scholarly journals Genetic Diversity Analysis of Genotype 2 Porcine Reproductive and Respiratory Syndrome Viruses Emerging in Recent Years in China

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Lei Zhou ◽  
Xiaorong Yang ◽  
Yuan Tian ◽  
Shuoyan Yin ◽  
Gang Geng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Hypervariable Region ◽  
Clinical Samples ◽  
Respiratory Syndrome Virus ◽  
Diversity Analysis ◽  
Coding Region ◽  
Genotype 2 ◽  
Orf5 Sequences ◽  
Complete Genomic

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by its extensive genetic diversity. Here we analyzed 101 sequences of NSP2 hypervariable region, 123 ORF3 sequences, and 118 ORF5 sequences from 128 PRRSV-positive clinical samples collected in different areas of China during 2008–early 2012. The results indicated that the amino acid identities of the three genes among these sequences were 87.6%–100%, 92.5%–100%, and 77%–100%, respectively. Meanwhile, 4 novel patterns of deletion and insertion in NSP2 region or GP5 were first found. The phylogenetic analysis on these 3 genes revealed that the Chinese PRRSV strains could be divided into three subgroups; majority of genes analyzed here were clustered in subgroup 3 with multiple branches; the strains with 30-aa deletion in NSP2-coding region were still the dominant virus in the field. Further phylogenetic analysis on four obtained complete genomic sequences showed that they were clustered into different branches with the Chinese corresponding representative strains. Our analyses suggest that the genetic diversity of genotype 2 PRRSV in the field displays a tendency of increasing in recent years in China, and the 30-aa deletion in NSP2-coding region should be no longer defined as the molecular marker of the Chinese HP-PRRSV.

scholarly journals The First Detection of Equine Coronavirus in Adult Horses and Foals in Ireland

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 946 ◽  
Author(s):  
Nemoto ◽  
Schofield ◽  
Cullinane
Keyword(s):  
Polymerase Chain Reaction ◽  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Clinical Samples ◽  
Enteric Disease ◽  
Coding Region ◽  
Chain Reaction ◽  
Diagnostic Laboratory ◽  
Polymerase Chain ◽  
Thoroughbred Foals

The objective of this study was to investigate the presence of equine coronavirus (ECoV) in clinical samples submitted to a diagnostic laboratory in Ireland. A total of 424 clinical samples were examined from equids with enteric disease in 24 Irish counties between 2011 and 2015. A real-time reverse transcription polymerase chain reaction was used to detect ECoV RNA. Nucleocapsid, spike and the region from the p4.7 to p12.7 genes of positive samples were sequenced, and sequence and phylogenetic analyses were conducted. Five samples (1.2%) collected in 2011 and 2013 tested positive for ECoV. Positive samples were collected from adult horses, Thoroughbred foals and a donkey foal. Sequence and/or phylogenetic analysis showed that nucleocapsid, spike and p12.7 genes were highly conserved and were closely related to ECoVs identified in other countries. In contrast, the region from p4.7 and the non-coding region following the p4.7 gene had deletions or insertions. The differences in the p4.7 region between the Irish ECoVs and other ECoVs indicated that the Irish viruses were distinguishable from those circulating in other countries. This is the first report of ECoV detected in both foals and adult horses in Ireland.

Genetic diversity and phylogenetic analysis of porcine reproductive and respiratory syndrome virus isolates in East China

2014 ◽  
Vol 24 ◽  
pp. 193-201 ◽  
Author(s):  
Xiaomin Wang ◽  
Kongwang He ◽  
Wenwen Zhang ◽  
Zhongtao Zhou ◽  
Aihua Mao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
East China ◽  
Respiratory Syndrome Virus ◽  
Virus Isolates

scholarly journals Analysis of Genetic Variation of Two NADC30-like Strains of Porcine Reproductive and Respiratory Syndrome Virus in China

