Molecular Epidemiology of Enteroviruses Associated with Hand, Foot, and Mouth Disease in the Mainland of China

Hand, foot, and mouth disease （HFMD） is a common contagious illness which occurs worldwide both sporadically and in epidemics. The disease mainly affects, children and the typical symptoms, which may resolve spontaneously, include mucocutaneous papulovesicular lesions on the hands, feet, mouth, and buttocks. In rare cases, however, the patients may also develop neurological complications such as neurogenic pulmonary edema,

Characterization of Avian Influenza A(H7N9) Virus Prevalence in Humans and Poultry in Huai′an,China：Molecular Epidemiology,Phylogenetic,and Dynamics Analyses

Objective To trace the source of human H7N9 cases in Huai＇an and elucidate the genetic characterization of Huai＇an strains associated with both humans and birds in live poultry market.Methods An enhanced surveillance was implemented when the first human H7N9 case was confirmed in Huai＇an.Clinical specimens,cloacal swabs,and fecal samples were collected and screened by real-time reverse transcription-polymerase chain reaction（RT-PCR） for H7N9 virus.The positive samples were subjected to further RT-PCR and genome sequencing.The phylodynamic patterns of H7N9 virus within and separated from Huai＇an and evolutionary dynamics of the virus were analyzed.Results Six patients with H7N9 infection were previously exposed to live poultry market and presented symptoms such as fever（〉38.0 °C） and headaches.Results of this study support the hypothesis that live poultry markets were the source of human H7N9 exposure.Phylogenetic analysis revealed that all novel H7N9 viruses,including Huai＇an strains,could be classified into two distinct clades,A and B.Additionally,the diversified H7N9 virus circulated in live poultry markets in Huai＇an.Interestingly,the common ancestors of the Huai＇an H7N9 virus existed in January 2012.The mean nucleotide substitution rates for each gene segment of the H7N9 virus were（3.09-7.26）×10-3 substitutions/site per year（95% HPD：1.72×10-3 to 1.16×10-2）.Conclusion Overall,the source of exposure of human H7N9 cases in Huai＇an was live poultry market,and our study highlights the presence of divergent genetic lineage of H7N9 virus in both humans and poultry specimens in Huai＇an.

Molecular Epidemiology and Sequencing of the G-L Intergenic Region of Rabies Viruses Isolated in China

一组 25 个狂犬病病毒(RABV ) ，从 24 条狗和一个人的盒子恢复了，在在 2004 和 2006 之间的中国从各种各样的区域被收集。G-L intergenic 区域的基因、种系发生的分析在 25 街 RABV 被执行孤立， CTN 疫苗 7 拉紧代。学习基于 519 bp 核苷酸顺序的比较，包含 G-L intergenic 区域。中国街紧张的核苷酸顺序相同从 95.5% ～ 100% 。种系发生的分析证明中国的所有孤立清楚地在 Lyssavirus 遗传型 1 支持了所有中国病毒的放置，他们根据他们的地理起源是分布式的。所有仔细中国紧张被联系，但是他们能仍然被划分成二个组：一些街紧张和一些 CTN 紧张。这研究基于 G-L Intergenic 区域的序列关于狂犬病病毒的分子的传染病学介绍细节。关键词狂犬病病毒 - 分子的传染病学 - G-L intergenic 区域 - 中国 CLC 数字 R373.33 基础条款：第 10 国家 five-year-plan (2004BA718 b03 ) 的关键技术 R&D

