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Background & objectives: BK virus (BKV) is a polyomavirus and cause of a common infection after renal transplantation which could be preceded to BKV-associated nephropathy. It has four main subtypes (I–IV). BKV subtypes II and III are rare, whereas subtype I shows a ubiquitous distribution. The objective of the present study was to investigate the prevailing BKV subtypes and subgroups in renal transplant patients in Sri Lanka. Methods: The presence of BKV in urine was tested through virus load quantification by real-time PCR from 227 renal transplant patients who were suspected to have BKV infection. Of these patients only 41 were found to be BKV infected (>103copies/ml) and those were subjected to conventional PCR amplification of VP1 gene followed by BKV genotyping via phylogenetic analysis based on DNA sequencing data. Results: Persistent BK viral loads varied from 1×103 to 3×108 copies/ml. Of the 41 patient samples, 25 gave positive results for PCR amplification of subtyping region of VP1 gene of BKV. BKV genotyping resulted in detecting subtype I in 18 (72%) and subtype II in seven (28%) patients. BKV subgroups of Ia, Ib-1 and Ib-11, and Ic were identified with frequencies of 6/18 (33.3%), 6/18 (33.3%), 5/18 (27.8%), and 1/18 (5.6%), respectively. Interpretation & conclusions: Findings from this preliminary study showed a high occurrence of subtype I, while the presence of subtype II, which is rare and less prevalent, was a novel finding for this Asian region. This emphasizes the need for further molecular and serological studies to determine the prevalence of different BKV subtypes in Sri Lanka
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Objective:To investigate the predominant types of enteroviruses and the characteristics of the VP1 gene of coxsackievirus A4 (CVA4) causing hand, foot and mouth disease (HFMD) in Yunnan Province from 2018 to 2020.Methods:Throat swab and stool samples were collected from HFMD cases and tested by real-time quantitative PCR for nucleic acid detection. The samples positive for enterovirus nucleic acids were used for viral isolation and sent to the National Center for Disease Control and Prevention. The VP1 gene of the isolated strains was sequenced and analyzed.Results:From 2018 to 2020, a total of 21 757 HFMD samples were collected, 16 457 (75.64%) of which were positive for enteroviruses. Altogether 533 strains were isolated from 4 114 positive samples that were selected for viral isolation, including 89 strains of enterovirus 71 (EVA71, 16.70%), 180 strains of coxsackievirus A16 (CVA16, 33.77%), 76 strains of CVA10 (14.26%), 118 strains of CVA6 (22.14%), 26 strains of CVA4 (4.88%) and 44 strains of other types (8.26%). HFMD occurred mainly in children under five years old with higher incidence in males than in females (1.35∶1). The incidence of HFMD reached the peak in the second and third quarters. In Yunnan Province, CVA4 mainly circulated in Qujing and Kunming, and was sporadically detected in Wenshan and Honghe. The VP1 gene was 915 bp in length. Twenty-six CVA4 strains belonged to C2 subtype, which were genetically far from the prototype strain AY421762-HighPoint. Mutations in the VP1 gene were found at multiple sites including 18, 23, 34, 102, 148, 164, 200, 262, 174, 275, 285 and 303. These strains showed 80.4%-99.0% homology in nucleotide sequence and 95.6%-99.0% in amino acid sequence. Nucleotide mutations were mostly synonymous mutations.Conclusions:CVA16, CVA6, EVA71 and CVA10 were the predominant enteroviruses causing HFMD in Yunnan Province from 2018 to 2020. The prevalence of CVA4 was also worthy of attention. CVA4 isolates in Yunnan Province belonged to C2 subtype, mainly circulating in the east and southeast of Yunnan Province and gradually becoming a cocirculating predominant strain. Long-term dynamic monitoring would be of great public health significance for improving the sensitivity of HFMD early warning.
