scholarly journals Genotypic analyses and virulence characterization ofGlaesserella parasuisisolates from Taiwan

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6960 ◽  
Author(s):  
Wei-Hao Lin ◽  
Hsing-Chun Shih ◽  
Chuen-Fu Lin ◽  
Cheng-Yao Yang ◽  
Chao-Nan Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Partial Correlation ◽  
Economic Losses ◽  
Swine Industry ◽  
High Genetic Diversity ◽  
Molecular Serotyping ◽  
Positive Rate ◽  
Polymerase Chain ◽  
Different Strains ◽  
Group 1

BackgroundGlaesserella(Haemophilus)parasuis(G. parasuis) causes severe economic losses in the swine industry. MultipleG. parasuisstrains can exist in single animals. Typing techniques are required for identifyingG. parasuisisolates. Different strains within a serovar display varying virulence. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) can assess the heterogeneity. The group 1 virulence-associated trimeric autotransporters (vtaA) gene is an indicator of virulence. The aim of this study was to characterize TaiwaneseG. parasuisisolates via molecular serotyping, vtaA PCR and ERIC-PCR.MethodsOne hundred and forty-five strains were collected between November 2013 and March 2017 in Taiwan and further examined by molecular serotyping, vtaA PCR and ERIC-PCR.ResultsThe dendrogram revealed heterogeneous genetic diversity within many clusters. Partial correlation between the ERIC-PCR clusters of different strains, serovars and lesion patterns was observed. Twelve herds (8.3%) infected with more than one strain. Group 1 vtaA positive rate reached 98.6%.DiscussionThis study showed the high genetic diversity ofG. parasuisin Taiwan by a high discriminatory capability of ERIC-PCR. Group 1 vtaA commonly exists inG. parasuisisolates and may play important roles in the pathogenesis of TaiwaneseG. parasuisisolates.

scholarly journals Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Sri Ramadiana ◽  
Dwi Hapsoro ◽  
Rusdi Evizal ◽  
Kukuh Setiawan ◽  
Agus Karyanto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Breeding Program ◽  
Similarity Coefficients ◽  
Robusta Coffee ◽  
Genomic Dnas ◽  
Polymerase Chain ◽  
Group Ii ◽  
Group 1

Abstract. Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.

scholarly journals Prevalence of bovine astroviruses and their genotypes in sampled Chinese calves with and without diarrhoea

2021 ◽  
Vol 102 (8) ◽  
Author(s):  
Jie Zhu ◽  
Mingpu Qi ◽  
Chuanwen Jiang ◽  
Yongchong Peng ◽  
Qingjie Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Binary Logistic Regression ◽  
Binary Logistic Regression Analysis ◽  
Strong Positive Correlation ◽  
High Genetic Diversity ◽  
Bovine Rotavirus ◽  
Calf Diarrhoea ◽  
Faecal Samples ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs

Bovine astrovirus (BoAstV) belongs to genus Mamastravirus (MAstV). It can be detected in the faeces of both diarrhoeal and healthy calves. However, its prevalence, genetic diversity, and association with cattle diarrhoea are poorly understood. In this study, faecal samples of 87 diarrhoeal and 77 asymptomatic calves from 20 farms in 12 provinces were collected, and BoAstV was detected with reverse transcription-polymerase chain reaction (RT-PCR). The overall prevalence rate of this virus in diarrhoeal and asymptomatic calves was 55.17 % (95 % CI: 44.13, 65.85 %) and 36.36 % (95 % CI: 25.70, 48.12 %), respectively, indicating a correlation between BoAstV infection and calf diarrhoea (OR=2.15, P=0.024). BoAstV existed mainly in the form of co-infection (85.53 %) with one to five of nine viruses, and there was a strong positive correlation between BoAstV co-infection and calf diarrhoea (OR=2.83, P=0.004). Binary logistic regression analysis confirmed this correlation between BoAstV co-infection and calf diarrhoea (OR=2.41, P=0.038). The co-infection of BoAstV and bovine rotavirus (BRV) with or without other viruses accounted for 70.77 % of all the co-infection cases. The diarrhoea risk for the calves co-infected with BoAstV and BRV was 8.14-fold higher than that for the calves co-infected with BoAstV and other viruses (OR=8.14, P=0.001). Further, the co-infection of BoAstV/BRV/bovine kobuvirus (BKoV) might increase the risk of calf diarrhoea by 14.82-fold, compared with that of BoAstV and other viruses (OR=14.82, P <0.001). Then, nearly complete genomic sequences of nine BoAstV strains were assembled by using next-generation sequencing (NGS) method. Sequence alignment against known astrovirus (AstV) strains at the levels of both amino acids and nucleotides showed a high genetic diversity. Four genotypes were identified, including two known genotypes MAstV-28 (n=3) and MAstV-33 (n=2) and two novel genotypes designated tentatively as MAstV-34 (n=1) and MAstV-35 (n=3). In addition, seven out of nine BoAstV strains showed possible inter-genotype recombination and cross-species recombination. Therefore, our results increase the knowledge about the prevalence and the genetic evolution of BoAstV and provide evidence for the association between BoAstV infection and calf diarrhoea.

