Bovine Astrovirus Surveillance in Uruguay Reveals High Detection Rate of a Novel Mamastrovirus Species

Viral infections affecting cattle lead to economic losses to the livestock industry worldwide, but little is known about the circulation, pathogenicity and genetic diversity of enteric bovine astrovirus (BoAstV) in America. The aim of this work was to describe the prevalence and genetic diversity of enteric BoAstV in dairy cattle in Uruguay. A total of 457 fecal and 43 intestinal contents from dairy calves were collected between July 2015 and May 2017 and tested by RT-PCR, followed by sequencing and phylogenetic analyses of the polymerase and capsid regions. Twenty-six percent (128/500) of the samples were positive. Three different species within the Mamastrovirus genus were identified, including Mamastrovirus 28, Mamastrovirus 33 (3 samples each) and an unclassified Mamastrovirus species (19 samples). The unclassified species was characterized as a novel Mamastrovirus species. BoAstV circulates in Uruguayan dairy cattle with a high genetic diversity. The eventual clinicopathological significance of enteric BoAstV infection in cattle needs further investigation.

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Distribution and genetic diversity of Enterovirus G (EV-G) on pig farms in Thailand

BMC Veterinary Research ◽

10.1186/s12917-021-02988-6 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Taveesak Janetanakit ◽

Supassama Chaiyawong ◽

Kamonpan Charoenkul ◽

Ratanaporn Tangwangvivat ◽

Ekkapat Chamsai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Characterization ◽

Rt Pcr ◽

Cross Sectional Survey ◽

High Genetic Diversity ◽

Cross Sectional ◽

Predominant Genotype ◽

Diarrhea Virus ◽

Pig Farms

Abstract Background Enterovirus G (EV-G) causes subclinical infections and is occasionally associated with diarrhea in pigs. In this study, we conducted a cross-sectional survey of EV-G in pigs from 73 pig farms in 20 provinces of Thailand from December 2014 to January 2018. Results Our results showed a high occurrence of EV-Gs which 71.6 % of fecal and intestinal samples (556/777) and 71.2 % of pig farms (52/73) were positive for EV-G by RT-PCR specific to the 5’UTR. EV-Gs could be detected in all age pig groups, and the percentage positivity was highest in the fattening group (89.7 %), followed by the nursery group (89.4 %). To characterize the viruses, 34 EV-G representatives were characterized by VP1 gene sequencing. Pairwise sequence comparison and phylogenetic analysis showed that Thai-EV-Gs belonged to the EV-G1, EV-G3, EV-G4, EV-G8, EV-G9 and EV-G10 genotypes, among which the EV-G3 was the predominant genotype in Thailand. Co-infection with different EV-G genotypes or with EV-Gs and porcine epidemic diarrhea virus (PEDV) or porcine deltacoronavirus (PDCoV) on the same pig farms was observed. Conclusions Our results confirmed that EV-G infection is endemic in Thailand, with a high genetic diversity of different genotypes. This study constitutes the first report of the genetic characterization of EV-GS in pigs in Thailand.

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Bluetongue in Europe – the risk of animal import from restricted zones

Medycyna Weterynaryjna ◽

10.21521/mw.6254 ◽

2019 ◽

Vol 75 (05) ◽

pp. 6254-2019

Author(s):

ANNA ORŁOWSKA ◽

MARCIN SMRECZAK ◽

JERZY ROLA

Keyword(s):

Genetic Diversity ◽

20Th Century ◽

Bluetongue Virus ◽

Viral Disease ◽

Economic Losses ◽

High Genetic Diversity ◽

Key Factor ◽

Vector Borne ◽

Sentinel Animals ◽

Free Status

Bluetongue (BT) is a vector-borne viral disease effecting ruminants caused by bluetongue virus (BTV), transmitted mainly by bites from midges of the genus Culicoides. Since the end of 20th century, BTV is endemic in several European countries and the disease is caused mainly by BTV-8 and BTV-4 infections. Bluetongue virus is characterized by high genetic diversity. To date, over 29 BTV serotypes have been documented, including recently discovered atypical serotypes BTV (25–27). The disease has a high economic impact as it causes economic losses due to animal mortality, reduced productivity and restrictions on the movement of animals. Several reports and numerous observations indicate the contribution of animal movements to the spread of BTV infections. Thus, bluetongue surveillance that includes testing of sentinel animals as well as virological testing of animals susceptible to BTV infection imported from restricted zones due to the presence of BTV is a key factor in maintaining a BT-free status