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Objective:To analyze the etiology of hand, foot and mouth disease (HFMD) cases collected from Wenshan prefecture from 2014 to 2018 and the molecular epidemiology of coxsackievirus A6(CV-A6).Methods:Viruses were isolated by RD cells and Hep-2 cells from stool samples collected from HFMD patients in Wenshan prefecture from 2014 to 2018. Virus RNA was extracted and virus VP4/VP2 junction region sequence was firstly amplified and sequenced by MD91 and OL68-1 primer pairs, then the virus serotype was determined. Virus entire VP1 gene sequences were determined by relative primer pairs according to the references. The reference sequences of CV-A6 virus entire VP1 gene were downloaded from the GenBank and the phylogenetic tree was constructed and the genetic characteristics and molecular epidemiology were analyzed.Results:During five years of study period, a total of 581 strains of enteroviruses (EVs) was isolated with an isolation rate of 20.40% (581/2 848). Among 581 strains, 74 strains were CV-A6, accounting for 12.74% (74/581); 124 were CV-A16, accounting for 21.34% (124/581); 374 were EV-A71, accounting for 64.37% (374/581); nine were other EVs, accounting for 1.55% (9/581). The entire VP1 sequences of 74 CV-A6 strains were filtered by constructing a phylogenetic tree and the completely same strains were excluded from analysis. We finally analyzed the phylogenetic characteristics of 22 strains isolated in this study with 52 reference strains. The results showed that all 22 Wenshan strains belonged to D3a sub-genotype, of which 21 strains belonged to cluster 1, and only one strain belonged to cluster 2.Conclusions:From 2014 to 2018, the outbreaks of HFMD in Wenshan prefecture were mainly caused by EV-A71, CV-A16 and CV-A6, accounting for 64.37%, 21.34% and 12.74% respectively. Phylogenetic analysis showed, similar to the situation in China, the sub-genotype D3a of CV-A6 was the predominant virus and the cluster 1 was the main sub-genotype in this outbreak.
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Objective@#To develop RT-nPCR assays for amplifying partial and complete VP1 genes of human enteroviruses (HEVs) from clinical samples and to contribute to etiological surveillance of HEV-related diseases.@*Methods@#A panel of RT-nPCR assays, consisting of published combined primer pairs for VP1 genes of HEV A-C and in-house designed primers for HEV-D, was established in this study. The sensitivity of each RT-nPCR assay was evaluated with serially diluted virus stocks of five serotypes expressed as CCID @*Results@#The sensitivity of RT-nPCR assays for amplifying partial VP1 gene of HEVs was 0.1 CCID @*Conclusion@#This RT-nPCR system is capable of amplifying the partial and complete VP1 gene of HEV A-D, providing rapid, sensitive, and reliable options for molecular typing and molecular epidemiology of HEVs in clinical specimens.
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Humans , Capsid Proteins/genetics , Enterovirus A, Human/genetics , Enterovirus B, Human/genetics , Enterovirus C, Human/genetics , Enterovirus D, Human/genetics , Molecular Epidemiology/methods , Molecular Typing/methods , Reverse Transcriptase Polymerase Chain Reaction/methodsABSTRACT
