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Objective:To analyze the molecular characteristics of hemagglutinin-neuraminidase (HN) gene of human parainfluenza virus type 3 (HPIV3) among the cases with acute respiratory tract infection (ARI) in Henan Province.Methods:Nasal/throat swab samples collected from patients with severe acute respiratory tract infection (SARI) in Luohe and patients with influenza-like illness (ILI) in Zhengzhou were used in this study. HPIV nucleic acids in the samples were detected using real-time fluorescent PCR. HPIV3-positive samples were subjected to RT-PCR for the amplification of HN genes and the sequences were analyzed with Sanger method. CExpress and MEGA7.0 software were used for sequences editing, evolution tree construction and gene sequence analysis.Results:A total of 374 throat swab samples collected form ARI cases in Luohe and Zhengzhou were tested and 20 (5.3%) of them were positive for HPIV3. Eighteen HPIV3 HN gene sequences were successfully amplified and all belonged to C3 subgroups, including 16 sequences of C3f genotype and two sequences of C3a genotype. The 18 HN gene sequences shared the homology of 97.6%-100.0% in nucleotide and 99.3%-100.0% in amino acid, but the differences between them and the prototype strain Wash/47885/57 were significant. There were 12 amino acid mutations shared by them, including four function-related mutations (H295Y, I391V, D556N and I53T). There were no significant differences in the nucleotide or amino acid sequences as compared with the epidemic strain of China/BCH4210A/2014.Conclusions:The C3f and C3a branches of HPIV3 were the epidemic genotypes in Henan Province in recent years and a local circulating prevalence might be established. Continuous and in-depth monitoring of HPIV3 C3 subtype would be of great significance for the prevention and control of HPIV3-associated diseases.
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Objective:To analyze the viral genome sequence of novel coronavirus infected persons in Baotou City, understand the mutation characteristics of novel coronavirus genome in the process of transmission among cases, and explore the transmission rule of novel coronavirus in the clustered populations.Methods:Nine throat swabs samples (No. 1 - 7, No. 9, and No. 10), two sputum samples (No. 8, No. 11, and No. 11 sample was from No. 10 case), and one surface smear sample (No.12, and No. 12 sample was from No. 10 case) were collected from 10 confirmed cases of novel coronavirus infection in Baotou City from January 25 to February 21, 2020. Samples 1 and 3 were from single cases, and the rest were from clustered cases. The virus genome was sequenced by metagenomic next-generation sequencing (mNGS), and single nucleotide polymorphism (SNP) mutation sites were screened by comparing with NC_045512, a reference strain of novel coronavirus. Combined with relevant epidemiological information, gene mutation, virus typing, and evolutionary traceability analysis were carried out.Results:The results of viral genome mNGS showed that 76 SNP mutation sites were detected in 12 samples compared with the reference strain NC_045512, including 3 (3.95%) transitions and 73 (96.05%) reversals. There were 19 (25.00%) synonymous mutations and 57 (75.00%) non-synonymous mutations. The analysis of nucleotide and amino acid variation sites showed that mutations were found at five sites (T2821C, C6548T, T16464C, G16858A and T251C) in all the clustered cases (cases 2, 4 - 10). In the single cases, sample 1 had mutations at C9245T and A15340T, and sample 3 had mutation at C13T. The virus typing analysis showed that the samples 1 and 3 belonged to the L type of novel coronavirus, while the rest belonged to the S type of novel coronavirus. The results of genomic evolutionary relationship analysis showed that all the samples could be divided into two branches. The branches of sample 1 and 3 belonged to single cases, and the rest belonged to family clustered cases.Conclusion:The genomic characteristics of the clustered cases of novel coronavirus infection in Baotou City are basically consistent with the epidemiological investigation results, and the transmission of the virus is mainly related to close contact and family gathering.
