RESUMO
Objective:To investigate the epidemiological characteristics, genotypes and genetic evolution of respiratory syncytial virus (RSV) isolated in Shanghai from April 2020 to December 2021, which was a period from the COVID-19 outbreak to the phase of regular epidemic prevention and control.Methods:This retrospective study collected the nasopharyngeal secretions or nasopharyngeal aspirates of children with acute respiratory tract infection (ARTI) admitted to the Shanghai Children′s Hospital from April 2020 to December 2021. PCR-capillary electrophoresis and RT-PCR were used for virus identification and the amplification of the gene fragment of the second hypervariable region of RSV G protein. Homology analysis and phylogenetic analysis were conducted using bioinformatics software. Chi-square test was used to compare the detection rates of RSV. Results:A total of 6 211 samples were collected and 13.62% (846/6 211) of them were positive for RSV. The positive rates of RSV in male and female patients were 14.07% (503/3 574) and 13.01% (343/2 637), respectively, with no significant gender difference (χ 2=1.467, P=0.226). The highest detection rate of RSV was found in children ≤6 months of age, and the rate of RSV infection decreased gradually with age (χ 2=352.942, P<0.001). No RSV-positive specimens were detected from April 2020 to August 2020, after which the detection rate of RSV gradually increased with two epidemic peaks occurring from December 2020 to February 2021 and from August to October 2021. The predominant epidemic subtype was RSV subtype B in 2020 and the first 9 months of 2021, which was gradually replaced by RSV subtype A in the last 3 months of 2021. The 176 strains of RSV subtype A obtained in this study were all ON1 genotype, and the nucleotide homology of the Shanghai epidemic strains was 90.20%-99.50%. All of the 250 strains of RSV subtype B were BA9 genotype, and the nucleotide homology of the Shanghai epidemic strains was 90.10%-100.00%. Conclusions:From April 2020 to December 2021, with the regular prevention and control of COVID-19, there is a change in the epidemic season of RSV. The prevalent genotypes of RSV subtypes A and B are ON1 and BA9, respectively, and the subtype A gradually replaces subtype B as the most prevalent subtype.
RESUMO
@#Objective To analyze the genetic characteristics of the entire VP1 gene of Coxsackievirus A16(CVA16) strains isolated from the feces of patients with hand,foot and mouth disease(HFMD) in Yunnan Province in 2019.Methods The virus was isolated from human embryonic lung diploid fibroblast(KMB-17) cells and African green monkey kidney(Vero)cells,and the primers for the complete VP1 gene sequence of CVA16 were designed.The target fragment was amplified by RT-PCR and sequenced;the complete VP1 sequence was analyzed by softwares such as MEGA 7.0 and Geneious 9.0.2.Results A total of 26 CVA16 strains were isolated,including eight KMB-17 isolates and 18 Vero isolates.Twenty CVA16isolates were randomly selected for analysis,and three isolates were found to have Bla and 17 B1b genotypes;the nucleotide and amino acid homology of 17 CVA16 B1b isolates were 93.8%—100% and 98.3%—100%,and the nucleotide and amino acid homology with other domestic isolates was 91.1 %—99.2% and 97.3%—99.0%,respectively;the nucleotide and amino acid homology of the three Bla isolates was 98.0%—98.1% and 99.3%,and those with other domestic Bla isolates was 88.7%—98.1% and 98.3%—99.7%,respectively;17 B1b isolates and other three Bla isolates showed the nucleotide and amino acid homology of 87.4%—88.4% and 97.3%—98.7%.Conclusion The CVA16 prevalent in Kunming in 2019 belonged to Bla and B1b genotypes,with B1b as the main strain,and all of them were prevalent strains in the mainland of China.