Neosporosis: An Overview of Its Molecular Epidemiology and Pathogenesis

Neospora caninum (N. caninum), a cyst-forming protozoan parasite, is a major cause of bovine abortions and neonatal mortality worldwide. N. caninum has a broad intermediate host range, and its sexual cycle occurs exclusively in canids. Another species of Neospora, Neospora hughesi (N. hughesi), has been identified and causes myeloencephalitis in horses. Although molecular epidemiology studies are in their infancy, the 18S ribosomal RNA (rRNA) and ITS1 regions within the small subunit ribosomal RNA (ssuRNA) and an N. caninum species-specific DNA probe (pNc5) have been used extensively to differentiate Neospora from other closely related apicomplexan parasites. While these repetitive regions have higher sensitivity and specificity than housekeeping or antigen genes, they suffer from low discriminatory power and fail to capture intra-species diversity. Similarly, although multiple minisatellite or microsatellite marker studies have shown clear geographic substructures within Neospora, strains are often misclassified due to a convergence in the size of different alleles at microsatellite loci, known as homoplasy. Only one strain, N. caninum Liverpool (Nc-Liv), has been genome sequenced and compared with its closest relative, Toxoplasma gondii (T. gondii). Hence, detailed population genomics studies based on whole-genome sequences from multiple strains worldwide are needed in order to better understand the current population genetic structure of Neospora, and ultimately to determine more effective vaccine candidates against bovine neosporosis. The aim of this review is to outline our current understanding of the molecular epidemiology and genomics of Neospora in juxtaposition with the closely related apicomplexan parasites Hammondia hammondi and T. gondii.

Biochemical and Molecular Epidemiology of Cancer

Examples of practical approaches to molecular epidemiology of human cancer are described. Biomarkers of carcinogen exposure or inherited host factors for cancer susceptibility are discussed. Major advances have been made in the detection of carcinogen-macromolecular adducts through the use of high performance liquid chromatography, immunoaffinity chromatography, the 32P-postlabeling assay, enzyme immunoassays, gas chromatography/mass spectroscopy and synchronous spectrophotofluorimetry. The polycyclic aromatic hydrocarbon- DNA adducts are the most extensively studied in this field and together with antibodies to these adducts found in human serum, they have become useful indicators of exposure to carcinogens. Assays for various kinds of alky 1-DNA adducts have also been developed and the presence of these adducts have been documented in human tissues. Carcinogen-protein adducts have proven to be useful molecular dosimeters of carcinogen exposure. For example, 4-aminobiphenyl hemoglobin adducts are highly correlated with exposure to tobacco smoke. The study of the molecular aspects of interindividual differences in the metabolism and activation of xenobiotics and other genetic markers [DNA-restriction fragment length polymorphisms (RFLPs), mutations, and functional loss of specific genes in carcinogenesis] is an emerging new field that is discussed in the context of genetic susceptibility to cancer. The cytochrome P450 phenotypes and acetylation phenotype are examples of genetic markers that indicate an individual's potential for metabolism of exogenous substances. Further, inherited genetic polymorphic markers, e.g., DNA-RFLPs at protooncogene loci (HRAS-1 and L-myc) have been examined in a case-control study of lung cancer. Data concerning mutations of protooncogenes (H-, K-, and N-RAS) and tumor suppressor genes (retinoblastoma and p53 genes) in various common cancers are providing evidence of multiple genetic lesions that occur during the multistage process of carcinogenesis.

Molecular epidemiology of hepatitis B virus in Asia

Although safe and effective vaccines against hepatitis B virus(HBV) have been available for three decades, HBV infection remains the leading cause of chronic hepatitis, cirrhosis and hepatocellular carcinoma(HCC) worldwide, especially in Asian countries. HBV has been classified into at least 9 genotypes according to the molecular evolutionary analysis of the genomic DNA sequence and shown to have a distinct geographical distribution. Novel HBV genotypes/subgenotypes have been reported, especially from Southeast Asian countries. The clinical characteristics and therapeutic effectiveness of interferon(IFN) and nucleos(t)ide analogues vary among different HBV genotypes. Mutations at T1653 C in subgenotype C2 from Japan and South Korea, C/A1753 T and C1858 T in subgenotype C1 from Vietnam, and C1638 T and T1753 V in subgenotype B3 from Indonesia were reported to be associated with advanced liver diseases including HCC. Genotype distribution in Japan has been changed by an increasing ratio of subgenotype A2 in chronic hepatitis B. While a large number of epidemiological and clinical studies have been reported from Asian countries, most of the studies were conducted in developed countries such as Taiwan, China, South Korea and Japan. In this review, the most recent publications on the geographical distribution of genetic variants of HBV and related issues such as disease progression and therapy in Asia are updated and summarized.

