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.

scholarly journals Genetic Diversity of the ORF5 Gene of Porcine Reproductive and Respiratory Syndrome Virus Isolates in Southwest China from 2007 to 2009

PLoS ONE ◽  
2012 ◽  
Vol 7 (3) ◽  
pp. e33756 ◽  
Author(s):  
Gefen Yin ◽  
Libo Gao ◽  
Xianghua Shu ◽  
Guishu Yang ◽  
Shuhao Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southwest China ◽  
Respiratory Syndrome Virus ◽  
Orf5 Gene ◽  
Virus Isolates

scholarly journals Multiplex RT-PCR assay to differentiate genotypes of porcine reproductive and respiratory syndrome virus in swine

2019 ◽  
Vol 18 (06) ◽  
pp. 8-13
Author(s):  
Phat X. Dinh
Keyword(s):  
Real Time ◽  
Clinical Samples ◽  
Respiratory Syndrome Virus ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Swine Industry ◽  
Diagnostic Challenge ◽  
Nsp2 Gene ◽  
Prrs Virus ◽  
Pcr Products

Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically important diseases to swine industry worldwide. Due to the heterogeneity of field isolates, accurate detection of the PRRS virus is a diagnostic challenge. Recently, co-infection with NA-PRRSV, EU-PRRSV and HP-PRRSV isolates continuously increases in many countries, resulting in a significant impact on PRRSV diagnostics and disease control on farms. To facilitate rapid diagnosis and reliable discrimination of NA-PRRSV, EU-PRRSV and HP-PRRSV, a multiplex RT-PCR assay was established with three pairs of primers targeting highly conservative regions of nsp2 gene with predicted multiplex RT-PCR products of 364 bp, 161 bp and 259 bp, respectively. The primer pairs were optimized to be highly specific for PRRSV genotypes and were able to detect the target gene at the limit of 102 copies/μL for each gene. Clinical samples were used to evaluate this multiplex RT-PCR in parallel with a commercial real-time RT-PCR kit. Results showed over 95.2% (20/21 samples) agreement between the mRT-PCR and the real-time RT-PCR kit. Hence, it indicated that this multiplex RT-PCR could be useful for rapid and deferential diagnosis of NA-PRRSV, EU-PRRSV and HP-PRRSV in swine farms.

scholarly journals Commensal Rodents in 19th Century Australasia: Diversity, Invasion Routes and the China Connection

2021 ◽  
Author(s):  
Andrew James Veale ◽  
Carolyn King ◽  
Wayne Johnson ◽  
Lara Shepherd
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Dna Sequences ◽  
Archaeological Site ◽  
House Mice ◽  
Mus Musculus Domesticus ◽  
The South ◽  
The North ◽  
Founding Population ◽  
Norway Rats

Abstract The present genetic diversity of commensal rodent populations is often used to inform the invasion histories of these species, and as a proxy for historical events relating to the movement of people and goods. These studies assume that modern genetic diversity generally reflects early colonising events. We investigate this idea by sequencing the mitochondrial DNA of rodent bones found in a 19th-century archaeological site in The Rocks area of Sydney, Australia, the location of the first historical European port. We identified 19th-century bones from two species, Rattus norvegicus and Mus musculus domesticus. We found six genetic haplotypes in the 39 Norway rats, showing either multiple early introductions or a diverse initial founding population. One of them was identical with Norhap01 common in the North Island of New Zealand, but none was like the haplotype Norhap02 found throughout the South Island. We found three haplotypes in seven house mice, all belonging to the dominant subspecies established in Australia, M.m. domesticus. There was no evidence for M. m. castaneus or M. m. musculus having established there. We had few modern R. norvegicus and M. musculus DNA sequences from Sydney, but those we had did tentatively support the hypotheses that (1) modern samples can represent at least a preliminary estimate of historical diversities and origins, and (2) Asian haplotypes of both Norway rats and of house mice reached the South Island of New Zealand early in colonial times direct from China rather than through Port Jackson.

scholarly journals Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus

2020 ◽  
Vol 58 (11) ◽  
Author(s):  
Christian Lalonde ◽  
Chantale Provost ◽  
Carl A. Gagnon
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Full Length ◽  
Clinical Samples ◽  
Respiratory Syndrome Virus ◽  
Whole Genome ◽  
Serum Samples ◽  
Diagnostic Laboratory ◽  
Prrsv Strain ◽  
Orf5 Gene