RESUMO
This study explored the genetic characteristics of the whole genome sequences of coxsackie virus A6 strains in Jiangsu province from 2013 to 2022,and analyzed the genetic evolution of each coding region of the full-length genome.To in-vestigate why coxsackievirus A6 has replaced enterovirus A71 and coxsackievirus A16 as the most predominant etiological agent for HFMD in Jiangsu province,we selected 35 CVA6 isolates circulating in Jiangsu province during 2013-2022 for whole ge-nome sequence amplification and analysis.Sequence alignment,homology analysis,phylogenetic analysis and genetic recombi-nation were performed with the DNASTAR,MEGA7.0 and similarity plots 3.5.1 software packages.We analyzed the impor-tant amino acid sites of CV-A6 in the Pl region and 3D region.The nucleotide and amino acid similarities of 35 CV-A6 full-length genomes were 87.5％-99.6％ and 97.0％-99.8％,respectively,and the nucleotide and amino acid sequence identity with the CV-A6 prototype strain was 80.3％-81.0％ and 94.7％-95.3％,respectively.On the basis of phylogenetic analysis of VP1 region sequences,the 34 CV-A6 strains in this study belonged to the D3a genotype,and only one strain belonged to the D2 genotype.According to the phylo-genetic analysis of 3D region sequences,four recombinant forms(RFs),RF-A,RF-L,RF-K and RF-C,appeared primarily in 2013-2022 in Jiangsu province.Recombination analysis demonstrated that CVA6s,which was prevalent in Jiang-su from 2013 to 2022,had high similarity to the CVA6 prototype strain Gdula in the structured protein sequences.However,in the non-structured protein sequences and noncoding regions,similarities were higher among CVA6s and prototype strains of other EV-A types.Amino acid mutation site analysis showed that multiple amino acid sites in the Pl and 3D regions varied fre-quently with respect to the prototype strain Gdula.These differences might have resulted in small changes in the capsid struc-ture and potential receptor-binding sites.In conclusion,by analyzing the whole genome sequence of CV-A6,this study advances understanding of the gene recombination and genetic evolution relationship of CV-A6 in Jiangsu Province;in addition,it may explain possible reasons why CV-A6 has become the main pathogen of HFMD in recent years,and it provides basic data for the prevention and control of CV-A6.
RESUMO
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.
RESUMO
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.
RESUMO
ObjectiveTo introduce the Hr gene of spontaneously mutated SHJHhr mice into BALB/cAShjh inbred mice with clear genetic background,and provide a basis for study on the molecular mechanism of Hr gene mutation-induced abnormal phenotype and the application of this model.Methods Using a backcross-intercross breeding method guided by phenotypic monitoring, mutant genes from SHJHhr mice bred by spontaneous mutation were introduced into inbred BALB/cAShjh mice by homozygous mutation introgression, and the mice were bred into BALB/cA.Cg.SHJHhr (abbreviated as C.Cg.SHJHhr) mice after 10 generations. The genotypes of 90 single nucleotide polymorphism (SNP) detection sites were analyzed in C.Cg.SHJHhr mice by multiplex PCR library construction followed by next generation sequencing. Then 14 biochemical locus marker genes were detected in C.Cg.SHJHhr mice according to the method of GB/T 14927.1-2008. Finally, whole genome exon sequencing was utilized to detect the mutated genes in this mouse. ResultsFrom May 2018 to March 2022, a total of 10 generations of backcross-intercross were conducted to complete the construction of the C.Cg.SHJHhr mouse line. Among the 90 SNPs loci detected, except for rs13484115 and rs13484116, all the other loci had the same genotype as the recipient mice BALB/cAShjh. The results of biochemical marker gene detection showed that all the 14 loci of the mouse were the same as those of the recipient mouse. Whole genome exon sequencing found that the mouse had 109 site mutations compared with the recipient mouse strain, including 71 synonymous mutations, 1 stopgain, 37 missense mutations, and 20 genes involved in protein sequence alterations (including the reported Hr gene). ConclusionC.Cg.SHJHhr mice were created. Through exon sequencing and genetic analysis, three Hr mutated genes and associated mutated genes that mainly cause phenotypic variations were identified, which provides a basis for expanding the application of C.Cg.SHJHhr mice in biomedical research.