Molecular epidemiology of HIV-1 strains in the south-east and east of Turkey

Objective:To detect the subtype characterization and drug-resistant mutations in HIV-1 strains after the refugee movement from Syria to Turkey between 2011 and 2014 in south east border lines. Methods: A total of 65 patients were included in this study, of which 57(88%) patients were antiretroviral therapy-naive patients. HIV-1 RNA was detected and quantii ed by realtime PCR assay. HIV-1 subtypes and circulating recombinant forms(CRFs) were identii ed by phylogenetic analysis(neighbor-joining method), and drug-resistant mutations were analyzed.Results: Three major HIV groups were indicated. Two of these groups were located in subtype B. The other group showed heterogeneity. Subtype B(48/65, 73.8%), followed by CRFs(12/65, 18.5%) was the most common strain. Subtype of CRFs consisted of CRF01_AE(9/65, 13.8%) and CRF02_AG(3/65, 4.6%). Subtype C(1/65, 1.5%), sub-subtypes A1(2/65, 3.1%) and F1(2/65, 3.1%) were also detected with low prevalence. The rate of overall primary antiretroviral resistance was 4.9%(3/61). Drug-resistant rate for non-nucleoside reverse transcriptase inhibitors was 4.9%. The thymidine analogue mutation rate was 13.1%(8/61).Conclusions: HIV molecular epidemiology studies are necessary to determine transmission patterns and spread. Subtype B and CRF01_AE, CRF02_AG are the most prevalent strains in the south-east of Turkey. However, subtype C, sub-subtypes A1 and F1 are of low prevalence but persist in the south-east of Turkey. In the near future, changing of HIV epidemiology will be possible in Turkey due to migration movement in border lines and resistance testing will play an important role in HIV management.

Molecular epidemiology of DNA repair gene polymorphisms and head and neck cancer

Although tobacco and alcohol consumption are two common risk factors of head and neck cancer （HNC）, other specific etiologic causes, such as viral infection and genetic susceptibility factors, remain to be understood. Hu- man DNA is often damaged by numerous endogenous and exogenous mutagens or carcinogens, and genetic vari- ants in interaction with environmental exposure to these agents may explain interindividual differences in HNC risk. Single nucleotide polymorphisms （SNPs） in genes involved in the DNA damage-repair response are reported to be risk factors for various cancer types, including HNC. Here, we reviewed epidemiological studies that have assessed the associations between HNC risk and SNPs in DNA repair genes involved in base-excision repair, nucleotide-excision repair, mismatch repair, double-strand break repair and direct reversion repair pathways. We found, however, that only a few SNPs in DNA repair genes were found to be associated with significantly in- creased or decreased risk of HNC, and, in most cases, the effects were moderate, depending upon locus-locus in- teractions among the risk SNPs in the pathways. We believe that, in the presence of exposure, additional pathway- based analyses of DNA repair genes derived from genome-wide association studies （GWASs） in HNC are needed.

Molecular Epidemiology of Nontuberculous Mycobacteria in a German CF Center and Clinical Course of NTM Positive Patients

Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.

Molecular Epidemiology and Risk Factors of Herpes Simplex Virus Type 2 in Pregnant Women

Background:Herpes simplex virus type 2(HSV-2)infection is the main cause of genital and neonatal herpes infections.It has considerable public health importance among women as the virus may lead to adverse outcomes in pregnancy and neonatal infection.This study determines the molecular epidemiology and risk factors ofHSV-2 infection among pregnant women.Methods:In this cross-sectional study,all pregnant women admitted to three university hospitals for natural birth and Caesarean sections were enrolled.HSV detection and typing were carried out based on PCR and reverse dot blotting method,respectively.ANOVA and bivariate correlations were used to analyze the data.Results:In this study,the prevalence of genital herpes infection was 5.7%.A significant positive correlation was found between age group<25 years and HSV-2 shedding(P=0.026).Twelve participants(60%)with HSV-2 shedding were younger than 25.A significant correlation was found between the presence of genital lesion and HSV-2(P=0.02).Among participants with HSV-2 infection,the use of condom was low.Neonatal complications were not seen in newborns from mothers with HSV-2 shedding.Conclusion:PCR assay may help in promoting early diagnosis and more effective treatment for patients.Also,it shortens hospital stay and enhances patients?condition.HSV-2 transmission is rapid following the onset of sexual activity and likely to result in the significant prevalence of genital disease.