ABSTRACT Porcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing. PRRSV PCR-positive serum, oral fluid, and tissue clinical samples submitted to the diagnostic laboratory for routine surveillance or diagnosis of PRRSV infection in Québec, Canada, swine herds were used. The PRRSV reverse transcription-quantitative PCR Cq values of the processed samples varied between 11.5 and 34.34. PRRSV strain genomes were isolated using a poly (A)-tail method and were sequenced with a MiSeq Illumina sequencer. Ninety-two full-length PRRSV genomes were obtained from 88 clinical samples out of 132 tested samples, resulting in a PRRSV WGS success rate of 66.67%. Three important deletions in ORF1a were found in most wild-type (i.e., not vaccine-like) strains. The importance of these deletions remains undetermined. Two different full-length PRRSV genomes were found in four different samples (three serum samples and one pool of tissues), suggesting a 4.55% PRRSV strain coinfection prevalence in swine. Moreover, six PRRSV whole genomes (6.52% of PRRSV strains) were found to cluster differently than they did under the ORF5 classification method. Overall, WGS of PRRSV enables better strain classification and/or interpretation of results in 9.10% of clinical samples than ORF5 sequencing, as well as allowing interesting research avenues.

scholarly journals Genetic diversity and biogeography in Chaetomorpha melagonium (Ulvophyceae, Cladophorales) based on internal transcribed spacer (ITS rDNA) sequences

2020 ◽  
Author(s):  
C Boedeker ◽  
F Leliaert ◽  
Giuseppe Zuccarello
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Base Pair ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Point Mutations ◽  
Its Sequences ◽  
The Arctic ◽  
Lsu Rdna ◽  
The North

© 2017 Walter de Gruyter GmbH, Berlin/Boston. Chaetomorpha melagonium is a morphologically distinct species of green algae that occurs throughout the North Atlantic, the North Pacific and the Arctic Ocean. In this study, we analyzed the intraspecific genetic diversity among 14 samples of C. melagonium from across the distribution range based on nuclear large subunit ribosomal DNA (LSU rDNA) and rDNA internal transcribed spacer (ITS) DNA sequences. All samples had identical LSU sequences. The ITS sequences had very few mutations that nevertheless divided the specimens into two groups: one included samples from Iceland, Svalbard, Massachusetts and Alaska with identical ITS sequences; members of this group differed in samples from Europe (France, Germany, Scotland, Sweden, and Wales) by three mutations (two point mutations and one five base pair indel). The European specimens had identical ITS sequences with the exception of a single sample from Brittany that differed by one base pair. The maximum ITS sequence divergence within the samples of C. melagonium was less than 0.5%. This low intraspecific variation in the frequently used highly variable ITS region is discussed in the context of past geological and climatic scenarios.

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.

Genetic diversity of Echinococcus spp. in Russia

Parasitology ◽  
2013 ◽  
Vol 140 (13) ◽  
pp. 1637-1647 ◽  
Author(s):  
SERGEY V. KONYAEV ◽  
TETSUYA YANAGIDA ◽  
MINORU NAKAO ◽  
GALINA M. INGOVATOVA ◽  
YAKOV N. SHOYKHET ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Sensu Stricto ◽  
European Russia ◽  
Altai Region ◽  
The North ◽  
History Of ◽  
European Genotype ◽  
The Rich ◽  
Echinococcus Spp

SUMMARYIn Russia, both alveolar and cystic echinococcoses are endemic. This study aimed to identify the aetiological agents of the diseases and to investigate the distribution of each Echinococcus species in Russia. A total of 75 Echinococcus specimens were collected from 14 host species from 2010 to 2012. Based on the mitochondrial DNA sequences, they were identified as Echinococcus granulosus sensu stricto (s.s.), E. canadensis and E. multilocularis. E. granulosus s.s. was confirmed in the European Russia and the Altai region. Three genotypes, G6, G8 and G10 of E. canadensis were detected in Yakutia. G6 was also found in the Altai region. Four genotypes of E. multilocularis were confirmed; the Asian genotype in the western Siberia and the European Russia, the Mongolian genotype in an island of Baikal Lake and the Altai Republic, the European genotype from a captive monkey in Moscow Zoo and the North American genotype in Yakutia. The present distributional record will become a basis of public health to control echinococcoses in Russia. The rich genetic diversity demonstrates the importance of Russia in investigating the evolutionary history of the genus Echinococcus.