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Objective:To analyze the etiological distribution and phylogenetic characteristics of hand, foot and mouth disease (HFMD) in Qujing city of Yunnan Province in 2020.Methods:Stool samples were collected from HFMD cases in Qujing city in 2020 and virus RNA was extracted directly from treated stool suspensions. Virus VP4 gene sequences were firstly amplified using MD91/OL68-1 primer pairs and sequenced, then the virus serotypes were determined by BLAST search on the GenBank. Virus entire VP1 gene sequences were amplified and sequenced. Virus serotypes were identified online using Enterovirus Genotyping Tool Version 0.1. Sequences of reference virus genotypes/sub-genotypes were downloaded according to references. Phylogenetic trees were constructed by MEGA5.2 software and the genetic characteristics were analyzed.Results:A total of 47 strains of enteroviruses (EVs) were detected with a detection rate of 10.22% (47/460). The detected viruses were coxsackievirus A4 (CVA4, 0.65%, 3/460), CVA6 (7.83%, 36/460), CVA10 (0.87%, 4/460) and CVA16 (0.87%, 4/460). All were enterovirus species A (EVA), while other group viruses were not detected. The predominant virus was CVA6, accounting for 7.83% (36/460). EVA71 was not detected. CVA4 strains of C2 and C4 subgenotypes were co-circulating strains in Qujing city. CVA6 subgenotype D3a and CVA16 subgenotype B1a were also circulated in Qujing city. All CVA10 strains were in a separate lineage.Conclusions:Similar to the previous situation in China, the detection rates of EVA71 and CVA16 were very low, even zero. This study showed that CVA6 was the predominant virus, indicating a HFMD outbreak caused by CVA6 in Qujing city in 2020. The phylogenetic analysis showed CVA10 isolates belonged to a separate lineage, which might be unique to Qujing city. Laboratory and molecular epidemiological surveillance of non-EVA71 and non-CVA16 viruses, especially CVA6 and CVA10 should be strengthened in the future.
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BACKGROUND: The Kazakhs mainly live in the Yili Kazakh Autonomous Prefecture in northwestern Xinjiang. About 80% of the Kazakhs live in the areas of Yili, Tacheng, and Altay. To fully understand the physical characteristics of Kazakhs, a viviperception and head and face measurements of Kazakhs at the age of 20 and 86 were performed in Gilgelang Township, Gongliu County, Xinjiang. OBJECTIVE: To grasp the morphological traits in the head and face of Kazakh adults in Xinjiang. METHODS: Thirty-one head-face indexes of 422 Kazakh adults (219 males and 203 females) from Jiergelang county, Xinjiang were investigated. Twelve physical indices of the head and face were calculated. RESULTS AND CONCLUSION: In the Kazakh group, the incidence of eye fold of the upper eyelid was 92.7%; the rate of mongoloid fold was 9.9%; the appearance rates of flat and vertical types was 6.6% and 93.4%, respectively; the appearance rates of convex, concave and straight nasal profiles were 7.8%, 36.5% and 55.7%, respectively; the appearance rates of oblique, vertical and horizontal nostril shapes were 69.5%, 20.8% and 9.7%, respectively; the appearance rates of the chin of straight type and convex type were 68.2% and 31.8%, respectively; the appearance rates of earlobe type and non-earlobe type were 96.7% and 3.3%, respectively; the appearance rates of forehead hairline and non-forehead hairline were 72% and 28%, respectively; the appearance rates of straight hair and curly hair were 99.1% and 0.9%, respectively. Most of Kazakh males have dolichocephaly and hyperdolichocephaly (81.7%, 52.5%), hypsicephaly (93.6%), aerocephaly (84%), hyrerleptorrhiny (98.2%), and hypercuryen (74%). Kazak females most have dolichocephaly and hyperdolichocephaly (76.4%, 55.7%), hypsicephaly (97%), aerocephaly (84%), hyrerleptorrhiny (98.2%), and hypercuryen (74%). The head-face characteristics of Kazak population belongs to the North Asian type of Mongoloid．.
