Late presentation (LP) of HIV infection remains a major challenge to epidemic control, leading to advanced immunodeficiency, poorer treatment outcomes, and ongoing transmission before diagnosis. Despite expanded testing and awareness efforts, a considerable proportion of people living with HIV (PLHIV) in China are still diagnosed late. This study analyzed 386,704 newly reported HIV cases (2019–2022) from the National HIV/AIDS Comprehensive Response Information Management System (CRIMS). Logistic regression was used to identify significant predictors of LP, and a Bayesian network was constructed to model the complex interrelationships among variables. Logistic regression identified several factors associated with LP of HIV. Key factors included being male (aOR = 1.3), over 60 (aOR = 3.36), Han ethnicity (aOR = 1.16), education at below senior high school (aOR = 1.1), being a farmer or worker (OR = 1.04), transient population (aOR = 1.18), engaging in homosexual transmission (aOR = 1.1), being examined at other institutions (hospitals) (aOR = 1.27), having non-marital partners(lifetime history), and a history of STDs (aOR = 1.03) (P < 0.05). Bayesian network analysis revealed that age, gender, and sample sources were the key factors associated with LP of HIV. Among them, age played a central role in the model, directly influencing occupation, transmission routes, education level, transient status, and non-marital partners. Ethnicity indirectly affected LP through occupation, while education influenced LP indirectly by shaping occupation, non-marital partners, and transient status. In addition, a history of STDs not only directly affected sample sources but also indirectly increased the risk of LP through transient population status. This mixed-model approach demonstrated that demographic, behavioral, and structural factors jointly contribute to LP in China through complex associative pathways. Integrating logistic and Bayesian frameworks provides a more comprehensive understanding of HIV diagnostic delays, informing precision-targeted testing and intervention strategies.

Tianjin, a major hub in northern China, faces rising HIV-1 infections dominated by CRF01_AE and CRF07_BC. This study elucidated their divergent transmission patterns and drug resistance dynamics to guide targeted interventions. This study included samples identified as CRF01_AE and CRF07_BC subtypes through various methods between 2013 and 2022. BEAST software was used to examine the spatiotemporal transmission patterns of these subtypes in Tianjin. By integrating HIV-TRACE, we constructed high-risk transmission clusters and identified drug resistance mutations (DRMs) based on the Stanford HIV Drug Resistance Database. Finally, the birth–death skyline serial (BDSKY) model was employed to dynamically assess the effective reproductive number (Re) of both subtypes to predict future transmission dynamics. CRF01_AE might be introduced in 1988 from Henan and Zhejiang, forming multiple small clusters (< 10 nodes) and spreading through both heterosexual and men who have sex with men (MSM) in Tianjin, while CRF07_BC from Chongqing and Guizhou, et al. in 2004, experiencing explosive local transmission and forming a large cluster of 170 nodes primarily among MSM under 30 years old (P < 0.05). Phylogenetic analysis indicated that CRF01_AE has a significantly higher evolutionary rate (2.08 × 10⁻3 vs. 1.48 × 10⁻3 substitutions/site/year, P < 0.05), while CRF07_BC demonstrates a greater cluster formation capacity (56.6

Antiretroviral therapy (ART) and ART adherence are crucial for preventing HIV transmission and prolonging the lifespan of people living with HIV (PLWH). Serostatus disclosure is a significant factor influencing both ART initiation and ART adherence. However, studies evaluating the impact of disclosure on ART initiation and ART adherence in mainland China have yielded inconsistent findings. This systematic review and meta-analysis aim to examine the associations between disclosure and both ART initiation and adherence. We systematically reviewed English databases (MEDLINE, Embase, Web of Science and the Cochrane Library) and Chinese databases (CNKI, WanFang, CQVIP, and SinoMed) to identify literature on factors that influence ART initiation and ART adherence from inception to Sep 24, 2024. Microsoft Excel 2019 sheet was used for data extraction. The data extraction sheet included information on the author’s names, publication year of the study, study design, study population, sample size, definition of adherence to ART, and study quality score. The Joanna Briggs Institute (JBI) critical appraisal checklist for prevalence studies was employed to assess the quality of the selected articles. Data were analyzed using STATA 17.0, and a random effects model was utilized to calculate pooled odds ratios (ORs) and 95

