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Objective:To analyze the prevalence of influenza B virus in Hangzhou from 2014 to 2020 and the genetic evolution of seven reassortant strains of influenza B virus.Methods:Influenza viruses were isolated from throat swabs collected from 16 943 patients with influenza-like illness in Hangzhou from January 2014 to December 2020. The subtypes of influenza viruses were identified by real-time RT-PCR. Eight genes ( PB2, PB1, PA, HA, NP, NA, MP and NS) of influenza B viruses were amplified with specific primers and then analyzed with nanopore sequencing and phylogenetic analysis. Results:From January 2014 to December 2020, there were 1 090 influenza B virus-positive samples, including 474 samples of Yamagata lineage and 616 samples of Victoria lineage, were identified in Hangzhou with an overall positive rate of 6.43% (1 090/16 943). Whole genomes of 228 strains of influenza B virus were obtained by nanopore sequencing and seven reassortant strains of influenza B virus were found. There were four reassortant influenza B viruses of Yamagata lineage with NA gene fragments from viruses of Victoria lineage, two strains of Yamagata lineage (H644_BY and H648_BY) with NP and NA gene fragments from Victoria lineage and one strain of Victoria lineage with PB2, PB1, PA and NS gene fragments from Yamagata lineage. Meanwhile, these seven strains possessed several mutations in the antigenic sites of HA and NA genes. Conclusions:Several rare reassortant strains of influenza B virus with epidemic potential were detected in Hangzhou from 2014 to 2020, which indicated that the traditional detection methods should be improved and more attention should be paid to the reassortant influenza B viruses and the match between epidemic and vaccine strains.
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In order to understand the prevalence and evolution of porcine reproductive and respiratory syndrome virus (PRRSV) in China and to develop subunit vaccine against the epidemic lineage, the genetic evolution analysis of PRRSV strains isolated in China from 2001 to 2021 was performed. The representative strains of the dominant epidemic lineage were selected to optimize the membrane protein GP5 and M nucleotide sequences, which were used, with the interferon and the Fc region of immunoglobulin, to construct the eukaryotic expression plasmids pCDNA3.4-IFNα-GP5-Fc and pCDNA3.4-IFNα-M-Fc. Subsequently, the recombinant proteins IFNα-GP5-Fc and IFNα-M-Fc were expressed by HEK293T eukaryotic expression system. The two recombinant proteins were mixed with ISA206VG adjuvant to immunize weaned piglets. The humoral immunity level was evaluated by ELISA and neutralization test, and the cellular immunity level was detected by ELISPOT test. The results showed that the NADC30-like lineage was the main epidemic lineage in China in recent years, and the combination of IFNα-GP5-Fc and IFNα-M-Fc could induce high levels of antibody and cellular immunity in piglets. This study may facilitate the preparation of a safer and more effective new PRRSV subunit vaccine.
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Humans , Animals , Swine , Porcine respiratory and reproductive syndrome virus/genetics , Porcine Reproductive and Respiratory Syndrome/prevention & control , HEK293 Cells , Viral Envelope Proteins/genetics , Antibodies, Viral , Viral Vaccines/genetics , Recombinant Proteins , Vaccines, SubunitABSTRACT