Objective To analyze the genetic characteristics of VP1 3'region of human coxsack-ievirus B2 (CV-B2) strains isolated from Yunnan province. Methods RT-PCR and gene sequencing were performed to analyze the VP1 3'region of 15 CV-B2 strains isolated from acute flaccid paralysis ( AFP) cases during 2005 to 2006, healthy children in 2013 and hand, foot and mouth disease (HFMD) cases in 2014 in Yunnan province. CV-B2 VP1 gene reference sequences were downloaded from the Genbank. Nucleotide (nt) and amino acid (aa) diversities were calculated by MEGA5. 2 software and a phylogenetic tree was constructed. Genetic and molecular epidemiological characteristics of CV-B2 strains circulating in Yunnan province were analyzed. Results A total of 15 CV-B2 strains were isolated, which were one from 232 AFP cases in 2005, one from 240 AFP cases in 2006, 12 from 400 healthy children in 2013 and one from 500 HFMD cases in 2014. Phylogenetic analysis of the 15 CV-B2 strains in Yunnan province and those down-loaded from the GenBank showed that CV-B2 could be genetically divided into five genotypes. The prototype strain Ohio-1 and one strain (01-1) isolated in Taiwan in 1988 belonged to genotype 1. Strains isolated in France in 2006, 2007 and 2010 belonged to genotype 2. Strains isolated in Yunnan, Shandong, Henan, Fu-jian and Taiwan belonged to genotype 3. Strains isolated in Russia, Yunnan AFP cases in 2005 and 2006 and India belonged to genotype 4. Strains isolated in Taiwan, Shandong and New South Wales, Australia be-longed to genotype 5. Different genotypes distributed in different countries/areas with some confined within specific countries/areas. Conclusions The 12 strains isolated from healthy children and one from HFMD cases in Yunnan province belonged to genotype 3, while the two strains isolated from AFP cases belonged to genotype 4. Diversities in nt and aa sequences between the strains isolated from the healthy children and HFMD case were only 0. 76％ and 0. 03％, respectively, indicating that they might come from the same transmission source. However, the nt and aa diversities between the isolates of genotype 3 ( from healthy children and HFMD case) and genotype 4 (from AFP cases in 2005 and 2006) were 15. 11％-15. 22％ and 2. 76％-2. 72％, respectively. Correlation of CV-B2 with AFP and HFMD was worthy of further study.
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Objective To detect the enterovirus VP4 and VP1 genes in 510 stool samples collect-ed from hand, foot and mouth disease ( HFMD) cases and analyze the phylogenetic characteristics of the en-tire VP1 genes of coxsackievirus A6 (CV-A6) strains in six prefectures/cities of Yunnan Province in 2018. Methods Viral RNA was abstracted from the stool samples. VP4 gene sequences were amplified by RT-PCR and sequenced using the MD91/OL68-1 primer pair to identify viral genotypes. Whole VP1 gene se-quences were amplified and sequenced using appropriate primer pairs. The whole VP1 gene sequences of CV-A6 reference strains were downloaded from GenBank. MEGA5. 2 software was used to analyze the simi-larity in nucleotide and amino acid sequences between different strains and phylogenetic tree was constructed for analysis of genetic characteristics and molecular epidemiology. Results VP4 and VP1 gene sequences were obtained from 57 out of 510 stool samples with a positive rate of 11. 17％ (57/510). There were 43 CV-A6 (8. 43％, 43/510), six CV-A10 (1. 17％, 6/510), two enterovirus A71 (EV-A71, 0. 39％, 2/510) and two CV-A9 (0. 39％, 2/510) strains. The other four strains were CV-A4 (0. 19％, 1/510), CV-A5 (0. 19％, 1/510), CV-B1 (0. 19％, 1/510) and E11 (0. 19％, 1/510). The phylogenetic analy-sis showed that all 43 CV-A6 strains belonged to sub-genotype D3. Conclusions In the 510 HFMD sam-ples, CV-A6 strains were mostly detected with a detection rate of 8. 43％ and accounted for 75. 44％ (43/57) of all isolates, followed by CV-A10 (1. 17％, 6/510) and EV-A71 (0. 39％, 2/510). There was a large HFMD outbreak mainly caused by CV-A6 in Yunnan Province in 2018. The outbreak was caused by CV-A6 of sub-genotype D3, as was the case with pervious outbreaks in China.