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Distribution and phylogenetic diversity of Anopheles species in malaria endemic areas of Honduras in an elimination setting

10.21203/rs.2.24779/v2 ◽

2020 ◽

Author(s):

Denis Escobar ◽

Krisnaya Ascencio ◽

Andrés Ortiz ◽

Adalid Palma ◽

Gustavo Fontecha

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

Public Health Problem ◽

Abundant Species ◽

Malaria Vectors ◽

Morphological Identification ◽

High Genetic Diversity ◽

Homogeneous Population ◽

Molecular Approaches ◽

Endemic Areas

Abstract Background: Anopheles mosquitoes are the vectors of malaria, one of the most important infectious diseases in the tropics. More than 500 Anopheles species have been described worldwide, and more than 30 are considered a public health problem. In Honduras, information on the distribution of Anopheles spp. and its genetic diversity is scarce. This study aimed to describe the distribution and genetic diversity of Anopheles mosquitoes in Honduras. Methods: Mosquitoes were captured in 8 locations in 5 malaria endemic departments during 2019. Two collection methods were used. Adult anophelines were captured outdoors using CDC light traps and by aspiration of mosquitoes at rest. The morphological identification was performed using taxonomic keys. Genetic analyses included the sequencing of a partial region of the cytochrome oxidase I gene (COI) and the ribosomal internal transcribed spacer 2 (ITS2). Results: A total of 1320 anophelines were collected and identified through morphological keys. Seven Anopheles species were identified. Anopheles albimanus was the most widespread and abundant species (74.02%). To confirm the morphological identification of the specimens, 175 and 122 sequences were obtained for COI and ITS2 respectively. Both markers confirmed the morphological identification. COI showed a greater nucleotide diversity than ITS2 in all species. High genetic diversity was observed within the populations of An. albimanus while An. darlingi proved to be a highly homogeneous population. Phylogenetic analyses revealed clustering patterns in An. darlingi and An. neivai in relation to specimens from South America. New sequences for An. crucians, An. vestitipennis, and An. neivai are reported in this study.Conclusions: Here we report the distribution and genetic diversity of Anopheles species in endemic areas of malaria transmission in Honduras. According to our results, both taxonomic and molecular approaches are useful tools in the identification of anopheline mosquitoes. However, both molecular markers differ in their ability to detect intraspecific genetic diversity. These results provide supporting data for a better understanding of the distribution of malaria vectors in Honduras.

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High Genetic Diversity in Flavobacterium psychrophilum Isolates from Healthy Rainbow Trout (Oncorhynchus mykiss) Farmed in the Same Watershed, Revealed by Two Typing Methods

Applied and Environmental Microbiology ◽

10.1128/aem.01398-20 ◽

2020 ◽

Vol 87 (2) ◽

Author(s):

Ségolène Calvez ◽

Nora Navarro-Gonzalez ◽

Charlène Siekoula-Nguedia ◽

Catherine Fournel ◽

Eric Duchaud

Keyword(s):