Objective:To analyze the genetic evolution and molecular characteristics of H5N8 avian influenza viruses (AIVs) isolated from the poultry in a live poultry market (LPM) in Urumqi, Xinjiang.Methods:Oropharyngeal and cloacal swabs of poultry were collected from a LPM in Urumqi in 2016. AIVs were isolated by inoculating swab samples into chicken embryos. Hemagglutination test and RT-PCR were used to identify the AIVs. The genes of isolated AIVs were amplified with the universal primers of AIV and whole-genome sequencing was also performed. Pairwise sequence alignment and analysis of phylogenetic and molecular characteristics were performed using BLAST, Clustal W, MEGA-X and DNAStar software.Results:Five H5N8 AIVs were isolated from poultry. These strains shared a nucleotide identity of 99.70%-100.00%, which indicated that they were from the same source, and were named XJ-H5N8/2016. Phylogenetic analysis based on hemagglutinin( HA), NS and PB2 genes showed that these isolates were clustered together with H5N8 AIVs isolated from the migratory swans in Hubei, Shanxi and Sanmenxia, and the ducks in India during 2016 to 2017. Moreover, they were also clustered together with H5N6 AIVs isolated from minks in China and the first case of human infection in Fujian. The phylogenetic tree of neuraminidase( NA) gene indicated the five isolates clustered together with H5N8 AIVs isolated from ducks in India in 2016, and the phylogenetic trees of PB1, MP, PA and NP genes showed that they were clustered together with H5N8 AIVs isolated from wild birds and poultry in Egypt, Cameroon, Uganda, Congo and other African countries in 2017. The HA cleavage sites of XJ-H5N8/2016 contained five consecutive basic amino acids, indicating high pathogenicity. Multiple mutations in the genes of XJ-H5N8/2016 could enhance its virulence and pathogenicity to mammals. Conclusions:The five strains of H5N8 AIVs isolated from the LPM were highly pathogenic and closely related to the H5N8 AIVs isolated from migratory birds and poultry in Hubei, Shanxi, Sanmenxia area, Africa and India during 2016 to 2017. Meanwhile, some of the viral genes were also closely related to the H5N6 AIVs isolated from the minks and human in China. Multiple mutations could increase the virulence and pathogenicity of AIVs to mammals, which could pose a potential threat to public health.
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Objective:To analyze the molecular evolution characteristics of HA and NA genes of influenza B/Yamagata (BY) and influenza B/Victoria (BV) lineage viruses in Guizhou Province, aiming to provide reference for scientific prevention and control of influenza. Methods:The prevalence of various types of influenza viruses in Guizhou Province from 2017 to 2021 was analyzed. The nucleic acid of influenza B viruses was extracted, and then the HA and NA genes were amplified by RT-PCR. Fourteen strains were sequenced and the sequences of 83 strains were obtained from GISAID. Homologies between the 97 influenza B viruses as well as the phylogenetic characteristics and amino acid site variations were analyzed. Results:Influenza A, BY and BV lineage viruses co-circulated in Guizhou Province and BV lineage was the predominant type. The homologies of HA and NA genes were 98.7%-99.4% and 98.4%-99.6% between BY lineage viruses and the reference vaccine strain B/PHUKET/3073/2013. BV lineage viruses shared 98.3%-99.3% and 98.9%-99.6% homologies with the reference vaccine strain B/Colorado/06/2017. The BY lineage strains in Guizhou Province mainly belonged to Y3 genetic group with HA gene in two branches of Y3-H1-2 and NA gene in three branches of Y3-N1-3. Three reassortant strains were found in Y3 clade. The isolated BV lineage strains mainly belonged to V1A-2 genetic group with HA gene in four branches of V1A-2 H1-4 and NA gene in five branches of V1A-2 N1-5. Twenty reassortant strains were found in V1A-2 clade and no inter-lineage reassortants were found. Analysis of variations at key amino acid sites showed that there was no mutation at epitopes in Y3 genetic group. However, there were point mutations at four main epitopes and a shift mutation in 190 helix in V1A-2 genetic group. There was no mutation in drug resistance sites. Conclusions:Various types of influenza viruses circulated in Guizhou Province. The homology between influenza B viruses and vaccine strains was decreasing. Different branches of HA and NA genes had been evolved and various forms of mutations were detected in the sequences. Intra-lineage reassortant strains and new varieties emerged. Surveillance of influenza B viruses should be strengthened.