Public health implications of Yersinia enterocolitica investigation:an ecological modeling and molecular epidemiology study

Background Yersinia enterocolitica has been sporadically recovered from animals,foods,and human clinical samples in various regions of Ningxia,China.However,the ecological and molecular characteristics of Y.enterocolitica,as well as public health concerns about infection in the Ningxia Hui Autonomous Region,remain unclear.This study aims to analyze the ecological and molecular epidemiological characteristics of Y.enterocolitis in order to inform the public health intervention strategies for the contains of related diseases.Methods A total of 270 samples were collected for isolation[animals(n=208),food(n=49),and patients(n=13)],then suspect colonies were isolated and identified by the API20E biochemical identification system,serological tests,biotyping tests,and 16S rRNA-PCR.Then,we used an ecological epidemiological approach combined with machine learning algorithms(general linear model,random forest model,and eXtreme Gradient Boosting)to explore the associations between ecological factors and the pathogenicity of Y.enterocolitis.Furthermore,average nucleotide identity(ANI)estimation,single nucleotide polymorphism(SNP),and core gene multilocus sequence typing(cgMLST)were applied to characterize the molecular profile of isolates based on whole genome sequencing.The statistical test used single-factor analysis,Chi-square tests,t-tests/ANOVA-tests,Wilcoxon rank-sum tests,and Kruskal–Wallis tests.Results A total of 270 isolates of Yersinia were identified from poultry and livestock(n=191),food(n=49),diarrhoea patients(n=13),rats(n=15),and hamsters(n=2).The detection rates of samples from different hosts were statistically different(χ^(2)=22.636,P<0.001).According to the relatedness clustering results,270 isolates were divided into 12 species,and Y.enterocolitica(n=187)is a predominated species.Pathogenic isolates made up 52.4%(98/187),while non-pathogenic isolates made up 47.6%(89/187).Temperature and precipitation were strongly associated with the pathogenicity of the isolates(P<0.001).The random forest(RF)prediction model showed the best performance.The prediction result shows a high risk of pathogenicity Y.enterocolitica was located in the northern,northwestern,and southern of the Ningxia Hui Autonomous Region.The Y.enterocolitica isolates were classified into 54 sequence types(STs)and 125 cgMLST types(CTs),with 4/O:3 being the dominant bioserotype in Ningxia.The dominant STs and dominant CTs of pathogenic isolates in Ningxia were ST429 and HC100_2571,respectively.Conclusions The data indicated geographical variations in the distribution of STs and CTs of Y.enterocolitica isolates in Ningxia.Our work offered the first evidence that the pathogenicity of isolates was directly related to fluctuations in temperature and precipitation of the environment.CgMLST typing strategies showed that the isolates were transmitted to the population via pigs and food.Therefore,strengthening health surveillance on pig farms in high-risk areas and focusing on testing food of pig origin are optional strategies to prevent disease outbreaks.

Genetic characterizations and molecular epidemiology of human echovirus 30 isolated from Ningxia,China

In October 2017,a small outbreak of echovirus 30(E30)associated with aseptic meningitis in nine cases occurred at a primary school in the Ningxia Hui Autonomous Region.That year,we observed a significant increase in E30 levels in an acute flaccid paralysis(AFP)case surveillance system.To investigate their phylogenetic relationships,we determined the whole genomic sequences of 12 strains isolated from aseptic meningitis cases,AFP cases,and healthy children.We found that the E30 strains circulating in Ningxia belong to two lineages(H and J).The strains isolated in 2010,2012,and 2016 belonged to the H lineage.In 2017,a new lineage,J,emerged as the dominant lineage.Phylogenetic trees were constructed based on the whole genome andP1,P2,andP3 regions;clustering with other types of enterovirus species B was found,suggesting that recombination events had occurred.The recombination sites were mainly in regions2B,2C,and3D.This study confirmed that the E30 strains in Ningxia in 2010,2012,and 2016 had different recombination patterns and were recombined with different enteroviruses.The 2017 epidemic E30 originated from another new lineage with a complex recombination pattern and formed an independent transmission chain in Ningxia.