PURPOSE:To understand the geographic origins, transmission hotspots, and drug resistance mutations (DRMs) of HIV-1 CRF08_BC in Zhejiang Province, China. METHODS:This study analyzed HIV-1 CRF08_BC pol sequences collected between 2020 and 2023. Bayesian inference was employed to investigate temporal epidemic trends, while HIV-TRACE and MCODE were used to identify transmission clusters (TCs), key hotspots and super-spreaders. DRMs associated with CRF08_BC were also characterized. Additionally, demographic data were integrated with these findings, allowing for a description of the transmission dynamics. RESULTS:This study revealed that CRF08_BC strains in Zhejiang likely originated from Guangxi, with significant transmission among individuals aged 50 and older, particularly those with low educational levels. Molecular transmission analysis showed that 58.9% of CRF08_BC sequences were in TCs, with geographic concentrations in Taizhou (TZ) and Lishui (LS). 14 large clusters maintained effective reproductive numbers (Re) above 1, representing considerable epidemic growth. Hangzhou (HZ) emerged as a key transmission hub, with 10 TCs showing active transmission. LS established strong epidemiological links with HZ, Ningbo (NB), Taizhou (TZ), and Wenzhou (WZ), creating a pattern of viral spread radiating from LS to surrounding areas. DRMs were identified in 76 cases (6.0%), with NNRTI and NRTI mutations exhibiting distinct geographic clustering. CONCLUSIONS:The CRF08_BC strains in Zhejiang likely originated from Guangxi and are mainly found in individuals aged 50 and older with low education. The current epidemic hotspots are in TZ and LS, where NNRTI and NRTI mutations are clustered, significantly impacting treatment efficacy.

Recreational drug use has been identified as a significant risk factor for the transmission of human immunodeficiency virus (HIV). This behavior is particularly prevalent among young men who have sex with men (YMSM). However, limited research has been conducted to investigate the correlation between recreational drug use and HIV incidence within this population. To examine HIV incidence and explore the association between recreational drug use and HIV incidence among YMSM. A retrospective cohort study was conducted by a local non-governmental organization (NGO) among MSM aged 18–24 years from October 2017 to December 2023 in Tianjin, China. Participants were included if they had at least two HIV test records during this period. HIV incidence density and its 95

This study aimed to conduct a comprehensive molecular epidemiology study of major HIV-1 subtypes in developed Eastern China (Zhejiang Province). Plasma samples and epidemiological information were collected from 4180 newly diagnosed HIV-1 positive patients in Zhejiang Province in 2021. Pol sequences were obtained to determine the subtypes via multiple analytical tools. HIV-1 molecular networks were constructed on the basis of genetic distances to analyze transmission patterns among major subtypes. Furthermore, the birth-death skyline (BDSKY) model was utilized to estimate the transmission risks associated with large clusters (LCs). In 4180 patients, 3699 (88.49

Using a comprehensive molecular epidemiological approach, we characterized the transmission dynamics of HIV-1 among the MSM population in Tianjin, China. Our findings revealed that 38.56% (386/1001) of individuals clustered across 109 molecular transmission clusters (TCs), with MSM aged 50 and below being the group most commonly transmitting HIV-1. Among the identified TCs, CRF01_AE predominated, followed by CRF07_BC. Notably, CRF07_BC demonstrated a higher propensity for forming large clusters compared to CRF01_AE. Birth-death skyline analyses of the two largest clusters indicated that the HIV/AIDS transmission may be at a critical point, nearly all had Re approximately 1 by now. A retrospective analysis revealed that the rapid expansion of these large clusters was primarily driven by the introduction of viruses in 2021, highlighting the crucial importance of continuous molecular surveillance in identifying newly emerging high-risk transmission chains and adapting measures to address evolving epidemic dynamics. Furthermore, we detected the transmission of drug-resistant mutations (DRMs) within the TCs, particularly in the CRF07_BC clusters (K103N, Y181C, and K101E) and CRF01_AE clusters (P225H and K219R), emphasizing the importance of monitoring to support the continued efficacy of first-line therapies and pre-exposure prophylaxis (PrEP). Recombination analyses indicated that complex recombinant patterns, associated with increased amino acid variability, could confer adaptive traits to the viruses, potentially providing a competitive advantage in certain host populations or regions. Our study highlights the potential of integrating molecular epidemiological and phylodynamic approaches to inform targeted interventions.