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@#Abstract: Objective The main aim of the study is to sequence the complete genome of two Getah virus strains (GS11-155 and HNDZ1712-1) isolated in Gansu Province and Hainan Province in 2011 and 2017 respectively and analyze the molecular and genetic evolution of the two strains compared with M1, which was first isolated in 1964 in Hainan Province, China. Methods Genome of two newly isolated Getah viruses were sequenced by virus gene amplification technique, and the genomic database of Getah viruses was established. The molecular characteristics and genetic evolution of the viruses were analyzed by bioinformatics software. Results The genome length of two new isolated Getah virus strains (GS11-155 and HNDZ1712-1) was 11 690 nt and 11 621 nt, respectively. Both strains had the structural characteristics of Alphavirus genome. Although the nucleotide sequence lengths of structural genes, non-structural genes and non-coding junction regions of the two strains were identical, the nucleotide sequence lengths of the 5' and 3' non-coding regions of the viral genomes were a few different. The 3'UTR repeats elements in the genomes of the two virus strains did not change. It was 97.7% and 98.1% different of nucleotide and amino acid homology between both strains of Getah virus, HNDZ1712-1 isolated in 2017 and M1 isolated in 1964 in Hainan Province. Interesting, Gansu 2011 cluster and Hainan 2017 cluster were emerged leading by both strains GS11-155 and HNDZ1712-1 respectively, those two clusters totally independent with M1 virus isolated from Hainan in 1964 in whole genome phylogenetic analysis first. Conclusions Although the HNDZ1712-1 was also isolated from mosquito samples in Hainan Province, it was in a completely different evolutionary branch from the M1 isolated from Hainan Island in 1964, and was closely related to the strain isolated from Gansu Province (GS11-155) thousands of kilometers away. It is suggested that the two new strains of Getah virus are different from the Getah virus isolated in 1964.
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Objective@#To explore the intra-host genetic evolution of HIV-1 pol gene via follow-up for treatment-naïve HIV infections, and estimate the infection time with Bayesian coalescent theory, so as to support the evaluation of HIV epidemic. @*Methods@#Five cases were recruited and followed up. The pol gene fragments were amplified for the characteristics of transmitted drug resistance ( TDR ) by RT-PCR. Bayesian coalescent theory was utilized to construct maximum clade credibility ( MCC ) tree for genetic evolution and calculate the time to the most recent common ancestor ( tMRCA ). @*Results@#The five cases were all male, and aged from 27 to 50 years old.Five to nine sampling times were obtained from each case, and the pol gene sequences from each case formed a unique subcluster (posterior probability: 100% ), with different evolution characteristics, in the MCC tree. The three cases in primary HIV-1 infection were estimated to be infected one to five months before the first positive reaction of HIV screening, whereas the two HIV-1 diagnosed cases at first screening were extrapolated to get infected fourteen months and seven months before diagnosis, respectively. One case with acute HIV-1 infection carried TDR mutation ( M46I ) , expressing fast disease progress and quasispecies variation. @*Conclusions@#The general infection time can be estimated by analyzing the characteristics of intra-host genetic evolution of HIV-1 pol gene with Bayesian coalescent theory, and this method can help to estimate the HIV epidemic.
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Rhus chinensis is an important economic species, which could provide raw materials for pharmaceutical and industrial dyes. Rhus chinensis is famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. We report here Rhus chinensis chloroplast genomes by de novo sequencing. The results show that the length of Rhus chinensis was 159 082 bp, exhibiting a typical four-part structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The length of LSC and SSC was 85 394 bp and 18 663 bp, respectively. The genomes contained 126 genes, including 88 protein encoding genes, 8 rRNA and 30 tRNA genes. In the chloroplast genome, 61.97% of the sequence were gene coding region. In the sequence of gene encoding region, the vast majority of sequences were protein encoding region, accounting for 86.65%, followed by rRNA (10 620 bp, 10.77%) and tRNA (2 540 bp, 2.58%). In Rhus chinensis chloroplast genome, only 8 genes contain introns, all containing 1 intron except ycf3 gene (2 introns). The Rhus chinensis chloroplast genome contains 755 SSR locies. SSR mainly consists of dinucleotide and mononucleotide, accounting for 60% (453) and 28.74% (217) respectively. The clustering results show that Anacardiaceae were closest to Rhus chinensis, followed by Aceraceae and Sapindaceae. This study provides a molecular basis for the classification of Rhus chinensis.
