of E. bieneusi were identified, including a novel genotype named HNB-I and a zoonotic genotype PigEbITS7. The discovery of these novel sequences provides meaningful data for epidemiological studies of the both pathogens. Meanwhile our results are also presented that the fruit bats infected with E. bieneusi , but not with Cryptosporidium , should be considered potential public health threats. [ABSTRACT FROM AUTHOR]

The facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes) is the causative agent of listeriosis, a severe invasive illness. This ubiquitous species is widely distributed in the environment, but infection occurs almost exclusively through ingestion of contaminated food. The pork production sector has been heavily affected by a series of L. monocytogenes -related foodborne outbreaks in the past around the world. Ready-to-eat (RTE) pork products represent one of the main food sources for strong-evidence listeriosis outbreaks. This pathogen is known to be present throughout the entire pig and pork production chain. Some studies hypothesized that the main source of contamination in final pork products was either living pigs or the food-processing environment. A detailed genomic picture of L. monocytogenes can provide a renewed understanding of the routes of contamination from pig farms to the final products. This review provides an overview of the prevalence, the genomic diversity and the genetic background linked to virulence of L. monocytogenes along the entire pig and pork production chain, from farm to fork. • Pork products have been linked to listeriosis outbreaks worldwide. • Listeria monocytogenes strains are found at all stages of the chain, from pigs at farm to pork products. • In-depth genomic characterization is mandatory to determine the origin of the clonal complexes involved in listeriosis cases. • Hypervirulent clones mostly originate from the farm, hypovirulent clones are selected at the processing stage. • More studies at the chain scale are needed. [ABSTRACT FROM AUTHOR]

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.