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Objective@#To detect the enterovirus VP4 and VP1 genes in 510 stool samples collected from hand, foot and mouth disease (HFMD) cases and analyze the phylogenetic characteristics of the entire VP1 genes of coxsackievirus A6 (CV-A6) strains in six prefectures/cities of Yunnan Province in 2018.@*Methods@#Viral RNA was abstracted from the stool samples. VP4 gene sequences were amplified by RT-PCR and sequenced using the MD91/OL68-1 primer pair to identify viral genotypes. Whole VP1 gene sequences were amplified and sequenced using appropriate primer pairs. The whole VP1 gene sequences of CV-A6 reference strains were downloaded from GenBank. MEGA5.2 software was used to analyze the similarity in nucleotide and amino acid sequences between different strains and phylogenetic tree was constructed for analysis of genetic characteristics and molecular epidemiology.@*Results@#VP4 and VP1 gene sequences were obtained from 57 out of 510 stool samples with a positive rate of 11.17% (57/510). There were 43 CV-A6 (8.43%, 43/510), six CV-A10 (1.17%, 6/510), two enterovirus A71 (EV-A71, 0.39%, 2/510) and two CV-A9 (0.39%, 2/510) strains. The other four strains were CV-A4 (0.19%, 1/510), CV-A5 (0.19%, 1/510), CV-B1 (0.19%, 1/510) and E11 (0.19%, 1/510). The phylogenetic analysis showed that all 43 CV-A6 strains belonged to sub-genotype D3.@*Conclusions@#In the 510 HFMD samples, CV-A6 strains were mostly detected with a detection rate of 8.43% and accounted for 75.44% (43/57) of all isolates, followed by CV-A10 (1.17%, 6/510) and EV-A71 (0.39%, 2/510). There was a large HFMD outbreak mainly caused by CV-A6 in Yunnan Province in 2018. The outbreak was caused by CV-A6 of sub-genotype D3, as was the case with pervious outbreaks in China.
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Objective@#To analyze the genetic characteristics of Coxsackievirus A4 isolated from Taian, 2017-2018.@*Methods@#Sixty throat swab samples of the children who visited Taian Maternal and Child Health Hospital during the year 2017-2018 and were diagnosed as hand, foot and mouth disease, were collected and aseptically inoculated. Fluorescent quantitative PCR analysis was performed using the universal primer for enteroviruses. The high-throughput sequencing was applied to the enterovirus-positive samples, and the full-length genome sequences of the viruses were obtained. Phylogenetic analysis was performed using Mega5.05 and RaxML respectively, and sequence homology and amino acid mutation sites were also analyzed using Mega5.05.@*Results@#Four whole genome sequences of CV-A4 isolated from infants aged 17-19 months old were obtained. Phylogenetic analysis of the full length CV-A4 genomes showed that apart from MG550920/AA/Henan/2016, the remaining CV-A4 strains from China (97.2%), including the four strains from Taian, fell within Group 3. The VP1 genes could be classified into four genotypes and 98.5% of the Chinese strains belonged to genotype D, and the four strains from Taian belonged to D2. It was notable that the Taian isolate A1/Taian is closely related to two strains C179 and C062 from Australia both in the complete genome and the VP1 gene, as well as one strain YT184R isolated from Yantai in 2016 by us. Compared with the prototype CV-A4 strain High Point, 18 amino acid mutations were found in the P1 region.@*Conclusions@#Both phylogenetic trees estimated using the complete genome and the VP1 gene sequences revealed that the four CV-A4 isolates from Taian fell within the same clade with the majority of CV-A4 strains circulating in China. Compared with the prototype CV-A4 strain, several amino acid variations have occurred in the P1 region, which warrants further investigation.