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Genome, Chloroplast , Genetics , Open Reading Frames , Phylogeny , Rhus , Classification , Genetics , Sequence Analysis, DNAABSTRACT
Objective To analyze the genetic and evolutionary properties of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF 1ab/S/M proteins and select antigen epitope sequences of mRNA vaccines. Methods: We analyzed the worldwide SARS-CoV-2 genome sequences in this study and have focused on the protein and nucleic acid sequences of the ORF 1ab/S/M. The neighbor-joining tree was employed to map the global distribution of genetic differences. Based on current research on SARS-CoV-2 and SARS-CoV-2 genetic differences, we predicted candidate mRNA vaccines for SARS-CoV-2. Results: The SARS-CoV-2 ORF 1ab nucleic acid sequence similarity is 100.0%, while the homology is 99.3% in the global hot region; the S-protein nucleic acid sequence similarity is 100.0%, while the homology is 97.5%; the M-protein nucleic acid sequence similarity is 100.0%, while the homology is 99.9%. Global distribution of ORF 1ab/S/M proteins indicates that there is a significant genetic difference between the Americas and Eurasia. Potential vaccine antigen epitope mRNA sequences (11 B cell responses and 13 T cell responses) were selected for SARS-CoV-2 ORF 1ab protein; 6 B cell responses and 4 T cell responses antigen epitope mRNA sequences were selected for the Spike protein; 3 B cell responses and 7 T cell responses antigen epitope mRNA sequences were selected for the membrane protein. Conclusion: There are significant genetic differences in the global hot spot of SARS-CoV-2 in the Americas and Eurasia. Through our new antigen design strategy to screen linear epitopes, we predicted many sequences in ORF 1ab/S/M coding region that potentially raising an immune response. Our study will benefit the discovery of the mRNA vaccine (tandem antigen epitope sequence), antibody discovery, and potentially understanding related immune mechanisms.
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Background@#Zika virus (ZIKV) has emerged as a global pathogen causing significant public health concerns. China has reported several imported cases where ZIKV were carried by travelers who frequently travel between China and ZIKV-endemic regions. To fully characterize the ZIKV strains isolated from the cases reported in China and assess the risk of ZIKV transmission in China, comprehensive phylogenetic and genetic analyses were performed both on all ZIKV sequences of China and on a group of scientifically selected ZIKV sequences reported in some of the top interested destinations for Chinese travelers.@*Methods@#ZIKV genomic sequences were retrieved from the National Center for Biotechnology Information database through stratified sampling. Recombination event detection, maximum likelihood (ML) phylogenetic analysis, molecular clock analysis, selection pressure analysis, and amino acid substitution analysis were used to reconstruct the epidemiology and molecular transmission of ZIKV.@*Results@#The present study investigated 18 ZIKV sequences from China and 70 sequences from 16 selected countries. Recombination events rarely happens in all ZIKV Asian lineage. ZIKV genomes were generally undergone episodic positive selection (17 sites), and only one site was under pervasive positive selection. All ZIKV imported into China were Asian lineage and were assigned into two clusters: Venezuela-origin (cluster A) and Samoa-origin cluster (cluster B) with common ancestor from French Polynesia. The time of most recent common ancestors of Cluster A dated to approximately 2013/11 (95% highest posterior density [HPD] 2013/06, 2014/03) and cluster B dated to 2014/08 (95% HPD 2014/02, 2015/01). Cluster B is more variable than Cluster A in comparison with other clusters, but no varied site of biological significance was revealed. ZIKV strains in Southeast Asia countries are independent from strains in America epidemics.@*Conclusions@#The genetic evolution of ZIKV is conservative. There are two independent introductions of ZIKV into China and China is in danger of autochthonous transmission of ZIKV because of high-risk surrounding areas. Southeast Asia areas have high risk of originating the next large-scale epidemic ZIKV strains.