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@#Objective To analyze genetic characteristics of hemagglutinin( HA) gene of H9N2 avian influenza viruses( AIVs) circulating in Anhui Province from 2013 to 2018． Methods All H9N2 positive samples tested by real－time polymerase chain reaction( PCＲ) were inoculated into specific patho- gen free ( SPF) chicken eggs for isolation and purification． Viral ＲNA was reversely transcribed into cD- NA and then amplified with gene specific primers． PCＲ products were sequenced and the gene sequences were analyzed using molecular and bioinformatics software． The DATAMONKEY online server was conducted to analyze selection pressure，and protein structure homology modelling was computed by the SWISS－MODEL server． Ｒesults 33 H9N2 AIVs isolated from live poultry markets belonged to h9．4．2．5 in the phylogenetic tree． The receptor binding sites of HA gene at 183，226 and 227 position were mutated into N，L and M，respectively． Meanwhile 189 and 190 sites presented with genetic polymorphism． Since 2015，all H9N2 viruses in this study carried 6 potential N－linked glycosylation sites． It was found that po- sition 160 of HA gene was subjected greater positive selection pressure，presented 7 spatial conformations at least． Conclusions The H9N2 viruses isolated from live poultry markets in Anhui Province possess the molecular characteristics of infecting mammals and the ability of antigenic drift，so we need to pay more attention to the genetic characteristics of the viruses．
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@#Zoonotic coronaviruses were discovered in the 1960s. Since then pathogenic human coronaviruses were identified beginning with the discovery of SARS-CoV in 2002. With the recent detection of SARS-CoV-2, there are now seven human coronaviruses. Those that cause mild diseases are the 229E, OC43, NL63 and HKU1, and the pathogenic species are SARS-CoV, MERS-CoV and SARS-CoV-2 Coronaviruses (order Nidovirales, family Coronaviridae, and subfamily Orthocoronavirinae) are spherical (125nm diameter), and enveloped with club-shaped spikes on the surface giving the appearance of a solar corona. Within the helically symmetrical nucleocapsid is the large positive sense, single stranded RNA. Of the four coronavirus genera (a,b,g,d), human coronaviruses (HCoVs) are classified under a-CoV (HCoV-229E and NL63) and b-CoV (MERS-CoV, SARS-CoV, HCoVOC43 and HCoV-HKU1). SARS-CoV-2 is a b-CoV and shows fairly close relatedness with two bat-derived CoV-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21. Even so, its genome is similar to that of the typical CoVs. SARS-CoV and MERS-CoV originated in bats, and it appears to be so for SARS-CoV-2 as well. The possibility of an intermediate host facilitating the emergence of the virus in humans has already been shown with civet cats acting as intermediate hosts for SARS-CoVs, and dromedary camels for MERS-CoV. Human-to-human transmission is primarily achieved through close contact of respiratory droplets, direct contact with the infected individuals, or by contact with contaminated objects and surfaces. The coronaviral genome contains four major structural proteins: the spike (S), membrane (M), envelope (E) and the nucleocapsid (N) protein, all of which are encoded within the 3’ end of the genome. The S protein mediates attachment of the virus to the host cell surface receptors resulting in fusion and subsequent viral entry. The M protein is the most abundant protein and defines the shape of the viral envelope. The E protein is the smallest of the major structural proteins and participates in viral assembly and budding. The N protein is the only one that binds to the RNA genome and is also involved in viral assembly and budding. Replication of coronaviruses begin with attachment and entry. Attachment of the virus to the host cell is initiated by interactions between the S protein and its specific receptor. Following receptor binding, the virus enters host cell cytosol via cleavage of S protein by a protease enzyme, followed by fusion of the viral and cellular membranes. The next step is the translation of the replicase gene from the virion genomic RNA and then translation and assembly of the viral replicase complexes. Following replication and subgenomic RNA synthesis, encapsidation occurs resulting in the formation of the mature virus. Following assembly, virions are transported to the cell surface in vesicles and released by exocytosis.
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Abstract INTRODUCTION The relationships between phagocytosis, and mucoid phenotype, plasmid profile and virulence, and resistance genetic characteristics of Klebsiella pneumoniae clinical isolates were evaluated. METHODS Thirty isolates were used to determine the mucoid aspect. Four were selected for analysis of phagocytosis by alveolar macrophages. RESULTS Thirty percent of the samples presented the mucoid phenotype. The phagocytosis rate ranged from 21.5% to 43.43%. Phagocytosis was not correlated with the plasmid profile, but was apparently correlated with mucoid phenotype and antibiotic susceptibility. CONCLUSIONS: Several virulence factors act in parallel in K. pneumoniae to impair host defense.