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Objective@#In this study we analyzed the genetic characteristics of echovirus 30 (E-30) VP1 gene sequences from Yunnan province isolated from viral meningitis (VM) cases in 2010-2013.@*Methods@#RT-PCR and VP1 gene sequencing were done for 9 E-30 strains isolated from VM cases in 2010-2013. VP1 gene sequences of E-30 reference strains were downloaded from the GenBank and their nucleotide (nt) and amino acid (aa) diversities were calculated by MEGA 5.1 software, the phylogenetic tree was constructed and the genetic characteristics and molecular epidemiology were analyzed.@*Results@#In 2010-2013, 9 strains of E-30 viruses were detected from 79 VM cases caused by echoviruses, accounting for 11.39%(9/79), the overall positive rate was 1.63%(9/553). Phylogenetic analysis revealed that E-30 strains can be divided into four genotypes (genotype A, B, C and D), and genotype D can be further divided into seven sub-genotypes. Nine Yunnan VM isolates were distributed in D7 sub-genotype, and can be further clustered into 3 branches: 5 strains isolated in 2010 were clustered in branch 1, it is evident that these viruses were responsible for an aseptic meningitis outbreak in Kunming in that year; one 2011 isolate, together with 2013 isolate and one isolate from healthy children in 2010 were clustered in branch 2, these two branches were Yunnan special branches, and two 2011 isolates had the highest homology with 2003 VM outbreaks′ strains isolated from Shandong, Jiangsu, and Zhejiang, showing that these strains may have the same evolutionary sources.@*Conclusions@#Nine Yunnan VM isolates were distributed in D7 sub-genotype, and these strains have different evolutionary sources, showing that at different times E-30 viruses in the same sub-genotypes branch might prevail in different areas.
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Objective To investigate the genetic evolution of VP1 gene of pathogenic coxsackievirus A16 (CV-A16) strain isolated from clinical hand,foot,and mouth disease (HFMD) patients.Methods A total of 160 HFMD cases with CV-A16-positive results were collected from hospitals in Kunming during January 2015 to June 2017.Fecal samples were collected.Real-time polymerase chain reaction (PCR) was used to detect the CV-A16 virus nucleic acid.The VP1 genes of CV-A16-positive samples were amplified by reverse transcription-PCR.The amplified positive products were sequenced and aligned.The homologies were identified and their subgenotypes were determined.The phylogenetic tree was constructed and homology modeling was conducted.Results All the 160 CV-A16 isolates were B2 subtypes.The genetic distance between detected strains of CV-A16 and the strains in Fujian,Beijing,Nanjing was 0.76.The genetic distance to the strains in Malaysia was 0.78,and to the strains in Australia was 1.86.Homologous modeling revealed that the amino acid sequence of the VP1 gene of the strain had a G227R mutation.Conclusions There is no major genetic variation in the CV-A16 strains during 3 years.CV-A16 isolates are close to those of epidemic strains in Beijing,Fujian and Malaysia,but are far fram the strains from Australia.
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Objective@#To analyze the VP1 region characteristics of coxsakievirus B4 (CoxB4) strain isolated from patients with hand, foot and mouth disease (HFMD) in Henan province and to compare the similarity and difference among these viruses isolated from different diseases.@*Methods@#The 134 samples were tested by reverse-transcription polymerase chain reaction (RT-PCR) and cell-culture-based isolation of CoxB4. The VP1 of 8 CoxB4 isolated was amplified using specific primers. The sequences were spliced, edited, analyzed and mapped into phylogenetic tree by bioinformatics software ATGC, lustalx1.83, BioEdit and MEGA4.0, respectively.@*Results@#The VP1 region length of Henan CoxB4 isolates were 852 bp. Compared with other CoxB4 strains released in GeneBank, the similarities of nucleotide and amino acid is 80.3%-97.0%, 96.1%-100%. The largest difference was 19.7% between Henan isolates and diabetes isolates, and 3.0% was the smallest difference with HFMD isolates. Phylogenetic tree analysis showed that Henan CoxB4 isolates belonged to Genotype V, and the isolates from HFMD were close to those of meningitis, distributed in a cluster. These isolates from diabetic patients were in another cluster.@*Conclusions@#There were Genotype V spreading and circulating of CoxB4 that infected HFMD patients in Henan.