Genetic Diversity ◽

Rainbow Trout ◽

Oncorhynchus Mykiss ◽

Clonal Complex ◽

Economic Losses ◽

High Genetic Diversity ◽

Content Type ◽

Flavobacterium Psychrophilum ◽

Sequence Types ◽

Apparently Healthy

ABSTRACT Flavobacterium psychrophilum affects salmonid health worldwide and causes economic losses. The genetic diversity of the pathogen must be considered to develop control methods. However, previous studies have reported both high and low levels of genetic diversity. The present longitudinal study aimed at assessing the genetic diversity of F. psychrophilum at a small temporal and geographic scale. Four farms located on the same watershed in France were studied. Rainbow trout (Oncorhynchus mykiss) batches were monitored, and apparently healthy individuals were sampled over 1 year. A total of 288 isolates were recovered from fish organs (gills and spleen) and eggs. Pulsed field gel electrophoresis revealed high genetic diversity. Multilocus sequence typing performed on a selection of 31 isolates provided congruent results, as follows: 18 sequence types (STs) were found, of which 13 were novel. The mean gene diversity (H = 0.8413) was much higher than that previously reported for this host species, although the sampling was restricted to a single watershed and 1 year. Seven isolates out of 31 were assigned to clonal complex ST10 (CC-ST10), which is the predominant clonal complex in the main salmonid production areas. A split decomposition tree reflected a panmictic population. This finding is important for aquaculture veterinarians in their diagnostic procedure, as the choice of adequate antibiotic treatment is conditioned by the correct identification of the causative agent. Furthermore, this study expands our knowledge on genetic diversity required for the development of an effective vaccine against F. psychrophilum. IMPORTANCE The bacterium Flavobacterium psychrophilum is a serious pathogen in many fish species, especially salmonids, that is responsible for considerable economic losses worldwide. In order to treat infections and to develop vaccines, the genetic diversity of this bacterium needs to be known. We assessed the genetic diversity of F. psychrophilum isolates from apparently healthy rainbow trout raised in several fish farms in the same watershed in France. Two different genotyping methods revealed high diversity. The majority of isolates were unrelated to clonal complex sequence type 10 (CC-ST10), the clonal complex that is predominant worldwide and associated with disease in rainbow trout. In addition, we found 13 novel sequence types. These results suggest that a diverse subpopulation of F. psychrophilum may be harbored by rainbow trout.

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High genetic diversity of hepatitis delta virus in eastern Turkey

The Journal of Infection in Developing Countries ◽

10.3855/jidc.3910 ◽

2014 ◽

Vol 8 (01) ◽

pp. 074-078 ◽

Cited By ~ 4

Author(s):

Yasemin Bulut ◽

Ibrahim Halil Bahcecioglu ◽

Cem Aygun ◽

Pinar Demirel Oner ◽

Ibrahim Ozercan ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Restriction Enzyme ◽

Hepatitis Delta Virus ◽

Rt Pcr ◽

Genotype I ◽

High Genetic Diversity ◽

Hepatitis Delta ◽

Hdv Genotype ◽

Delta Virus

Introduction: Hepatitis delta virus (HDV) is a serious cause of liver-related mortality in patients infected with hepatitis B virus (HBV). Determination of genotypes of HDV and phylogenetic analysis are important for better understanding the pathogenesis of the liver diseases associated with HBV infection. The aim of this study was to determine the genotype or genotypes of HDV among chronically infected patients with HBV in eastern Turkey. Methodology: A group of 113 patients infected with HBV and HDV were included in this study. The samples taken from the patients were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) and restriction enzyme cleavage. Results: According to the results of the restriction enzyme analysis, all of the RT-PCR products were determined to be HDV genotype I. Furthermore, for phylogenetic analysis and genotyping, 40 of HDV RT-PCR positive products were sequenced. Phylogenetic analysis of the sequences showed that all of the samples were infected with HDV genotype I. In addition, the results of the alignment analysis showed that the sequences of clinical samples were 82%-95% similar. Conclusion: These results indicate that high genetic diversity of the virus is possible in endemic areas such as Turkey.

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Inter- and intra-variant genetic heterogeneity of human coronavirus OC43 strains in France

Journal of General Virology ◽

10.1099/vir.0.82065-0 ◽

2006 ◽

Vol 87 (11) ◽

pp. 3349-3353 ◽

Cited By ~ 17

Author(s):

Astrid Vabret ◽

Julia Dina ◽

Thomas Mourez ◽

Stéphanie Gouarin ◽

Joëlle Petitjean ◽

...