2017 ◽  
Vol 11 (1) ◽  
pp. 90-97
Author(s):  
Zhi Zhou ◽  
Jiajun Wu ◽  
Shuo Zhang ◽  
Bo Hou ◽  
Tao Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
North America ◽  
Untranslated Region ◽  
Respiratory Syndrome Virus ◽  
Nucleotide Deletion ◽  
Complete Genomes ◽  
Swine Herds

Background: NADC30-like strains of porcine reproductive and respiratory syndrome virus first appeared in Chinese swine herds in 2012. Objective and Method: To explore the possible genetic diversity of these strains, we sequenced and analyzed the complete genomes of two NADC30-like strains. These isolates shared 95.4% homology with NADC30. Result: The two strains displayed a discontinuous deletion of 131 amino acids in NSP2, mutations of amino acids in GP3 and GP5, and a 3-nucleotide deletion in the 3′ untranslated region. Phylogenetic analysis showed that the two isolates formed a new branch and clustered in a subgroup with NADC30 isolates from North America. Conclusion: We conclude that the above two NADC30-like strains may have been introduced from North America to China, where they acquired new genetic diversity.

scholarly journals Molecular detection and genetic diversity of porcine circovirus type 3 in commercial pig farms in Xinjiang province, China

2019 ◽  
Vol 63 (4) ◽  
pp. 481-488
Author(s):  
Qiao Mengfan ◽  
Wang Xifeng ◽  
Zhang Guowu ◽  
Meng Qingling ◽  
Qiao Jun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus ◽  
Clinical Samples ◽  
Molecular Characteristics ◽  
Pig Farms ◽  
Commercial Farms ◽  
Type 3 ◽  
And Control

AbstractIntroductionPorcine circovirus type 3 (PCV3) is a newly discovered porcine circovirus. The molecular characteristics and genetic evolution of PCV3 in Xinjiang province, China still being unclear, the aim of the study was their elucidation.Material and MethodsA total of 393 clinical samples were collected from pigs on commercial farms in nine different regions of Xinjiang and phylogenetic analysis based on full-length Cap genes was performed.ResultsThe prevalence at farm level was 100%, while in all the tested samples it was 22.39%. Nine PCV3 strains were detected in Xinjiang province and they shared 98.9–99.3% nucleotide and 97.5–100.0% Cap gene amino acid sequence identities with other epidemic strains from China and abroad. Compared with other epidemic strains of PCV3, there were 26 base mutation sites in the Cap gene in the nine Xinjiang strains, resulting in the mutation of amino acids at positions 20, 24, 75, 77, 108, 111 and 206. Phylogenetic analysis showed that these strains can be divided into two different genetic groups, to the first of which five strains affiliated and divided between subgroups 1.1 and 1.2, and to the second of which the other four strains affiliated and similarly divided between subgroups 2.1 and 2.2.ConclusionPCV3 circulates widely among commercial pig farms in Xinjiang province, China, and displays obvious genetic diversity. The results provide epidemiological information useful for the prevention and control of PCV3 infection in the pig industry.

scholarly journals Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259531
Author(s):  
Mariana Kikuti ◽  
Juan Sanhueza ◽  
Carles Vilalta ◽  
Igor Adolfo Dexheimer Paploski ◽  
Kimberly VanderWaal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Production Systems ◽  
Sequence Data ◽  
The United States ◽  
Respiratory Syndrome Virus ◽  
Viral Diversity ◽  
Wild Type ◽  
Routine Monitoring ◽  
Genotype 2

Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.

scholarly journals Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amer Al-Jawabreh ◽  
Suheir Ereqat ◽  
Kamal Dumaidi ◽  
Hanan Al-Jawabreh ◽  
Abedelmajeed Nasereddin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Haplotype Network ◽  
Health Concern ◽  
Diversity Analysis ◽  
High Genetic Diversity ◽  
Genetic Diversity Analysis ◽  
First Time