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Objective To investigate the etiology of hand,foot and mouth disease (HFMD) and to analyze the genetic characteristics of three prevalent enteroviruses in Qingdao in 2015. Methods City-wide surveillance data in 2015 were used to analyze the epidemiological characteristics of HFMD in Qingdao. RNA samples extracted from throat swab of HFMD cases were examined for general enteroviruses (EVs) such as enterovirus 71(EV71), coxsackievirus A16 (CA16) and CA6 by real-time RT-PCR. Full-length VP1 genes of EV-positive specimens were amplified and sequenced. Sequencing results were phylogenetically analyzed using MEGA 7.0 software package. Results A total of 804 patients with HFMD were identified from 1 176 patients in 2015. CA6 (41.4%),EV71 (31.6%) and CA16 (15.3%) were the predominant EVs causing HFMD. Children 5 years of age and under accounted for 80.3% of the 804 HFMD cases. CA6 was responsible for 48.9% of HFMD cases in children under 3 years old. The epidemic subtypes of EV71 and CA16 in Qingdao were C4a and B1b,respectively. Twenty-eight randomly selected CA6 strains were all classified into type A genome. Conclusion CA6, EV71 and CA16 were the prevalent pathogens causing HFMD in Qingdao in 2015. CA6 became the most predominant pathogen,mainly targeting children under 3 years old. C4a remained the prevailing subtype of EV71,while different from the co-prevalence of B1a and B1b subtypes in the past,B1b became the predominant subtype of CA16. CA6 strains circulating in Qingdao in 2015 mainly belonged to type A genome and evolved into multiple smaller branches. However, CA6 strains isolated in Qingdao in 2015 and 2013 located in different branches.
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Objective To investigate the characteristics of VP1 gene hypervariable region in hu-man enterovirus type 68(HEV68)strains isolated in China. Methods Nucleotide sequences of the VP1 gene in the Chinese strains and strains isolated in other countries were aligned by using Clustal W in the MEGA6 program. The phylogenetic trees were constructed by using Neighbor-Joining(NJ)method in the MEGA6 program. Sequence of the amino acids encoded by that region was analyzed by compared with that of the standard strain Fermon. Results A total of 80 strains of EV68 had been isolated in China by the end of 2015. Most of the mutations occurred in BC and DE loops. The mutation sites lied in the VP1 gene of Chi-nese isolates were at 83,89,91,94,96,97,98,102,109,139,141,142,143,144 and 147. Glycine was missing from most of the amino acid sequences encoded by the VP1 gene of Chinese strains. The phylo-genetic analysis indicated that 53 and 21 EV68 strains isolated in China belonged to B and C clades,respec-tively. Conclusion Compared with the standard strain Fermon,the Chinese strains changed a lot in BC-loop and DE-loop,which were associated with the antigenicity and virulence of EV68. The EV68 strains iso-lated in China belonged to B and C clades.
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Objective In order to investigate etiology and molecular-epidemiological characteristics of enterovirus associated encephalitis (EAE) in Zhejiang,2008-2012.Method Cerebrospinal fluid and stool specimens were collected from suspected EAE patients,who were admitted to our hospitals.RD and Hep-2 cell lines were used to isolate enterovirus (EV).Serotypes of these EV isolates were identified through neutralization test by using serotype specific anti-sera.VP 1 genes of these isolates were sequenced,compared and used for the construction of phylogenetic tree.Results 127 (20.6％) human enterovirus (HEV) strains were isolated from 616 samples,which were collected from 610 patients.Serotypes of these EV isolates,including 60 coxsackievirus (CV),and 67 Echovirus (E) appeared to be CVA9,CVB1,CVB3-5,E3,E4,E6,E9,El4,E25 and E30,respectively.Predominant EV serotypes on EAE from 2008 to 2012 were seen as CVB3,CVB5,E6,E30 and E30,respectively.The full length of VP1 genes from different EV isolates was between 834 and 918 nucleotides.The VP1 gene similarities between these isolates and the reference strains were from 76.7％ to 85.0％ (nucleotides level) and 91.1％ to 97.9％ (amino acids level).The VP1 genes from E6 serotype isolates appeared most diverged,reaching 20.4％ (nucleotides level) attd 4.8％ (amino acids level).Based on the generated phylogenetic tree,all the EV isolates were fallen on the same branch of HEV-B,and the isolates in the same serotype formed one sub-branch,suggesting there existed geographical and temporal effects.E6 isolates diverged into two branchlets.Conclusion EVs from HEV-B were the etiologic agents for EAE in Zhejiang province from 2008 to 2012.All these EV isolates showed 12 serotypes,with predominant isolates varied every year.E30 was determined as the most dominant serotype while serotype E6 diverged into two sub-genetypes.