RESUMO
@#Abstract: Objective To understand the phenotypic and genetic characteristics of Yersinia pestis strains isolated from Himalayan marmot natural focus area and domestic rat plague focus area in southern China, and provide reference for mastering the pathogenic characteristics of Yersinia pestis of two plague foci. Methods A total of 412 of Yersinia pestis strains isolated from Himalayan marmot plague focus and domestic rat plague focus of southern China were subjected to to sorbitol fermentation assays, virulence factor, different region (DFR) typing, and clustered regularly interspaced palindromic repeats (CRISPR) typing. Results The biochemical types of Y. pestis from the two plague foci showed distinct regional distribution features. Five biochemical phenotypes were identified in Yersinia pestis isolated from Himalayan marmot natural focus area, while only one biochemical phenotype was identified in strains isolated from the domestic rat plague focus of Southern China. Most of the Yersinia pestis isolated from the two plague foci were capable of producing the virulence factors of Fl and PstI. Among the strains from Himalayan marmot focus, 70.53% (201/285) were VW-positive, 75.09% (214/285) were Pgm-positive, 20.00% (57/285) of the strains were Pgm-negative, and 5.26% (15/285) were Pgm mixed-type strains. Among strains from domestic rat plague focus of southern China, 37.80% (48/127) were VW-positive, 29.13% (37/127) were Pgm-positive, 58.27% (74/127) were Pgm-negative, and 12.60% (16/127) were Pgm mixed-type strains. DFR typing revealed 22 genotypes of Y. pestis from the Himalayan marmot plague focus, with the main genotypes being type 5, 7, 8, 10, 19, 32 and 49. All strains from domestic rat plague focus area in southern China belonged to type 9. CRISPR typing revealed that all strains from the Himalayan marmot natural focus were classified into 7 CRISPR gene clusters and 14 CRISPR genotypes, with the main genotypes being G7, G22, G26-a1'and G22-A1'. All strains from domestic rat plague focus area in southern China belonged to CRISPR genotype G30, with the gene cluster being Ca8. Conclusions The phenotypes and genotypes of the Yersinia pestis of Himalayan marmot plague focus are diverse, with an obvious characteristics of geographical distribution. The phenotype and genotype of the Yersinia pestis of domestic rat plague focus of Southern China are single. DFR and CRISPR genotyping methods with phenotypic characteristics can effectively identify the Yersinia pestis isolated from the two plague foci, thereby meeting the needs of identification and traceability research.
RESUMO
@#Abstract: Objective To analyze the results of the surveillance of hand, foot and mouth disease (HFMD) pathogens in Baoshan City, Yunnan Province in 2022, and to analyze the genetic characteristics of the main epidemic strain coxsackievirus A16 (CVA16), in order to provide scientific basis for the prevention and control of HFMD. Methods Samples of hand, foot and mouth disease cases in Baoshan City submitted to Yunnan Province in 2022 were selected, the samples were processed, and the viral nucleic acid was extracted, and the Enterovirus (EV) VP4/VP2 binding region gene was amplified with primers (MD91/OL68-1) and sequenced. The sequence was BLAST searched in GenBank to determine the virus type, and then the full sequence of VP1 region was amplified with relevant primers of each type of virus and sequenced. Viruses were identified by using Enterovirus Genotyping Tool Version 1.0. according to the reference documents, the reference sequences were downloaded for making the phylogenetic tree, and the test results were statistically analyzed. Results A total of 307 clinical samples of hand-foot-mouth disease in Baoshan City in 2022 were detected by real-time RT-PCR. There were 280 laboratory-confirmed cases (91.21%), among which the detection rate of CVA16 was 55.05% (169/307), EV-A71 was 3.58% (11/307), and other enteroviruses were 32.57% (100/307). Of the 206 HFMD test specimens, the VP4/VP2 junction and VP1 gene sequences of enterovirus were amplified and identified, and 29 enterovirus strains were obtained, with a positive virus rate of 14.08% (29/206). All viruses belonged to group A and were divided into 3 serotypes, which included 27 strains of CVA16 (93.10%, 27/29), 1 strain of EV-A71 (3.45%, 1/29), and 1 strain of CVA10 (3.45%, 1/29). Group B, C, and D viruses were not detected. The positive rate of VP4/VP2 binding region and VP1 region of coxsackievirus A16 gene in Baoshan City in 2022 was 13.11% (27/206). The genetic evolution analysis showed that the 27 strains of CVA16 belong to B1a subtype and can be divided into two evolutionary branches. Conclusions In 2022, the main epidemic strain of HFMD in Baoshan City, Yunnan Province is CVA16 gene, belonging to B1a subtype, which can be divided into two branches, indicating 2 transmission chains prevalent in Baoshan City. Future efforts should focus on strengthening surveillance, improving the quality of monitoring, and understanding the characteristics of viral prevalence..