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Objective To analyze the prevalence of influenza A (H3N2) virus in Hangzhou be-tween 2012 and 2017 and to investigate the genetic variations in hemagglutinin ( HA) and neuraminidase ( NA) . -ethods Throat swab samples were collected for viral isolation from 12185 patients with suspected influenza in Hangzhou area from January 2012 to December 2017. Influenza virus subtypes were identified by real-time RT-PCR. HA and NA genes of some isolated Influenza A (H3N2) viruses were amplified with spe-cific primers and then analyzed by sequencing and phylogenetic analysis. Results Influenza A (H3N2) virus was the predominant subtype circulating in Hangzhou during 2012 to 2017. It caused high morbidity in elderly people (Z=81. 039, P<0. 05). Most of the isolated influenza A (H3N2) viruses belonged to the phylogenetic clades of 3C. 3a and 3C. 2a. These viruses shared a homology of 96. 7％-100％ in nucleotide sequences of both HA and NA genes, but possessed several HA and NA mutations in antigenic sites. Con-clusions Influenza A (H3N2) virus was an important pathogen causing influenza epidemics in Hangzhou during 2012 to 2017. HA and NA genes showed many mutations in antigenic sites. No drug resistant virus was reported.
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Comparative analysis of the variations in HA 1 gene of the influenza A (H3N2) virus and the vaccine recommended were conducted in Shangluo city of China,during the surveillance year of 2014-2015.In this study,we collected the samples of H3N2 subtype strain from the Shanglou City of China during the surveillance period of 2014-2015.The strain was cultured in MDCK cells,HA gene fragment was amplified by RT-PCR and the nucleotide sequence was determined.Sequence alignment was performed using the clustax2.1 software.The phylogenetic tree was constructed by Mega6.0 software and was analyzed by Neighboring-joining method.Results showed that the homology of isolated strain during 2014-2015 was 97.2 ％-99.9％ and homology with the recommended vaccine strain A/Texas/50/2012 was 97.3％-98.5％.The amino acid sequence of the HA 1 gene of the isolated strain was compared with that of the vaccine strain.The major antigenic determinants of the isolates in 2014,having mutations were section B,Y159F,S198P,while the major antigenic determinants of isolates in 2015,having amino acid mutations were A zone G142R,B region S159F,S198P.These results indicated that the key antigenic determinant of influenza H3N2 subtype strain in Shangluo City has changed in 2014-2015 and A/Texas/50/2012 vaccine component is no more effective.Hence,there is an urgent need to update the influenza H3N2 subtype vaccine components and in future we should be deeply concerned about the evolution ofinfluenza H3N2 gene trends.
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The high prevalence of influenza A virus is identified in Hunan Province because of the high density of poultry farms. To survey the variations of H9N2 subtype avian influenza virus in Hunan province, we analyzed HA and NA genes of 10 virus strains isolated from different areas of Hunan Province. All these strains belong to the Eurasian lineage, Y280-like sub-lineage. The cleavage sites in their HA genes were all RSSR↓GLT, corresponding to the feature of low pathogenic AIV. All strains had an L (Leu) at the site 234 in the HA genes, indicating the ability of binding with the SAα-2,6 receptor. NA gene stalk deletions at aa 63-65 were also detected from all the isolates, indicating a possibility of increased virus replication in mammals. Our findings suggest that more attention should be paid to the surveillance of H9N2 influenza virus and its direction of reassortment.
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Objective To study the epidemiological characteristics and genetic evolution of human bocavirus ( HBoV ) infection in hospitalized children with severe acute respiratory infection ( SARI ) in Hangzhou.Methods A total of 1388 clinical specimens were collected from children with SARI admitted in Affiliated Children' s Hospital, Zhejiang University School of Medicine from January 2011 to December 2014.HBoV1-4 and other respiratory pathogens were identified by fluorescent real -time polymerase chain reaction (fRT-PCR).The VP1 gene in HBoV1 positive samples was amplified and sequenced for genetic analysis with Clustal X and MEGA 6.0.Chi-square test and Fisher exact probability were used to analyze the data.Results Eighty five HBoV positive samples were detected from 1388 samples (6.12％), among which 83 (97.65％) were HBoV1 positive and 2 (2.35％) were HBoV2 positive.The positive rates of HBoV in males and females were 6.54％and 5.35％(χ2 =0.780, P>0.05).The posititve detection rate of HBoV in all age groups was statistically significant (χ2 =47.446,P <0.01).The detection rate in children aged 6 months-1 year was highest (12.84％), in children aged >3 years was lowest (1.64％), in children aged ≤6 months and aged 1-3 years was 3.04％ and 3.33％, respectively.The detection rate of HBoV in summer was the highest (14.97％), followed by that in autumn (7.14％), spring (3.19％) and winter (1.97％) (χ2 =58.807, P<0.01).The detection rates of HBoV in 2011 to 2014 were 7.39％, 7.31％, 5.58％ and 4.72％ (χ2 =3.447, P >0.05 ).The co-infection rate with other respiratory pathogens was 62.35％.The main pathogens were human rhinovirus (33.96％), parainfluenza virus (28.30％) and respiratory syncytial virus (20.75％).The incidence of anhelation and wheezing in HBoV positive group was higher than that in HBoV negative group (χ2 =15.161 and 13.914, P <0.01). Sequence analysis of VP 1 gene showed that 44 isolates belonged to the same branch ( clade 1 ) as Swedish strain ST2, and 2 isolates HZ12-S32 and HZ12-S199 belonged to a separated branch.Conclusion HBoV is an important causative agent of hospitalized children with SARI in Hangzhou area and has high co -infection with other respiratory pathogens.Most of the strains belong to the same clade as the Swedish strain ST 2, and two strains of HZ12-S32 and HZ12-S199 are identified in a separated clade.