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Foot-and-mouth disease virus (FMDV) is highly contagious and responsible for huge outbreaks among cloven hoofed animals.The aim of the present study is to evaluate a plasmid DNA immunization system that expresses the FMDV/O/IRN/2007 VP1 gene and compare it with the conventional inactivated vaccine in an animal model.The VP1 gene was sub-cloned into the unique Kpn I and BamH I cloning sites of the pcDNA3.1+ and pEGFP-N1 vectors to construct the VP1 gene cassettes.The transfected BHKT7 cells with sub-cloned pEGFP-N1-VP1 vector expressed GFP-VP1 fusion protein and displayed more green fluorescence spots than the transfected BHKT7 cells with pEGFP-N1 vector,which solely expressed the GFP protein.Six mice groups were respectively immunized by the sub-cloned pcDNA3.1+-VP1 gene cassette as the DNA vaccine,DNA vaccine and PCMV-SPORT-GMCSF vector (as molecular adjuvant) together,conventional vaccine,PBS (as negative control),pcDNA3.1+ vector (as control group) and PCMV-SPORT vector that contained the GMCSF gene (as control group).Significant neutralizing antibody responses were induced in the mice which were immunized using plasmid vectors expressing the VP1 and GMCSF genes together,the DNA vaccine alone and the conventional inactivated vaccine (P＜0.05).Co-administration of DNA vaccine and GMCSF gene improved neutralizing antibody response in comparison with administration of the DNA vaccine alone,but this response was the most for the conventional vaccine group.However,induction of humeral immunity response in the conventional vaccine group was more protective than for the DNA vaccine,but T-cell proliferation and IFN-γ concentration were the most in DNA vaccine with the GMCSF gene.Therefore the group that was vaccinated by DNA vaccine with the GMCSF gene,showed protective neutralizing antibody response and the most Th1 cellular immunity.
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Objective To study the composition of variant and point mutations of Norovirus GⅡ.4 in Guiyang regions.Methods From June to November 2010,cases information and fecal specimens were collected from guard-hospitals in Guiyang regions,who had caught the acute-gastroenteritis.Noroviruses in specimens were detected by a real-time reverse transcription polymerase chain reaction(real-time RT-PCR),and then partial genotyped norovirus-positive clinical samples (in random) were cloned and sequenced in VP1 gene code.Furthermore,the gene sequences were compared with the published variants at home and abroad of norovirus(GⅡ.4),including the phylogenetic analyses of genomes and variation of amino acids within individual sites.Results Those 267 specimens were GⅡ-norovirus-positive(62.68％) in 426 clinical samples.There were nine GⅡ.4-norovirus-positive VP1 gene-sequences available,and two subtype-norovirus variants (GⅡ.4 2008a and G Ⅱ.4 2008b variant) were epidemic in 2010,Guizhou province.The homology between and in subgroups were 95.90％-96.72％ and 99.45％-100％.Two amino acids within individual sites were apt to mutate.Conclusion Norovirus GⅡ genotype were predominant in summer and fall acute gastroenteritis in 2010 for Guiyang regions,and the variants were diversity.
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In the present study, epidemiological survey and molecular characterization of hepatitis A virus during an outbreak in five Tunisian childcare centers in El-Mahres during October and November 2006 were carried out. Five well-water and five drinking water samples were included in the present study. Serological investigation and molecular characterization were carried out. All patients were IgM seropositive and the viral genome was detected in all clinical and well-water samples whereas it was not detected in drinking water from the five childcare centers. Sequence analysis showed that all Tunisian strains belong to sub-genotype IA. The genetic profile of the VP1/2A junction showed that the outbreak isolates underwent an amino acid substitution which was absent in virus's strains detected previously in Tunisia. Further studies need to be conducted to evaluate the emergence of the virus's strains in clinical and water samples and more epidemiological data need to be collected about the risk factors which may contribute to acute hepatitis.