Abstract Objectives SARS-CoV-2, severe respiratory syndrome coronavirus-2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS-CoV-2 in Palestine in fall 2020. Results To achieve these aims, whole genome sequencing of SARS-CoV-2, phylogenetic analysis, haplotype networking and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS-CoV-2 genome sequences, in which cluster-I comprised the majority of clusters by 90%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster-I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima’s D and Fu-Li’s-F tests (− 2.11 and 2.74, respectively), highest number of mutations (Eta = 120), highest number of haplotypes (h = 17), and highest average number of nucleotide differences between any two sequences (S = 118). The study confirmed the high genetic diversity among the Palestinian of SARS-CoV-2 which possessed high number of mutations including one which was reported for the first time.

scholarly journals Phylogenetic Analysis of the Hypervariable Region of the 18S rRNA Gene of Cryptosporidium Oocysts in Feces of Canada Geese (Branta canadensis): Evidence for Five Novel Genotypes

2004 ◽  
Vol 70 (1) ◽  
pp. 452-458 ◽  
Author(s):  
Kristen L. Jellison ◽  
Daniel L. Distel ◽  
Harold F. Hemond ◽  
David B. Schauer
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Hypervariable Region ◽  
Pcr Amplification ◽  
The United States ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Canada Geese ◽  
Pcr Products

ABSTRACT To assess genetic diversity in Cryptosporidium oocysts from Canada geese, 161 fecal samples from Canada geese in the United States were analyzed. Eleven (6.8%) were positive for Cryptosporidium spp. following nested PCR amplification of the hypervariable region of the 18S rRNA gene. Nine PCR products from geese were cloned and sequenced, and all nine diverged from previously reported Cryptosporidium 18S rRNA gene sequences. Five sequences were very similar or identical to each other but genetically distinct from that of Cryptosporidium baileyi; two were most closely related to, but genetically distinct from, the first five; and two were distinct from any other sequence analyzed. One additional sequence in the hypervariable region of the 18S rRNA gene isolated from a cormorant was identical to that of C. baileyi. Phylogenetic analysis provided evidence for new genotypes of Cryptosporidium species in Canada geese. Results of this study suggest that the taxonomy of Cryptosporidium species in geese is complex and that a more complete understanding of genetic diversity among these parasites will facilitate our understanding of oocyst sources and species in the environment.

Genetic diversity analysis of the ORF5 gene in porcine reproductive and respiratory syndrome virus samples from South China

2012 ◽  
Vol 60 (1) ◽  
pp. 157-164 ◽  
Author(s):  
Zong-Xi Cao ◽  
Pei-Rong Jiao ◽  
Yu-Mao Huang ◽  
Hong-Yang Qin ◽  
Liu-Wu Kong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South China ◽  
Dna Sequences ◽  
Clinical Samples ◽  
Respiratory Syndrome Virus ◽  
Specific Amino Acid ◽  
The North ◽  
Glycosylation Sites ◽  
Pcr Products ◽  
Orf5 Gene

To understand the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) in South China, we collected 231 clinical samples from pigs with suspected PRRSV infection in Guangdong between 2007 and 2009. We found that 74 of 231 samples were positive by RT-PCR. The PCR products of the ORF5 gene of 35 isolates from different farms were sequenced and their DNA sequences were compared to 23 other PRRSV isolates in the GenBank. We found that the nucleotide similarity among all South China isolates ranged from 87.6% to 100%, and all belonged to the North American genotype. Most of them were classified into subgenotype I, but the rest mapped to subgenotypes III, V or VI. Those in subgenotypes I and III were found to be highly variable in the primary neutralising epitope (PNE) with a specific amino acid mutation (F39/L39→I39), and a few isolates in subgenotypes I and III isolates also had a mutation at L41 (L41→S41). PRRSV isolates in subgenotypes III, V and VI had less potential glycosylation sites than those in subgenotype I. Our data contribute to the understanding of molecular variation of PRRSV in South China.

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