Introduction: A comprehensive analysis of nationwide survival trends for people living with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS, PLWHA) from the initial reported case to present has not been conducted. This study evaluated the survival outcomes of PLWHA reported in China from 1985 to 2022. Methods: We analyzed data from PLWHA recorded in the National HIV/AIDS Comprehensive Response Information Management System from 1985 to 2022. Survival rates were calculated using Kaplan- Meier curves, and factors associated with survival time were analyzed using Cox proportional hazard models. Results: Progressive relaxation of antiretroviral therapy initiation criteria led to significant improvements in survival rates across different diagnostic periods in China. The 1-year and 5-year cumulative survival rates increased from 85.2% and 66.1% in the 1985-2003 cohort to 91.1% and 81.4% in the 2016-2022 cohort. Cox proportional hazard analysis revealed elevated mortality risks among males, individuals aged >= 65 years, those with injection drug use or other transmission routes, hospital-tested patients, and those with lower CD4 counts at diagnosis or without treatment. Conclusions: Antiretroviral therapy has effectively reduced mortality risk among PLWHA in China. Future efforts should focus on expanding HIV testing to reduce the proportion of late diagnoses with lower CD4 counts and providing targeted, differentiated services for older populations to further decrease mortality risk among PLWHA.

Objective Reducing the prevalence of treatment failure among people living with HIV (PLHIV) on highly active antiretroviral therapy (HAART) is crucial for improving individual health and reducing disease burden. This study aimed to assess existing evidence on treatment failure and its associated factors among PLHIV in mainland China. Methods We conducted a comprehensive search of PubMed, Web of Science, Cochrane Library, WanFang, China National Knowledge Infrastructure, and SinoMed databases. Relevant studies on treatment failure among PLHIV in mainland China until September 2022 were searched, including cross-sectional, case-control, and cohort studies. The primary outcome was treatment failure, and secondary outcomes were the potential influencing factors of treatment failure. We performed a meta-analysis to pool each outcome of interest, including meta-regression, subgroup, publication bias, and sensitivity analyses. Results A total of 81 studies were deemed eligible and included in the final meta-analysis. The pooled treatment failure prevalence among PLHIV in mainland China was 14.40% (95% confidence interval [CI]:12.30–16.63), of which the virological and immunological failure prevalence was 10.53% (95%CI:8.51–12.74) and 18.75% (95%CI:15.44–22.06), respectively. The treatment failure prevalence before and after 2016 was 18.96% (95%CI:13.84–24.67) and 13.19% (95%CI:10.91–15.64). Factors associated with treatment failure included good treatment adherence (odds ratio [OR] = 0.36, 95%CI:0.26–0.51), baseline CD4 counts>200 cells/μL (OR = 0.39, 95%CI:0.21–0.75), HAART regimens containing Tenofovir Disoproxil Fumarate (TDF) (OR = 0.70, 95%CI:0.54–0.92), WHO clinical stage III/IV (OR = 2.02, 95%CI:1.14–3.59) and age≥40 years (OR = 1.56, 95%CI:1.23–1.97). Conclusion The prevalence of treatment failure among PLHIV receiving HAART in mainland China was low and tended to decline. Poor adherence, low baseline CD4 count, HAART regimens without TDF, advanced clinical stage, and old age were contributing factors for treatment failure. Relevant intervention programs are needed with increasing treatment adherence through behavioral intervention or precise intervention targeting older adults.