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Humans , Disease Outbreaks , Immunoglobulin M , Sequence Analysis, DNA , Sequence Analysis, Protein , Hepatitis Viruses/genetics , Diagnostic Techniques and Procedures , Methods , Patients , Water SamplesABSTRACT
Objective To discuss the prevalence of non-EV71,non-CA16 virus strains of hand,foot and mouth disease(HFMD) in Guangdong province between 2008 and 2009,and analyze the genetic evolution of these non-EV71,non-CA16 virus strains.Methods Isolated viruses from stool samples collected from outpatient and in-patient cases of HFMD between 2008 and 2009 by human rhabdomyosarcoma(RD) cell and HEp-2 cell,cultures that exhibited a characteristic enterovirus cytopathic effect were evaluated by RT-PCR.Those strains which identified non-EV71,non-CA16 were analyzed by VP1 sequencing and then were identified by BLAST program.A phylogenetic tree was constructed using the Neighor-Joinning method in the MEGA 4.0 software.Results Twenty-two virus strains of non-EV71,non-CA16 were obtained,and nine of the twenty-two virus strains in 2008 were classified into CA2,CA4,and CB3 by BLAST; thirteen of the twenty-two virus strains in 2009 were classified into EV80,Echo13,Echo30,CBS,Echo24,CA10,CA6,and poliovirus 1 by BLAST.The honology of all strains was low,and all the strains belonged to CA,CB,Echoviruses,Enterovirus and poliovirus subgroup.Conclusion Except for EV71 and CA16 was a major causative agent in prevail of HFMD in Guangdong province between 2008 and 2009,there also existed other subgroup Enterovirus.The other twenty-two strains respectively belonged to CA,CB,Echoviruses,Enterovirus and poliovirus subgroup,and none of those strains was predominant.Muti-species Enterovirus occurred concomitantly.
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Enterovirus 71 (EV71) is a common cause of Hand, foot, and mouth disease (HFMD) and may also cause severe neurological diseases, such as encephalitis and poliomyelitis-like paralysis. To examine the genetic diversity of EV71, we determined and analyzed the complete VP1 sequences (891 nucleotides) from nine EV71 strains isolated in Fuyang, China. We found that nine EV71 strains isolated were over 98% homologous at the nucleotide level and 93%-100% homologous to members of the C4 subgenogroup. At the amino acid level, these Fuyang strains were 99% -100% homologous to one another, 97%-100% homologous to members of the C4 subgenogroup, and the histidine(H) at amino acid position 22 was conserved among the Fuyang strains. The results indicate that Fuyang isolates belong to genotype C4, and an H at position 22 appears to be a marker for the Fuyang strains.
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The complete genomic sequence of Duck hepatitis virus 1 (DHV-1) ZJ-V isolate was sequenced and determined to be 7 691 nucleotides (nt) in length with a 5'-terminal un-translated region (UTR) of 626 nt and a 3'-terminal UTR of 315 nt (not including the poly(A) tail). One large open reading frame (ORF) was found within the genome (nt 627 to 7 373) coding for a polypeptide of 2 249amino acids. Our data also showed that the poly (A) tail of DHV-1 has at least 22 A's. Sequence comparison revealed significant homology (from 91.9% to 95.7%) between the protein sequences of the virus in the Picornaviridae family, its genome showed some unique characteristics. DHV-1 contains 3copies of the 2A gene and only 1 copy of the 3B gene, and its 3'-NCR is longer than those of other picornaviruses. Phylogenetic analysis to do sequence homology based on the VP1 protein sequences showed that the ZJ-V isolate shares high sequence homology with the reported DHV-1 isolates (from 92.9% to 99.2%), indicating that DHV-1 is genetically stable.