Preliminary molecular epidemiology of the Staphylococcus aureus in lower respiratory tract infections： a multicenter study in China

Background Staphylococcus aureus （S. aureus） remains as an important microbial pathogen resulting in community and nosocomial acquired infections with significant morbidity and mortality. Few reports for S. aureus in lower respiratory tract infections （LRTIs） have been documented. The aim of this study was to explore the molecular epidemiology of S. aureus in LRTIs in China.Methods A multicenter study of the molecular epidemiology of S. aureus in LRTIs was conducted in 21 hospitals in Beijing, Shanghai and twelve other provinces from November 2007 to February 2009. All the collected S. aureus strains were classified as minimum inhibitory concentration （MIC）, mecA gene, virulence genes Panton-Valentine Leukocidin （PVL） and y-hemolysin （hlg）, staphylococcal cassette chromosome mec （SCCmec） type, agr type, and Multilocus Sequence Typinq （MLST）.Results Totally, nine methicillin-sensitive S. aureus （MSSA） and 29 methicillin-resistant S. aureus （MRSA） strains were isolated after culture from a total of 2829 sputums or bronchoalveolar lavages. The majority of MRSA strains （22/29） had a MIC value of 〉512 μg/ml for cefoxitin. The mecA gene acting as the conservative gene was carried by all MRSA strains. PVL genes were detected in only one S. aureus strain （2.63%, 1/38）. The hlg gene was detected in almost the all S. aureus （100% in MSSA and 96.56% in MRSA strains）. About 75.86% of MRSA strains carried SCCmec Ⅲ. Agr type 1 was predominant （78.95%） among the identified three agr types （agr types 1,2, and 3）. Totally, ten sequence type （ST） of S. aureus strains were detected. A new sequence type （ST1445） was found besides confirming ST239 as the major sequence type （60.53%）. A dendrogram generated from our own MLST database showed all the bootstrap values 〈50%. Conclusion Our preliminary epidemiology data show SCCmec Ⅲ, ST239 and agr type 1 of S. aureus as the predominant strains in LRTIs in Mainland of China.

Recent transmission of Mycobacterium tuberculosis in China： the implication of molecular epidemiology for tuberculosis control

Tuberculosis （TB） has remained an ongoing concern in China. The national scale-up of the Directly Observed Treatment, Short Course （DOTS） program has accelerated the fight against TB in China. Nevertheless, many challenges still remain, including the spread of drug-resistant strains, high disease burden in rural areas, and enormous rural-to-urban migrations. Whether incident active TB represents recent transmission or endogenous reactivation has helped to prioritize the strategies for TB control. Evidence from molecular epidemiology studies has delineated the recent transmission of Mycobacterium tuberculosis （M. tuberculosis） strains in many settings. However, the transmission patterns of TB in most areas of China are still not clear. Studies carried out to date could not capture the real burden of recent transmission of the disease in China because of the retrospective study design, incomplete sampling, and use of low-resolution genotyping methods. We reviewed the implementations of molecular epidemiology of TB in China, the estimated disease burden due to recent transmission of M. tuberculosis strains, the primary transmission of drug-resistant TB, and the evaluation of a feasible genotyping method of M. tuberculosis strains in circulation.

Molecular epidemiology of coxsackievirus A16 circulating in children in Beijing, China from 2010 to 2019