RESUMO
Objective:To analyze the whole-genome sequences of coxsackievirus A10 (CVA10) strains isolated in Jiangsu Province from 2015 to 2022 and their molecular epidemiological characteristics.Methods:Forty-five CVA10 isolates circulating in Jiangsu Province during 2015 to 2022 were selected for whole-genome sequencing. Phylogenetic trees were constructed based on the whole genome, VP1, P1, P2 and P3 sequences of CVA10 strains. Bioinformatics software, including DNAStar, MEGA7.0 and Similarity plots3.5.1, was used for analysis of homology, genetic recombination and major amino acid variation sites.Results:The nucleotide and amino acid sequence homology of the whole-genome sequences of 45 CVA10 strains was 90.3%-99.1% and 97.9%-99.8%, respectively. The nucleotide sequence homology of P1 region was the highest (92.1%-100.0%), while the nucleotide sequence homology of P3 region ranged from 84.7% to 100.0%. In contrast to the diversity of nucleotide sequences, the amino acid sequences of each region were conserved. A phylogenetic analysis based on the complete VP1 sequences of CVA10 strains revealed eight genotypes: A-H. The CVA10 isolates in Jiangsu Province and other prevalent strains in China mainly belonged to genogroup C. Results of the phylogenetic analysis based on the whole-genome sequences and complete VP1 sequences were consistent. Phylogenetic analysis bases on different gene segments and Simplot recombination analysis revealed that Jiangsu isolates GD07/Lianyungang/2017 and N180/Suqian/2016 showed high homology with the CVA10 prototype in the P1 region, but had recombination sites with other strains of enterovirus group A in the P2, P3, 5′-UTR and 3′-UTR regions. Compared with the prototype strain AY421767/Kowalik/2004, the Jiangsu isolates showed frequent variations in the VP1 region and many other major amino acid sites, which might result in some imperceptible changes in capsid structure and potential receptor-binding sites.Conclusions:By analyzing the evolution and genetic recombination features of CVA10 strains at the genome level in Jiangsu Province, this study elucidated the influence of genetic recombination and amino acid site mutation on CVA10 infection, providing basic data for the prevention and control of hand-foot-mouth disease in Jiangsu Province.
RESUMO
Objective:To investigate the molecular features of hand, foot and mouth disease (HFMD) caused by coxsackievirus A10 (CVA10) in Qingdao and analyze the clinical features of mild and severe cases.Methods:A total of 6 677 cases of HFMD routinely monitored by Qingdao Women and Children Hospital from 2014 to 2021 were enrolled. Throat swab samples were collected. Clinical data of these cases were retrospectively analyzed. Virus nucleic acid was extracted from the samples and the serotypes of enteroviruses were identified. The VP1 genes of CVA10 strains were amplified and sequenced. A phylogenetic tree based on the VP1 gene sequences was constructed using MEGA7. 0 software. SPSS23.0 software was used for statistical analysis.Results:There were 285 cases positive for CVA10, including 183 males and 102 females, and children under five years old accounted for 89.8%. Most of CVA10 infection occurred between the months of April to September. The count of white blood cells, the percentage of neutrophils, the concentration of hemoglobin, and the levels of aspartate aminotransferase and alanine transaminase were significantly higher in severe patients than in mild patients. Besides, chest radiography and brain CT revealed more abnormalities in severe patients, and the duration of ECG monitoring was longer in them. Compared with mild cases, severe cases developed rash early than fever with rash mostly on buttocks ( P<0.05). Phylogenetic analysis showed that most of the CVA10 strains circulating in Qingdao between 2014 and 2021 belonged to clade Ⅰ, and there were two variations A23V and I283V in the amino acid sequence of clade Ⅰ. Conclusions:This study showed that children of all ages were susceptible to CVA10, especially those under five years old. CVA10 showed complex and diverse epidemic trends in different regions and years.
RESUMO
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.
RESUMO
@#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．
RESUMO
@#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.
RESUMO
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．.
RESUMO
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.
RESUMO
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.
RESUMO
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.
RESUMO
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.
RESUMO
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.
RESUMO
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.