INTRODUCTION:The COVID-19 epidemic control and prevention strategies affected people's sexual activities and behaviors. Little was known about long-term effects of COVID-19 prevention and control strategies on sexual behaviors among men who have sex with men (MSM). This study aimed to examine changes in risky sexual behaviors of MSM before and after the local epidemic. METHODS:An online survey was conducted nationwide from June 1 to June 10, 2022. MSM aged 16 years and above, residing in China were recruited through convenience sampling. A generalized estimating equation model with modified Poisson regression was used to analyze changes in multiple sexual partners, unprotected sex, mobility for sexual activity, and recreational substance use before and after the local epidemic. RESULTS:Compared to the pre-pandemic (36.5%), the prevalence of multiple sexual partners (11.5%) significantly decreased during the local epidemic and then increased after the local epidemic (25.2%) but remained lower than pre-pandemic, as did the prevalence of unprotected sex (31.1%, 19.4%, and 26.1%), mobility for sexual activity (7.5%, 2.8%, and 4.1%) and recreational substance use (47.7%, 27.2%, and 39.5%). Compared to the pre-pandemic, higher declines in the prevalence of risky sexual behaviors during the local epidemic existed among MSM living without a regular partner (44% decrease in unprotected sex and 46% in recreational substance use), with a bachelor's degree and above (70% decrease in multiple sex partners, 39% in unprotected sex, 67% in mobility for sexual activity and 44% in recreational substance use), higher incomes (70% decrease in multiple sex partners), self-identified gay or bisexual/unsure (38-71%), and HIV infection (49-83% decrease respectively in these four indicators). After the local epidemic, the declines in the above indicators compared to the pre-pandemic were correspondingly. And higher declines existed among MSM living without a regular partner (8% decrease in unprotected sex and 13% in recreational substance use), with a bachelor's degree and above (33% decrease in multiple sex partners), higher incomes (55% decrease in mobility for sexual activity), self-identified gay (51% decrease in mobility for sexual activity), and HIV infection (32%, 68%, 24% decrease respectively in unprotected sex, mobility for sexual activity and recreational substance use). CONCLUSIONS:Risky sexual behaviors reduced considerably during the local epidemic, then seemed rebounded after the outbreak but wouldn't return to pre-pandemic levels. More attention should be paid to vulnerable people with lower socio-economic status, HIV-positive, and sexual minorities for sustained HIV and COVID-19 prevention.

分析江西一例免疫缺陷患者体内连续采集的15份粪便标本中分离到的Ⅲ型脊髓灰质炎病毒的全长VP1区基因特征.将从15份标本中分离到的14株Ⅲ型iVDPVs进行噬斑纯化,每个病毒随机挑取10个噬斑,接着进行逆转录-聚合酶链反应扩增,测定获取到的154株iVDPVs全长VP1区序列.通过系统发育分析和BEAST程序探究iVDPV病毒的进化特征,估算其进化速率和口服脊灰减毒活疫苗(attenuated oral polio vaccine,OPV)初始感染时间.14株iVDPVs与Ⅲ型脊髓灰质炎减毒疫苗株(Sabin Ⅲ)核苷酸和氨基酸同源性分别为97.8％～98.7％和97.6％～98.3％.相较于Sabin Ⅲ,14株iVDPVs VP1区第54位氨基酸发生了 A→V的突变,这可能导致温度敏感表型和衰减表型的改变.根据拓扑结构系统发育树被划分为3个Lineages,其中17049-1-8,17049-2-2和17049-2-9分别属于Lineage 1和Lineage 2,其余属于Lineage 3.具有Lineage 3序列特征的克隆是优势克隆,呈现出随时间持续分化的特征.BEAST程序估算的14株iVDPVs全长VP1区核苷酸平均进化速率为9.29×10-3/位点/年(95％置信区间:2.81×10-3-1.59×10-2),OPV初始感染时间为2012年11月 18 日.MCC 树(maximum clade credibility tree)显示前4个遗传分支的分化仅用了 40 d.14株Ⅲ型iVDPVs具有高度相关性,它们感染患儿后进化非常迅速,在慢性感染的早期便开始了谱系的分化.突变的不断积累和关键位点的改变可以引起iVDPVs神经毒力的变化,导致患儿出现AFP症状.iVDPV病例持续的排毒给脊灰根除目标的实现带来了巨大挑战,在脊髓灰质炎消灭的最后阶段及时调整免疫策略,继续维持较高的免疫覆盖率,保持iVDPV监测的灵敏性显得十分重要.