Keyword(s):

Genetic Diversity ◽

Cell Culture ◽

Respiratory Tract ◽

Respiratory Infections ◽

Rt Pcr ◽

Human Coronavirus ◽

High Genetic Diversity ◽

Close Relationship ◽

Respiratory Tract Illness

Human coronavirus OC43 (HCoV-OC43) causes acute, self-limited respiratory infections. A close relationship between bovine coronaviruses (BCoVs) and HCoV-OC43 has recently been demonstrated. This study includes seven clinical, non-cell culture-adapted, contemporary HCoV-OC43 strains detected in France in 2003. By using RT-PCR and clonal sequencing of the S1 gene of HCoV-OC43, the inter-variant heterogeneity of the HCoV-OC43 circulating strains was studied and the intra-variant diversity was assessed by investigation of a quasispecies cloud. This paper brings to the forefront a high genetic diversity of circulating HCoV-OC43 variants. Genetically different groups are defined among the variants described in this study. One of these variants holds characteristics of an outlier and presents a deletion of 12 nt, also found in BCoV strains. Moreover, the presence of HCoV-OC43 as a quasispecies cloud in vivo during an acute respiratory-tract illness was discovered. It has also been revealed that quasispecies-cloud sizes are similar for the two viral populations tested.

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High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

Microbiology ◽

10.1099/0022-1317-81-1-243 ◽

2000 ◽

Vol 81 (1) ◽

pp. 243-255 ◽

Cited By ~ 76

Author(s):

M. Bousalem ◽

E. J. P. Douzery ◽

D. Fargette

Keyword(s):

Genetic Diversity ◽

Mosaic Virus ◽

Statistical Tests ◽

Phylogenetic Analyses ◽

Natural Populations ◽

High Genetic Diversity ◽

Single Clade ◽

Cultivated Species ◽

Selection Of

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis–Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3′-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis–D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

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Genetic stability of equine arteritis virus during horizontal and vertical transmission in an outbreak of equine viral arteritis

Journal of General Virology ◽

10.1099/0022-1317-80-8-1949 ◽

1999 ◽

Vol 80 (8) ◽

pp. 1949-1958 ◽

Cited By ~ 47

Author(s):

Udeni B. R. Balasuriya ◽

Jodi F. Hedges ◽

Steven A. Nadler ◽

William H. McCollum ◽

Peter J. Timoney ◽

...

Keyword(s):

Genetic Diversity ◽

Vertical Transmission ◽

Genetic Stability ◽

Phylogenetic Analyses ◽

Equine Arteritis Virus ◽

Rt Pcr ◽

Persistently Infected ◽

Equine Viral Arteritis ◽

N Proteins

An imported carrier stallion (A) from Europe was implicated in causing an extensive outbreak of equine viral arteritis (EVA) on a Warmblood breeding farm in Pennsylvania, USA. Strains of equine arteritis virus (EAV) present in the semen of two carrier stallions (A and G) on the farm were compared to those in tissues of foals born during the outbreak, as well as viruses present in the semen of two other stallions that became persistently infected carriers of EAV following infection during the outbreak. The 2822 bp segment encompassing ORFs 2–7 (nt 9807–12628; which encode the GS, GP3, GP4, GL, M and N proteins, respectively) was directly amplified by RT–PCR from semen samples and foal tissues. Nucleotide and phylogenetic analyses confirmed that virus present in the semen of stallion A initiated the outbreak. The genomes of viruses present in most foal tissues (10/11) and serum from an acutely infected mare collected during the outbreak were identical to that of virus present in the lung of the first foal that died of EVA. Virus in the placenta of one foal differed by one nucleotide (99·9% identity) from the predominant outbreak virus. The relative genetic stability of viruses that circulated during the outbreak contrasts markedly with the heterogeneous virus populations variously present in the semen of persistently infected stallions on the farm. These findings are consistent with the hypothesis that the carrier stallion can be a source of genetic diversity of EAV, and that outbreaks of EVA can be initiated by the horizontal aerosol transmission of specific viral variants that occur in the semen of particular carrier stallions.