Background Coxsackievirus A16(CVA16)is one of the major etiological agents of hand,foot and mouth discase(HFMD).This study aimed to investigate the molecular epidemiology and evolutionary characteristics of CVA16.Methods Throat swabs were collected from children with HFMD and suspected HFMD during 2010-2019.Enteroviruses(EVs)were detected and typed by real-ime reverse transcription-polymerase chain reaction(RT-PCR)and RT-PCR.The genotype,evolutionary rate,the most recent common ancestor,population dynamics and selection pressure of CVA16 were analyzed based on viral protein gene(VPI)by bioinformatics software.Results A total of 4709 throat swabs were screened.EVs were detected in 3180 samples and 814 were CVA16 positive.More than 81%of CVA 16-positive children were under 5 years old.The prevalence of CVA 16 showed obvious periodic fluctuations with a high level during 2010--2012 followed by an apparent decline during 2013--2017.However,the activities of CVA16 increased gradually during 2018-2019.All the Beijing CVA16 strains belonged to sub-genotype BI,and B Ib was the dominant strain.One B Ic strain was detected in Bejing for the first time in 2016.The estimated mean evolutionary rate of VPI gene was 4.49x 103 substitution/site/year.Methionine gradually fixed at site-23 of VP1 since 2012.Two sites were detected under episodic positive selection,one of which(site-223)located in neutralizing linear epitope PEP71.Conclusions The dominant strains of CVA 16 belonged to clade B lb and evolved in a fast evolutionary rate during 2010-2019 in Beiing.To provide more favorable data for HFMD prevention and control,it is necessary to keep attention on molecular epidemiological and evolutionary characteristics of CVA16.

Molecular epidemiology of serotype 19A Streptococcus pneumoniae isolated from children in Beijing, 1997-2006

Background Despite the prevalence of Streptococcus pneumoniae serotype 19A, the molecular characteristics of this serotype are yet to be fully elucidated. The aim of this study was therefore to determine the homology of the serotype 19A in China. Methods Pulsed-field gel electrophoresis and multilocus sequence typing were done to these forty-nine serotype 19A isolates to investigate the relationship between the strains prevalent in Beijing and other regions. Results From 1997 to 2006, the percentage of serotype 19A isolates increased. The susceptibility rate to penicillin and amoxicillin decreased and the resistance rate to cefuroxime increased. ST320 was the most prevalent ST, followed by ST3546. There were six new STs identified in our study. The serotype 19A strains were classified into six different pulsed-field gel electrophoresis （PFGE） patterns. ST320, which was associated with two different PFGE patterns （A and D）, accounted for 32 isolates, and ST3546, which was associated with two PFGE patterns （B and E）, accounted for eight isolates. Conclusions From 2003 onwards, ST320 was the most common ST and the rate of resistance to cefuroxime increased significantly. Further long-term surveys of Streptococcus pneumoniae serotype 19A are required to monitor ST prevalence and antimicrobial resistance, in this important human pathogen.

Molecular Epidemiology of Staphylococcus aureus among Patients with Skin and Soft Tissue Infections in Two Chinese Hospitals

Background：Staphylococcus aureus is one of the predominant causes of skin and soft tissue infections （SSTIs）,but limited data were available regarding the characterization of S.aureus from SSTIs patients in Jiangsu Province in China.We aimed to investigate the molecular epidemiology ofS.aureus among SSTIs patients in two hospitals of Jiangsu Province.Methods：Sixty-two patients with SSTIs from two Chinese hospitals in Jiangsu Province were enrolled in this study,and 62 S.aureus isolates were collected from February 2014 to January 2015.S.aureus isolates were characterized by antimicrobial susceptibility testing,toxin gene detection,and molecular typing with sequence type,Staphylococcus protein A gene type,accessorygeneregulator（agr）group,and Staphylococcal cassette chromosome mec type.Results：Sixteen （25.8%） methicillin-resistant S.aureus （MRSA） isolates were detected,and there was no isolate found resistant to vancomycin,teicoplanin,sulfamethoxazole-trimethoprim,and linezolid.The sei was the toxin gene most frequently found,and no lukS/F-PV-positive isolates were detected among the SSTIs＆#39; patients.Molecular analysis revealed that ST398 （10/62,16.1%;2 MRSA and 8 methicillin-susceptible S.aureus） to be the dominant clone,followed by ST5 （8/62,12.9%） and ST7 （8/62,12.9%）.Conclusions：The livestock ST398 was the most common clone among patients with S.aureus SSTIs in Jiangsu Province,China.Surveillance and further studies on the important livestock ST398 clone in human infections are necessarily requested.