Objective:To analyze the pathogen spectrum and genetic characteristics of the main pathogens of hand, foot, and mouth disease (HFMD) in Chongqing from 2017 to 2018.Methods:Chongqing Children's Hospital was selected as the study object. Nucleic acid detection information of 1 071 patients diagnosed with HFMD from 2017 to 2018 was collected. The enterovirus serotypes of 810 samples were identified. There were 175 samples remaining unidentified for serotypes. Eighty-six samples were enterovirus-negative. Through virus isolation, nucleic acid concentration and gene sequencing, the above 261 samples were tested to obtain a complete pathogen spectrum of HFMD in this area. MEGA 7.0 software was used to construct phylogenetic trees of the four major pathogens for the study of genetic characteristics.Results:Except for 3 samples that were identified as Human parechovirus (HPeV), 258 samples were positive for enterovirus by the improved identification method. Among them, coxsackievirus A6 (CVA6) was the dominant serotype, followed by enterovirus A71 (EV-A71). There were also 13 serotypes of CVA16, CVA10 and other enteroviruses. The phylogenetic analysis results showed that the serotypes of CVA6 in Chongqing were all D3a sub-genotype, while the dominant gene subtypes of EV-A71, CVA10 and CVA16 were C4a, C2b and B1b, respectively. These four dominant genotypes co-evolved with the genotypes in other areas of China.Conclusions:This study improved the detection rate of enterovirus by optimizing the identification method, and further defined the pathogen spectrum of HFMD in Chongqing. The dominant pathogen of HFMD was CVA6 in Chongqing from 2017 to 2018, followed by EV-A71, and both serotypes were also the main pathogen causing severe HFMD in Chongqing area.

In 2013, a case of immunodeficiency vaccine-derived poliovirus (iVDPV) was identified in Jiangxi Province, China. In this study, we purified 14 type 3 original viral isolates from this case and characterized the molecular evolution of these iVDPVs for 298 days. Genetic variants were found in most of the original viral isolates, with complex genetic and evolutionary relationships among the variants. A phylogenetic tree constructed based on the P1 region showed that these iVDPVs were classified into lineage A and B. The dominant lineage B represents a major trend in virus evolution. The nucleotide substitution rate at the third codon position (3CP) estimated by the BEAST program was 1.76 x 10-2 substitutions/site/year (95% HPD: 1.23-2.39 x 10-2). The initial OPV dose was given dating back to March 2013, which was close to the time of the last OPV vaccination, suggesting that OPV infection may have originated with the last dose of vaccine. Recombinant analysis showed that these iVDPVs were inter-vaccine recombinants with two recombination patterns, S3/S2/S1 and S3/S2/S3/S2/S1. Whole genome sequence analysis revealed that key nucleotide sites (C472U, C2034U, U2493C) associated with the attenuated phenotype of Sabin 3 have been replaced. Temperature sensitivity test showed that all tested strains were temperature-sensitive, except for the variant Day11-5. Interestingly, we observed that the variant Day11-5 temperature resistance properties may be associated with the Lys to Met substitution at the VP2-162 site. Serological test and whole genome sequence analysis showed that the seropositivity rate remained high, and mutations in the antigenic sites did not significantly alter neutralization ability.

BackgroundThe diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.Materials and methodsWe implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.ResultsIn this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.ConclusionOverall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.