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Humans , Phagocytosis/genetics , Virulence/genetics , Drug Resistance, Microbial/genetics , Virulence Factors/genetics , Klebsiella pneumoniae/genetics , Anti-Bacterial Agents/pharmacology , Phagocytosis/physiology , Phenotype , Plasmids , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/pathogenicityABSTRACT
Objective@#To analyze the genotypes, amino acid vatiations and molecular epidemiological characteristics of respiratory syncytial virus (RSV) infection in pediatric patients in Gansu province for the future research.@*Methods@#A total of 4 556 respiratory tract specimens were colleted from pediatric patients under 10 years of age in five cities in Gansu from 2012 to 2017. These specimens were tested for RSV and its subtypes.The coding region of the RSV G gene was amplified using reverse transcription-polymerase chain reaction (RT-PCR) and sequenced for RSV positive specimens. Sequences were edited using DNA Star software. Sequence alignment and phylogenetic trees were built by MEGA 6.0 software.@*Results@#Out of 4 556 specimens, 1 135 (24.91%) were positive for RSV, totally 216 G protein sequences were obtained. RSV A isolates were clustered into three genotypes: NA1、NA3 and ON1. The nucleotides and amino-acid homology was 84.9%-100% and 77.3%-100%, respectively. The nucleotides and amino-acid homology between this study and prototype long strain was 81.2%-83.3% and 74.1%-88.0%. RSV B isolates were clustered into only BA9 one genotypes. The nucleotides and amino-acid homology was 97.7%-100% and 95.8%-100%, respectively. The nucleotides and amino-acid homology between this study and prototype CH18537 strain was 84.9%-85.7% and 77.9%-80.1%.@*Conclusions@#The genetic characteristics and the amino-acid changes were analyzed systematically using data of RSV G gene collected from 2012 to 2017 in Gansu province in this study. These data were used for analyses of the etiology, control and prevention of RSV infection.
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Objective@#To understand the epidemiological characteristics of influenza A(H1N1)pdm09 virus in Sichuan population during the monitoring period of 2018-2019, and to clarify the antigenic variation, the gene characteristics and the matching of current epidemic strains, vaccine strains, representative strains at home and abroad.@*Methods@#A total of 118 strains of influenza A(H1N1)pdm09 virus isolated in Sichuan region influenza network laboratory from April 2018 to March 2019 were selected. The hemagglutination inhibition (HI) assay was conducted for antigen analysis. The HA and NA genes of 16 strains with low-response strains were sequenced. Phylogenetic analysis and amino acid locus variation analysis were applied using BioEdit and MEGA5.0 software.@*Results@#The result of the antigen analysis demonstrated that more than 95% of the A(H1N1) pdm09 influenza viruses detected were similar to the WHO recommended vaccine strain A/Michigan/45/2015. The analysis of HA gene characteristics showed that some low-response strains had amino acid site variation in the Sa, Sb and Cb regions of the HA protein. A total of 15 low-response strains belonged to the 6B.1 branch. And their evolutionary relationship were close to the representative strains A/beijin-xicheng/SWL1633/2018 and A/brisbane/02/2018, which were popular at home and abroad. Compared with A/sichuan/1/2009, there are mutations involving 6, 14 and 1 amino acid sites in the antigen-determining regions (Sa, Sb, Ca and Cb), non-determined regions and receptor binding site(RBS) respectively. No amino acid site mutations related to resistance to NA gene were found.@*Conclusions@#In 2018-2019, the epidemic A(H1N1) pdm09 influenza virus in Sichuan is consistent with the global epidemic characteristics, which also matched with vaccine strains recommended by WHO in the northern hemisphere. Compared with A/sichuan/1/2009 which was the first isolated in China in 2009, there were amino acid sites mutations in antigen-determining region and receptor binding site of the HA protein, and the transmembrane region of the NA protein, drug and antibody binding sites.