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Objective To inquire into the molecular epidemiology of enterovirus 71 ( EV71 ) in our region by analyzing the whole genome characteristics and genetic evolution of EV 71 strains isolated from Guizhou area. Methods The throat swabs samples of hospitalized children with hand,foot and mouth disease in Guizhou province from 2013 to 2015 were collected,the virus nucleic acid were extracted,then the whole genome of virus were piecewise amplified by reverse transcription polymerase chain reaction( RT-PCR) and sequenced. Sequencing results were edited and spliced by DNAMAN8. 0 software,then the viral genome se-quences were compared with genome sequences of other EV71 strains in the genebank by Blastn,the phyloge-netic tree was constructed by the Neighbor-Joining method in MEGA5. 2 software. Results The whole ge-nome sequences of 17 EV71 strains were successfully isolated and amplified,the whole genome length of 17 EV71 isolates was 7405 base pair,encoded about 2193 amino acids. The 17 isolates were divided into ten species of amino acid sequences by 12 differences of amino acid among the strains,different sequences and clinical types had not shown regularity and correlation. The nucleotide homology in VP1 region,5′untranslat-ed region(5′UTR) and 3′untranslated region (3′UTR) were high among 17 EV71 isolates. The results that the whole genome of 17 EV71 isolates was compared with representative strains of EV71 A,B,C genotype and coxsakievirus A 16 ( CA16) showed that 17 EV71 isolates had higher homology with EV71 C4a sub-type,95. 3%-98. 1%,and the lowest homology with CA16. The phylogenetic tree was constructed based on nucleotide sequence of the whole genome,VP1 region and 5′untranslated region of 17 isolates showed that the 17 isolates were clustered into one cluster,and were clustered in the same branch with C4a isoforms,the phy-logenetic relationships among different regions were different. Conclusion The popular genotype of EV71 strains in Guizhou area for 2013-2015 was C4a subtype,consistenting with the genotype of popular EV71 in other regions of China. EV71 strains hasn′t the antigen transformation and input of a new subtype temporari-ly,but exist nucleotide and amino acid changes,so need be chronically and dynamically monitored. There is no correlation between the amino acid sequence difference of 17 EV71 isolates and the state of an illness.