Genetic diversity of the ORF5 gene of porcine reproductive and respiratory syndrome virus isolates in China from 2006 to 2008

2009 ◽  
Vol 144 (1-2) ◽  
pp. 136-144 ◽  
Author(s):  
Yan-Jun Zhou ◽  
Hai Yu ◽  
Zhi-Jun Tian ◽  
Guo-Xin Li ◽  
Xiao-Fang Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syndrome Virus ◽  
Orf5 Gene ◽  
Virus Isolates

scholarly journals Genetic diversity and biogeography in Chaetomorpha melagonium (Ulvophyceae, Cladophorales) based on internal transcribed spacer (ITS rDNA) sequences

2020 ◽  
Author(s):  
C Boedeker ◽  
F Leliaert ◽  
Giuseppe Zuccarello
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Base Pair ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Point Mutations ◽  
Its Sequences ◽  
The Arctic ◽  
Lsu Rdna ◽  
The North

© 2017 Walter de Gruyter GmbH, Berlin/Boston. Chaetomorpha melagonium is a morphologically distinct species of green algae that occurs throughout the North Atlantic, the North Pacific and the Arctic Ocean. In this study, we analyzed the intraspecific genetic diversity among 14 samples of C. melagonium from across the distribution range based on nuclear large subunit ribosomal DNA (LSU rDNA) and rDNA internal transcribed spacer (ITS) DNA sequences. All samples had identical LSU sequences. The ITS sequences had very few mutations that nevertheless divided the specimens into two groups: one included samples from Iceland, Svalbard, Massachusetts and Alaska with identical ITS sequences; members of this group differed in samples from Europe (France, Germany, Scotland, Sweden, and Wales) by three mutations (two point mutations and one five base pair indel). The European specimens had identical ITS sequences with the exception of a single sample from Brittany that differed by one base pair. The maximum ITS sequence divergence within the samples of C. melagonium was less than 0.5%. This low intraspecific variation in the frequently used highly variable ITS region is discussed in the context of past geological and climatic scenarios.

scholarly journals SELECTION AND ASSESSMENT OF ISSR-MARKERS FOR ANALYSIS OF SEPARATE CATTLE POPULATIONS

2021 ◽  
Vol 61 ◽  
pp. 137-145
Author(s):  
О. M. Мaherovska
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Dairy Cattle ◽  
Dna Sequences ◽  
Biological Material ◽  
Dna Polymorphism ◽  
Molecular Genetic ◽  
Issr Markers ◽  
Dna Fragments ◽  
Pcr Products

The article covers molecular genetic analysis of intermicrosatellite DNA sequences of dairy cattle productivity. Molecular markers based on DNA polymorphism were used for this monitoring. Such markers make it possible to assess quickly the genetic polymorphism of taprin in the herd. Іnsofar as a large number of intermicrosatellite repeats is in the genome of cattle, that increases the probability of detecting polymorphic loci. The ISSR markers selected for the study are based on multiclocus synthesis in polymerase chain reaction (PCR) and allow an objective study of the breed and interbreed diversity. And it makes possible to assess quickly and accurately genetic diversity for the presence of genes associated with economically useful traits. The purpose of this work is the selection and evaluation of ISSR-markers for the analysis and study of genetic diversity of Ukrainian and imported breeds of dairy cattle. Samples of biological material from representatives of three herds of cattle (Ukrainian Red-and-White spotted dairy, Montbeliard breed and their crossbreeds) were selected for the study by the method of groups-analogues. For the analysis of this material the generally accepted zootechnical methods of studying of a selection material and methods of an estimation of animals on molecular – genetic markers are included. According to standard methods, DNA was isolated from peripheral blood lymphocytes using a set of reagents "DNA Sorb B". Amplification of total DNA with ISSR primers was performed on a thermal cycler "Tertsyk" ("DNA technology" of the Russian Federation). Electrophoretic separation of DNA fragments was performed in an agarose gel according to conventional methods. The size of the obtained PCR products was detected using a molecular weight marker SM1343. As a result of the study of the biological material of these animals, the obtained ISSR-PCR products were quite heterogeneous. The vast majority of polylocus spectra had clear discrete bands, but there were amplicons without clear discrete bands. Analyzing the results of the study of the genetic structure of animals of the Ukrainian Red-and-White dairy breed, using primers ISSR-1, ISSR-2, ISSR-3 and ISSR-4, the range of obtained PCR products ranges from 250 bp. up to 3000 bp. The range of amplification products in Montbeliard animals has a smaller range and ranges from 250 bp, respectively. up to 1500 bp.The obtained amplicons for the use of primers ISSR-1 and ISSR-2, ISSR-3 and ISSR-4 in the turf of Ukrainian Red-and-White dairy and Montbeliard breeds have sizes from 350 bp to 2000 bp. Having analyzed the information you can determine the distribution of the number and length of DNA fragments using 4 ISSR-markers. The total number of amplified DNA fragments varies depending on the primer from 21 to 106, and their size ranges from 250 BP up to 3000 bp. Based on the analysis of DNA plymorphism, it is possible to assess the heterogeneity of selected populations of cattle. Thus, as a result of studying the genetic structure of animals of two breeds of dairy cattle and their crossbreeds by intermicrosatellite DNA loci, their individual polymorphism was revealed. The amplification products have significant variations depending on the primer used. Primers ISSR-1 and ISSR-2 were the most informative for the analysis of cattle DNA polymorphism.

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