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

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

scholarly journals Astrovirus in Reunion Free-Tailed Bat (Mormopterus francoismoutoui)

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1524
Author(s):  
Léa Joffrin ◽  
Axel O. G. Hoarau ◽  
Erwan Lagadec ◽  
Marie Köster ◽  
Riana V. Ramanantsalama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rna Viruses ◽  
Mammalian Species ◽  
Rdrp Gene ◽  
Chain Reaction ◽  
Rna Dependent Rna Polymerase ◽  
Nested Polymerase Chain Reaction ◽  
High Genetic Diversity ◽  
Partial Rdrp ◽  
Polymerase Chain

Astroviruses (AstVs) are RNA viruses infecting a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from 21 June 2016 to 4 September 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. Phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

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

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.

scholarly journals Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1842
Author(s):  
Marcos Paulo Carrera Menezes ◽  
Amparo Martinez Martinez ◽  
Edgard Cavalcanti Pimenta Filho ◽  
Jose Luis Vega-Pla ◽  
Juan Vicente Delgado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Allele Number ◽  
Hair Samples ◽  
The Mean ◽  
Polymerase Chain ◽  
Single Sequence ◽  
Brazilian Populations

The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.

scholarly journals WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2419
Author(s):  
Frank Vandenbussche ◽  
Elisabeth Mathijs ◽  
Marylène Tignon ◽  
Tamara Vandersmissen ◽  
Ann Brigitte Cay
Keyword(s):  
Genetic Diversity ◽  
Large Scale ◽  
Control Strategies ◽  
Added Value ◽  
Respiratory Syndrome Virus ◽  
Serum Samples ◽  
Swine Industry ◽  
High Genetic Diversity ◽  
Rate Analysis ◽  
Phylogenetic Cluster

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic studies only target the highly variable open reading frame (ORF) 5, for which an extensive database is available. In this study, we performed whole-genome sequencing (WGS) on a collection of 124 PRRSV-1 positive serum samples that were collected over a 5-year period (2015–2019) in Belgium. Our results show that (nearly) complete PRRSV genomes can be obtained directly from serum samples with a high success rate. Analysis of the coding regions confirmed the exceptionally high genetic diversity, even among Belgian PRRSV-1 strains. To gain more insight into the added value of WGS, we performed phylogenetic cluster analyses on separate ORF datasets as well as on a single, concatenated dataset (CDS) containing all ORFs. A comparison between the CDS and ORF clustering schemes revealed numerous discrepancies. To explain these differences, we performed a large-scale recombination analysis, which allowed us to identify a large number of potential recombination events that were scattered across the genome. As PRRSV does not contain typical recombination hot-spots, typing PRRSV strains based on a single ORF is not recommended. Although the typing accuracy can be improved by including multiple regions, our results show that the full genetic diversity among PRRSV strains can only be captured by analysing (nearly) complete genomes. Finally, we also identified several vaccine-derived recombinant strains, which once more raises the question of the safety of these vaccines.

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

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.

scholarly journals Genetic Diversity and Prevalence of Porcine Circovirus Type 2 in China During 2000-2019

2021 ◽  
Vol 8 ◽  
Author(s):  
Ning Li ◽  
Jing Liu ◽  
Jiali Qi ◽  
Feng Hao ◽  
Lei Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Wide Distribution ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus Type 2 ◽  
Amino Acid Sequences ◽  
Porcine Circovirus ◽  
Economic Losses ◽  
Swine Industry ◽  
Emerging Virus

As the major pathogen for porcine circovirus-associated disease (PCVAD), porcine circovirus type 2 (PCV2) is no longer treated as an emerging virus anymore. The wide distribution of PCV2 infection in China causes huge economic losses in the swine industry. Currently, it is generally believed that PCV2 has eight genotypes (PCV2a to PCV2h), with PCV2a, PCV2b, and PCV2d being widely distributed. To comprehensively explore the genetic diversity and prevalence of PCV2 in China, PCV-2 sequences submitted from China in the GenBank database were retrieved. With a total of 714 PCV2 strains were retrieved, we found that early-submitted PCV2 sequences were mainly collected from coastal provinces in the southeast part of China, which may indicate PCV2 was initially circulating in those regions. From 2002 to 2008, PCV2b was the dominant prevalent genotype in those retrieved sequences. From 2009, PCV2d became the dominant genotype in those sequences, dropping a hint that a potential shift of PCV2b to PCV2d might occur in 2009, which is similar to the patterns at the global level. In addition to the PCV2a, PCV2b, and PCV2d genotypes, novel strains were also characterized. We further revealed that the amino acid sequences consistency of PCV2a Cap is higher than those in other genotypes. Together, this study provided clues for the possible prevalent genotypes and dynamics of genetic diversity in China from 2000 to 2019.

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

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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