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Case Report: First Report and Phylogenetic Analysis of Porcine Astroviruses in Chile

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.764837 ◽

2021 ◽

Vol 8 ◽

Author(s):

Carlos Flores ◽

Naomi Ariyama ◽

Benjamín Bennett ◽

Juan Mena ◽

Claudio Verdugo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

The United States ◽

Swine Industry ◽

High Genetic Diversity ◽

Monophyletic Cluster ◽

Genetic Lineages ◽

Young Pigs ◽

Human Astroviruses ◽

Porcine Astrovirus

Porcine Astrovirus (PoAstV) causes mild diarrhea in young pigs and is considered an emerging virus in the swine industry worldwide. PoAstV has high genetic diversity and has been classified into five genetic lineages, PoAstV1–5. In Chile, only human astroviruses have been reported. This study aimed to determine the presence and genetic diversity of PoAstV circulating in intensive pig farms in Chile. Seventeen Chilean intensive swine farms from Valparaíso, Metropolitana, O'Higgins, Ñuble and Araucanía regions were sampled. A selection of oral fluid and fecal material samples from 1–80 days-old pigs were collected and analyzed using next-generation sequencing. The circulation of PoAstV was confirmed in all studied farms. We obtained complete or partial sequences of PoAstV-2 (n = 3), PoAstV-4 (n = 2), and PoAstV-5 (n = 7). In 15 out of 17 farms, we detected more than one lineage co-circulating. Phylogenetic analyses grouped the seven PoAstV-5 strains in a monophyletic cluster, closely related to the United States PoAstV-5 strains. The three PoAstV-2 were located into two separate sub-clusters. PoAstV-4 sequences are also grouped in two different clusters, all related to Japanese strains. Thus, our results indicate that PoAstV circulates in Chile with high frequency and diversity. However, the lack of reference sequences impairs local evolution patterns establishment and regional comparisons. This is the first contribution of PoAstV genomes in Latin America; more studies are needed to understand the diversity and impact of PoAstV on swine health.

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Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

Veterinary Sciences ◽

10.3390/vetsci8120329 ◽

2021 ◽

Vol 8 (12) ◽

pp. 329

Author(s):

Mitzilin Zuleica Trujano-Chavez ◽

Reyna Sánchez-Ramos ◽

Paulino Pérez-Rodríguez ◽

Agustín Ruíz-Flores

Keyword(s):

Genetic Diversity ◽

Candidate Genes ◽

Genetic Resistance ◽

Principal Component ◽

Clinical Mastitis ◽

Snp Markers ◽

Economic Losses ◽

High Genetic Diversity ◽

A Value ◽

Candidate Loci

Mastitis is a disease that causes significant economic losses, since resistance to mastitis is a difficult trait to be improved due to its multifactorial occurrence. Therefore, our objective was to characterize a Mexican Braunvieh cattle population for genetic resistance and susceptibility to mastitis. We used 66 SNP markers for 45 candidate genes in 150 animals. The average heterozygosity was 0.445 ± 0.076, a value higher than those reported for some European breeds. The inbreeding coefficient was slightly negative for resistance to subclinical (−0.058 ± 0.055) and clinical (−0.034 ± 0.076) mastitis, possibly due to low selection for the immunological candidate genes that influence these traits. The genotypic profiles for the candidate loci per K-means group were obtained, as well as the group distribution through the graphics of the principal component analysis. The genotypic profiles showed high genetic diversity among groups. Resistance to clinical mastitis had the lowest presence of the heterozygous genotypes. Although the percentage of highly inbred animals (>50%) is up to 13.3%, there are highly heterozygous groups in terms of the studied traits, a favorable indicator of the presence of genetic diversity. The results of this study constitute evidence of the genetic potential of the Mexican Braunvieh population to improve mastitis-related traits.

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