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Objective To inquire into the molecular epidemiology of enterovirus 71 ( EV71 ) in our region by analyzing the whole genome characteristics and genetic evolution of EV 71 strains isolated from Guizhou area. Methods The throat swabs samples of hospitalized children with hand,foot and mouth disease in Guizhou province from 2013 to 2015 were collected,the virus nucleic acid were extracted,then the whole genome of virus were piecewise amplified by reverse transcription polymerase chain reaction( RT-PCR) and sequenced. Sequencing results were edited and spliced by DNAMAN8. 0 software,then the viral genome se-quences were compared with genome sequences of other EV71 strains in the genebank by Blastn,the phyloge-netic tree was constructed by the Neighbor-Joining method in MEGA5. 2 software. Results The whole ge-nome sequences of 17 EV71 strains were successfully isolated and amplified,the whole genome length of 17 EV71 isolates was 7405 base pair,encoded about 2193 amino acids. The 17 isolates were divided into ten species of amino acid sequences by 12 differences of amino acid among the strains,different sequences and clinical types had not shown regularity and correlation. The nucleotide homology in VP1 region,5′untranslat-ed region(5′UTR) and 3′untranslated region (3′UTR) were high among 17 EV71 isolates. The results that the whole genome of 17 EV71 isolates was compared with representative strains of EV71 A,B,C genotype and coxsakievirus A 16 ( CA16) showed that 17 EV71 isolates had higher homology with EV71 C4a sub-type,95. 3%-98. 1%,and the lowest homology with CA16. The phylogenetic tree was constructed based on nucleotide sequence of the whole genome,VP1 region and 5′untranslated region of 17 isolates showed that the 17 isolates were clustered into one cluster,and were clustered in the same branch with C4a isoforms,the phy-logenetic relationships among different regions were different. Conclusion The popular genotype of EV71 strains in Guizhou area for 2013-2015 was C4a subtype,consistenting with the genotype of popular EV71 in other regions of China. EV71 strains hasn′t the antigen transformation and input of a new subtype temporari-ly,but exist nucleotide and amino acid changes,so need be chronically and dynamically monitored. There is no correlation between the amino acid sequence difference of 17 EV71 isolates and the state of an illness.
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Resumen El virus chikungunya pertenece al género Alphavirus, de la familia de los Togaviridae. Es transmitido por artrópodos, en particular por la picada de especies de mosquitos, tales como Aedes aegypti y Aedes albopictus. El curso clínico característico de la infección incluye fiebres, artralgias y exantema. Desde que fue reportado en 1952 en los límites de Tanzania y Mozambique ha generado brotes de enorme significado epidemiológico. Recientemente fue causado un brote en las Américas por una cepa del virus, aparentemente, asiática. En esta revisión presentamos su filogenia, estructura y organización del genoma. Enfatizaremos en el mecanismo de multiplicación y la expresión genética. Finalmente, la interacción virus-huésped y sus mecanismos de adaptación a vectores específicos también son discutidos.
Abstract Chikungunya virus belongs to the Alphavirus genus of the family Togaviridae. It is transmitted by arthropods, in particular by the biting of mosquito species such as Aedes aegypti and Aedes albopictus. The characteristic clinical course of the infection includes fever, arthralgia, and rash. Since it was reported on 1952 on the borders of Tanzania and Mozambique, it has been triggered outbreaks with tremendous epidemiological significance. Recently an outbreak was caused in the Americas by an apparent Asian strain of this virus. In this review we present its phylogeny, structure and genome organization. We will emphasize the mechanism of replication and gene expression. Finally, the virus-host interaction and its mechanisms of adaptation to specific vectors are also discussed.
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The list of animal viruses has been frequently added of new members raising permanent concerns to virologists and veterinarians. The pathogenic potential and association with disease have been clearly demonstrated for some, but not for all of these emerging viruses. This review describes recent discoveries of animal viruses and their potential relevance for veterinary practice. Dogs were considered refractory to influenza viruses until 2004, when an influenza A virus subtype H3N8 was transmitted from horses and produced severe respiratory disease in racing greyhounds in Florida/USA. The novel virus, named canine influenza virus (CIV), is considered now a separate virus lineage and has spread among urban canine population in the USA. A new pestivirus (Flaviviridae), tentatively called HoBi-like pestivirus, was identified in 2004 in commercial fetal bovine serum from Brazil. Hobi-like viruses are genetically and antigenically related to bovine viral diarrhea virus (BVDV) and induce similar clinical manifestations. These novel viruses seem to be widespread in Brazilian herds and have also been detected in Southeast Asia and Europe. In 2011, a novel mosquito-borne orthobunyavirus, named Schmallenberg virus (SBV), was associated with fever, drop in milk production, abortion and newborn malformation in cattle and sheep in Germany. Subsequently, the virus disseminated over several European countries and currently represents a real treat for animal health. [...] Finally, the long time and intensive search for animal relatives of human hepatitis C virus (HCV) has led to the identification of novel hepaciviruses in dogs (canine hepacivirus [CHV]), horses (non-primate hepaciviruses [NPHV] or Theiler's disease associated virus [TDAV]) and rodents. For these, a clear and definitive association with disease is still lacking and only time and investigation will tell whether they are real disease agents or simple spectators.