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Objective@#To investigate the genetic characteristics of VP1 coding region of enterovirus Coxsackievirus A16(CV-A16) and etiological features of hand, foot and mouth disease (HFMD) in 2017 in Xining city.@*Methods@#The pharyngeal swab specimens were collected from HFMD patients, and detected by real-time reverse transcription-polymerase chain reaction (RT-PCR). For CV-A16 positive samples, virus isolation was performed. Then RNA was extracted, and then VP1 coding region was amplified by RT-PCR. The phylogenetic tree was constructed by comparing with other genotypes and sub-genotypes strains of EV-A71.@*Results@#It was shown that 70 strains of CV-A16 were isolated from 2017 to 2018 in Xining city. In 2017, 10 strains were isolated and divided into two different lineages by phylogenetic analysis, 3 strains of B1a and 7 stains of B1b. In 2018, 60 stains were isolated, which were all belong to B1b.@*Conclusions@#B1a and B1b of CV-A16 are prevalent in Xining city from 2017 to 2018, in which B1b is the prominent isolates.
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Objective@#To evaluate the effect of vaccine and provide scientific evidence for prevention and control of influenza virus, this study aims to analyze the characteristics of genomic variation of influenza A (H1N1) pdm09 viruses in Inner Mongolia.@*Methods@#The 16 viral strains were selected randomly according to the influenza A (H1N1) pdm09 viruses isolated from network laboratories in Inner Mongolia, 2013-2017. The hemagglutinin(HA) and neuraminidase(NA) genomic sequences were obtained by using RT-PCR and sequencing, and genomic characteristics were analyzed via bioinformatics.@*Results@#Compared to the A/California/07/2009 vaccine strain, the relatively obvious variation of antigen of influenza A (H1N1) pdm09 viruses in Inner Mongolia since 2014, and the vaccine provided a poor protection to influenza A (H1N1) pdm09 virus infection, while the A/Michigan/45/2015 vaccine strain recommended by WHO recently has a satisfactory protective effects. Several viral isolates from Inner Mongolia increased the binding force of virus in human upper respiratory tract because of D222N and D222G substitution within HA. E119K and H275Y substitution within NA gene of viral strains, suggesting that the viruses were resistant to NA inhibitors.@*Conclusions@#The influenza A (H1N1) pdm09 viruses had gradual variations as time went on, and the WHO recommended vaccine was relatively lagging. Virulent strains and drug-resistant strains appeared in the population, and the genetic characteristics of influenza virus surveillance should be strengthened to find the new mutants of virus in time, which provide evidence for the prevention and control of influenza.
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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 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 molecular epidemiology, genetic variations and evolution of enterovirus 71 (EV71) strains isolated in Jiangsu Province from 2009 to 2018.@*Methods@#Statistical methods were used to analyze the data about epidemiological characteristics and results of pathogen detection in cases with EV71 infection in Jiangsu Province from 2009 to 2018. The complete VP1 sequences of 80 EV71 strains were amplified and sequenced for analysis of diversity and phylogenesis.@*Results@#A total of 41 858 enterovirus-positive hand, foot and mouth disease cases were reported in Jiangsu Province from 2009 to 2018. EV71 was the predominant pathogen, accounting for 36.52%, and responsible for most of the severe cases. However, the percentage of EV71 among all pathogens gradually decreased over time. EV71 infection reached the peak in April to June and mainly occurred in children aged six months to five years old with higher incidence in males than in females. In terms of regional distribution, EV71 infections were characterized by area clustering in Jiangsu Province, mainly detected in Nanjing, Suzhou, Wuxi and Lianyungang. The 80 EV71 isolates belonged to C4a genotype. Nucleotide differences between them and three vaccine strains (H07, FY23 and FY7VP5)were 0.6%-5.5%, 0.8%-5.7% and 1.9%-6.9% and amino acid difference were 0-1.4%, 0.3%-2.0% and 0.3%-2.0%, respectively. Amino acid mutations in the epitopes of the 80 EV71 strains did not marked by years or regions.@*Conclusions@#EV71 strains showed obvious epidemiological characteristics in time, population and regional distribution in Jiangsu Province from 2009 to 2018.All of the 80 EV71 isolates belonged to C4a subgenotype. The nucleotide sequences between them and the vaccine strains varied greatly, but the homology of amino acids was relatively high, indicating the existence of some synonymous mutations and no risk of antigenic drift. This study would provide reference for EV71 vaccination in Jiangsu Province.