Clinical characteristics and molecular epidemiology of human metapneumovirus in children with acute lower respiratory tract infections in China, 2017 to 2019: A multicentre prospective observational study

Human metapneumovirus(HMPV) infection is one of the leading causes of hospitalization in young children with acute respiratory illness. In this study, we prospectively collected respiratory tract samples from children who were hospitalized with acute lower respiratory tract infection in six hospitals in China from 2017 to 2019. HMPV was detected in 145 out of 2733 samples(5.3%) from the hospitalized children. The majority of HMPV-positive children were under the age of two(67.6%), with a median age of one year. HMPV can independently cause acute lower respiratory tract infection in young children, while all patients showed mild clinical symptoms. Of all the co-infected patients, HMPV was most commonly detected with enterovirus(EV) or rhinovirus(RhV)(38.0%),followed by respiratory syncytial virus(RSV)(32.0%). The highest detection rate occurred from March to May in both northern and southern China. Out of 145 HMPV positive samples, 48 were successfully typed, of which 36strains were subgrouped into subtypes A2c(75%), eight strains were included in subtype B1(16.7%), and four strains were included in subtype B2(8.3%). Moreover, 16 A2c strains contained 111-nucleotide duplications in the G gene. Twenty-seven complete HMPV genomes were successfully obtained, and 25(92.6%) strains belonged to subtype A2c, whereas one strain was included in subgroup B1 and another was included in subgroup B2. A total of 277 mutations were observed in the complete genomes of 25 A2c strains. All results presented here improve our understanding of clinical characteristics and molecular epidemiology of HMPV infection in children.

Molecular epidemiology of Giardia duodenalis infection in humans in Southern Ethiopia:a triosephosphate isomerase gene-targeted analysis

Background:Giardia duodenalis is a species complex consisting of multiple genetically distinct assemblages.The species imposes a major public health crisis on developing countries.However,the molecular diversity,transmission dynamics and risk factors of the species in these countries are indeterminate.This study was conducted to determine the molecular epidemiology of G.duodenalis infection in asymptomatic individuals in Southern Ethiopia.Methods:From March to June 2014,fresh stool samples were collected from 590 randomly selected individuals.Socio-demographic data were gathered using a pre-tested structured questionnaire.The genotyping was done using triosephosphate isomerase gene-based nested polymerase chain reaction and DNA sequencing.The genetic identity and relatedness of isolates were determined using the basic local alignment search tool and phylogenetic analysis.Risk factors associated with G.duodenalis infection were analysed using binary and multinomial logistic regression models.Results:The results showed that 18.1%(92/509)of the study subjects were infected by G.duodenalis.Among the isolates,35.9%(33/92)and 21.7%(20/92)were sub-typed into assemblages A and B,respectively,whereas 42.4%(39/92)showed mixed infections of A and B.Most of the assemblage A isolates(94%,31/33)were 100%identical to sequences registered in GenBank,of which the majority belonged to sub-assemblage AII.However,the high genetic variability and frequency of double peaks made sub-genotyping of assemblage B more problematic and only 20%(4/20)of the isolates matched 100%with the sequences.The risk factors of age(P=0.032)and type of drinking water source(P=0.003)both showed a significant association with the occurrence G.duodenalis infection.Conclusions:This study established the endemicity of G.duodenalis in Southern Ethiopia.Infection with assemblage A was more frequent than with assemblage B,and the rate of infection was higher in children and in municipal/tap and open spring water consumers than the other groups.Sub-typing of assemblage B and determining the origin of double peaks were challenging.The present study confirms the need for further inclusive studies to be conducted focusing on sub-types of assemblage B and the origin of heterogeneity.

A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019

Human respiratory syncytial virus(RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015–2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A(RSV-A) was the predominant subgroup during this research period except in2016. Totally, 535 sequences of the second hypervariable region(HVR-2) of the G gene were obtained. Combined with182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1(512),NA1(6) and GA5(3), respectively;while 196 RSV-B sequences fell in BA9(193) and SAB4(3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258 Q and H266 L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than10%, while the sequences with T290 I and T312 I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites(296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015–2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.