O número de vírus animais cresce continuamente, causando preocupação permanente a virologistas e veterinários. O potencial patogênico e associação com doença tem sido claramente demonstrado para alguns - mas não para todos - vírus emergentes. Esse artigo apresenta uma breve revisão das recentes descobertas de vírus animais e a sua potencial relevância para saúde animal. Cães eram considerados refratários aos vírus da influenza até 2004, quando um vírus influenza A subtipo H3N8 foi transmitido de equinos e causou doença respiratória severa em cães galgos na Flórida/EUA. O novo vírus, denominado vírus da influenza canina (CIV), agora considerado uma linhagem distinta do vírus da influenza equina, disseminou-se na população canina urbana dos EUA. Um novo Pestivirus (Flaviviridae) - provisoriamente denominado pestivírus Hobi-like - foi identificado em 2004 em soro fetal bovino importado do Brasil. Os vírus Hobi-like são genética e antigenicamente relacionados com o vírus da diarreia viral bovina (BVDV) e induzem manifestações clínicas semelhantes. A sua origem e distribuição são desconhecidas, mas estão aparentemente disseminados no rebanho brasileiro e já foram identificados no sudeste asiático e na Europa. Em 2011, um novo buniavírus transmitido por mosquitos, denominado vírus Schmallemberg (SBV), foi associado com febre, redução da produção de leite, abortos e malformações fetais em bovinos e ovinos da Alemanha. [...] Finalmente, a longa e intensiva busca por vírus animais relacionados ao vírus da hepatite C humana (HCV) tem levado a identificação de "novos" pestivírus em cães (canine hepacivirus [CHV]), equinos (hepacivirus de não-primatas [NPHV] ou vírus associado à doença de Theiler [TDAV]) e em roedores. Para estes, uma associação clara e definitiva com doença ainda não foi demonstrada e apenas tempo e investigação irão dizer se são patógenos reais ou apenas espectadores.
Subject(s)
Animals , Communicable Diseases, Emerging/veterinary , Selection, Genetic/genetics , Gyrovirus/genetics , Hepacivirus/genetics , Alphainfluenzavirus/genetics , Orthobunyavirus/genetics , Pestivirus/genetics , Hepatitis E virus/geneticsABSTRACT
[Objective]This study was designed to investigate the genetic evolution of the neuraminidase(NA)gene of seasonal A/H1N1 and 2009 novel A/H1N1 inflilenza virus,and discuss the genetic variation of influenza A virus.[Methods]The virus strains were separately isolated from the clinical samples collected in 2006 and 2009,and then identified as seasonal A/H1N1 and novel A/H1N1.The full length of the NA gene of these strains was amplified by RT-PCR.Then the genetic evolution and mutations of important functional sites were analyzed.[Results]The homology of NA gene between the 2009 novel A/H1N1 isolates and 2006 seasonal A/H1N1 isolates was low(77.9%～78.8%),so was the homology of NA gene between the 2009 novel A/H1N1 isolates and representative strains of different periods and 1979-2001 WHO recommended vaccine strains(78.1%～79.3%).But compared with the WHO recommended vaccine strains of 2009 novel A/H1N1,the homology reached more than 99%.The genetic evolution analysis revealed that NA gene of 2009 novel A/H1N1 had the closest genetic relationship with the swine influenza A virus(A/swine/Belgium/1/1983)from Eurasian Iineage,and some of the antigenic sites and neuraminidase active sites of NA gene of seasonal A/H1N1 were mutated after 2005.[Conclusion]The NA gene of 2009 novel A/H1N1 may originate from Eurasian Iineage of swine influenza virus.The variation of NA gene of seasonal A/H1N1 has occurred in a certain degree.Hence,it is very necessary to continuously monitor the variant of influenza A virus.