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Objective To analyze the molecular epidemiology, genetic variations and evolution of enterovirus 71 (EV71) strains isolated in Jiangsu Province from 2009 to 2018. Methods Statistical meth-ods were used to analyze the data about epidemiological characteristics and results of pathogen detection in cases with EV71 infection in Jiangsu Province from 2009 to 2018. The complete VP1 sequences of 80 EV71 strains were amplified and sequenced for analysis of diversity and phylogenesis. Results A total of 41858 enterovirus-positive hand, foot and mouth disease cases were reported in Jiangsu Province from 2009 to 2018. EV71 was the predominant pathogen, accounting for 36. 52％, and responsible for most of the severe cases. However, the percentage of EV71 among all pathogens gradually decreased over time. EV71 infection reached the peak in April to June and mainly occurred in children aged six months to five years old with higher incidence in males than in females. In terms of regional distribution, EV71 infections were character-ized by area clustering in Jiangsu Province, mainly detected in Nanjing, Suzhou, Wuxi and Lianyungang. The 80 EV71 isolates belonged to C4a genotype. Nucleotide differences between them and three vaccine strains (H07,FY23 and FY7VP5) were 0. 6％-5. 5％, 0. 8％-5. 7％ and 1. 9％-6. 9％ and amino acid difference were 0-1. 4％, 0. 3％-2. 0％ and 0. 3％-2. 0％, respectively. Amino acid mutations in the epitopes of the 80 EV71 strains did not marked by years or regions. Conclusions EV71 strains showed ob-vious epidemiological characteristics in time, population and regional distribution in Jiangsu Province from 2009 to 2018. All of the 80 EV71 isolates belonged to C4a subgenotype. The nucleotide sequences between them and the vaccine strains varied greatly, but the homology of amino acids was relatively high, indicating the existence of some synonymous mutations and no risk of antigenic drift. This study would provide reference for EV71 vaccination in Jiangsu Province.
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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 analyze the variations and drug resistance of influenza A (H3N2) viruses in Jiangsu Province in 2017, and provide evidence for prevention and control strategies on influenza. Methods Reverse transcription polymerase chain reaction (RT-PCR) was used for the sequencing of H3N2 subtype influenza strains. The influenza reference sequences were obtained from the global shared influenza site GISAID. The sequence alignment and phylogenetic analysis were performed using MAGE7.0 software. Viral resistance was analyzed by a neuraminidase inhibition assay. Results The H3N2 subtype influenza isolates and vaccine strains belonged to the 3C.2a branch of the H3 subtype. Some of the strains showed amino acid mutations on the immune-related sites named N121K, T135K and N171K. The isolates were sensitive to the flu drugs oseltamivir and zanamivir. Conclusion The H3N2 epidemic strains in Jiangsu have genetic recombination within subtypes and are still sensitive to neuraminidase inhibitors. As the H3N2 influenza virus mutations continue, a close monitoring of the viral genetic evolution and the drug resistant genes should be guaranteed.
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Objective To investigate the genetic variation and epidemiological characteristics of influenza B virus in Xinxiang to provide policy basis for local influenza vaccination. Methods The influenza surveillance data in Xinxiang from January 2012 to February 2019 was analyzed. 23 isolated influenza B virus were randomly selected for hemagglutinin (HA) and neuraminidase (NA) gene sequencing. Sequence alignment was conducted by using DNAman software and phylogenetic tree analysis was conducted using Neighbor-Joining method. Results Yamagata (BY) and Victoria (BV) strains of influenza B virus circulated alternately every other year in Xinxiang, mainly among people aged 0-15 years (91.4%). The dominant influenza B lineages from 2015 to 2016 and from 2017 to 2018 did not match the corresponding trivalent vaccine strain of the year. The HA phylogenetic tree revealed that 87.5% (7/8) of BV strains coexisted with the vaccine strain in one branch, while 88.98% (8/9) of BY strains from 2013 to 2015 were not in the same branch as the corresponding vaccine strain, with 5 epitope site mutions N116K, S150L, N165Y, D196N and N202S. No drug-resistant site mutation was identified in the NA gene. A total of 6 intra-lineage reassortants were identified. Conclusions The influenza B lineage in the trivalent vaccine recommended by WHO did not match the dominant circulating B lineage of Xinxiang in some epidemic year. Therefore, quadrivalent vaccines are recommended to use in susceptible population, especially under the age of 15. In addition, there are large variations in HA gene of the epidemic BY strain compared with the corresponding vaccine. Then, a vaccine more sutable for the epidemic strains in China is expected to be developed.
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Objective To analyze the genetic characteristics of mumps virus ( MuV) isolated from an outbreak in Henan province in 2016 and to provide reference data for the control of mumps in Henan prov-ince. Methods Swab specimens were collected from a mumps outbreak in Henan province in 2016. One virus strain was selected for whole genome sequencing after virus isolation and genotyping. MEGA7. 0 soft-ware was used to construct phylogenetic tree, to calculate P-distance and to analyze the characteristics of genes encoding small hydrophobic protein ( SH ) , fusion protein ( F ) and hemagglutinin neuraminidase ( HN) . Results Five swab specimens were collected in the outbreak and five MuV strains were successfully obtained. Phylogenetic analysis showed that all of them belonged to genotype F with a P-distance of 0. 047 (0. 046-0. 049 ) with the reference strain. The P-distance among the five MuV strains was 0. 001 ( 0-0. 003). Results of the whole genome sequencing of one MuV strain showed that the P-distance with the ref-erence virus was 0. 053 (0. 018-0. 072) and the smallest P-distance with genotype F was 0. 018. Compared with the vaccine strain (HQ416907. 1), the amino acid at 28-30 site of SH protein was IML. The 91, 195 and 383 amino acid sites in F protein were related to the pathogenicity of MuV, but no mutations were found in these sites. Some mutations were found in HN protein, such as P354Q, E356D and K464N, which were associated with the immunological characteristics of MuV. Conclusions MuV strains isolated from the out-break in Henan province in 2016 belonged to genotype F. The genetic characteristics of these MuV strains were similar to those prevalent in other provinces of China.
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Objective@#To analyze the epidemiological characteristics and the pathogenic features of the influenza B virus strains circulating in Anhui province during 2017-2018 influenza surveillance year.@*Methods@#The antigenic characteristics of influenza B virus was analyzed with reference ferret anti-sera. The hemagglutinin (HA) and neuraminidase (NA) genes of influenza B viruses isolated in Anhui during this period were obtained by Sanger dideoxy sequencing. Then the phylogenetic trees and amino acid mutations were analyzed respectively.@*Results@#During 2017-2018 influenza season, the activity of B Yamagata lineage virus were stronger than B Victoria lineage virus. Most of B Yamagata lineage viruses had close antigenic relation with the vaccine strain B/Phuket/3073/2013(93.3%), but D196 N substitution was detected on HA protein in all of Yamagata lineage viruses. All of B Victoria lineage viruses had close antigenic relation with the vaccine strain B/Brisbane/60/2008(100%), meanwhile I117 V and N129D were found on HA protein. Phylogenetic analysis on B influenza viruses indicated that Yamagata clade 3 and Victoria clade 1A were predominant strains, however we found that two strains had intra-clade reassortants between HA and NA gene. The NA gene of all strains did not find a molecular mutation that was less sensitive to neuraminidase.@*Conclusions@#The WHO recommended influenza vaccine could protect from influenza B virus isolated from Anhui province. However, it is still necessary to pay close attention to its significant epitope variation in order to update the vaccine candidates in time.