Echovirus, a member of the Enterovirus B (EV-B) family, has led to numerous outbreaks and pandemics, causing a broad spectrum of diseases. Based on the national hand, foot, and mouth disease (HFMD) surveillance system, seven strains of echovirus 33 (E33) were isolated from Mainland of China between 2010 and 2018. The whole genomes of these strains were isolated and sequenced, and phylogenetic trees were constructed based on the gene sequences in different regions of the EV-B prototype strains. It was found that E33 may be recombined in the P2 and P3 regions. Five genotypes (A–E) were defined based on the entire VP1 region of E33, of which the C gene subtype was the dominant gene subtype at present. Recombinant analysis showed that genotype C strains likely recombined with EV-B80, EV-B85, E13, and CVA9 in the P2 and P3 regions, while genotype E had the possibility of recombination with CVB3, E3, E6, and E4. Results of Bayesian analysis indicated that E33 may have appeared around 1955 (95% confidence interval: 1945–1959), with a high evolutionary rate of 1.11 × 10−2 substitution/site/year (95% highest posterior density (HPD): 8.17 × 10−3 to 1.4 × 10−2 substitution/site/year). According to spatial transmission route analysis, two significant transmission routes were identified: from Australia to India and from Oman to Thailand, which the E33 strain in Mainland of China likely introduced from Mexico and India. In conclusion, our study fills the gaps in the evolutionary analysis of E33 and can provide important data for enterovirus surveillance.

Nineteen CVA9 isolates were obtained between 2010 and 2019 from six provinces of mainland China, using the HFMD surveillance network established in China. Nucleotide sequencing revealed that the full-length VP1 of 19 CVA9 isolates was 906 bases encoding 302 amino acids. The combination of the thresholds of the phylogenetic tree and nucleotide divergence of different genotypes within the same serotype led to a value of 15–25%, and enabled CVA9 worldwide to be categorized into ten genotypes: A–J. The phylogenetic tree showed that the prototype strain was included in genotype A, and that the B, C, D, E, H, and J genotypes disappeared during virus evolution, whereas the F, I, and G genotypes showed co-circulation. Lineage G was the dominant genotype of CVA9 and included most of the strains from nine countries in Asia, North America, Oceania, and Europe. Most Chinese strains belonged to the G genotype, suggesting that the molecular epidemiology of China is consistent with that observed worldwide. The 165 partial VP1 strains (723 nt) showed a mean substitution rate of 3.27 × 10−3 substitution/site/year (95% HPD range 2.93–3.6 × 10−3), dating the tMRCA of CVA9 back to approximately 1922 (1911–1932). The spatiotemporal dynamics of CVA9 showed the spread of CVA9 obviously increased in recent years. Most CVA9 isolates originated in USA, but the epidemic areas of CVA9 are now concentrated in the Asia–Pacific region, European countries, and North America. Recombination analysis within the enterovirus B specie (59 serotypes) revealed eight recombination patterns in China at present, CVB4, CVB5, E30, CVB2, E11, HEV106, HEV85, and HEV75. E14, and E6 may act as recombinant donors in multiple regions. Comparison of temperature sensitivity revealed that temperature-insensitive strains have more amino acid substitutions in the RGD motif of the VP1 region, and the sites T283S, V284M, and R288K in the VP1 region may be related to the temperature tolerance of CVA9.

Objective:To construct a scientific molecular typing criteria for coxsackievirus B5 (CVB5) according to the basic principles of molecular typing for enteroviruses (based on the cut-off value of 15%-25% difference in the entire nucleotide sequence of VP1 region). Methods:The entire VP1 coding regions of all 69 CVB5 strains isolated from mainland of China from 2001 to 2021 were amplified by reverse transcription-polymerase chain reaction using the Chinese Hand, Foot, and Mouth Disease (HFMD) Laboratory Network Platform. The nucleotide sequencing and analyses were also performed. The 742 complete sequences of VP1 coding region (849 nucleotides) of CVB5 in GenBank by the end of February 16, 2022 were downloaded and filtered. The phylogenetic tree with maximum likelihood method for the study of CVB5 genotyping criteria was constructed using MEGA 7.0 software with the bootstrap value of 1000.Results:Nucleotide and amino acids sequence similarity between 69 CVB5 isolates from the Chinese mainland and CVB5 prototype strain (Faulkner strain) ranged from 77.3% to 81.6% and 93.2% to 95.3%, respectively. The phylogenetic tree showed that CVB5 worldwide could be divided into 4 different branches. The average differences in nucleotides and amino acids within the branch were 7.3%-13.4% and 1.9%-3.3%, respectively. The average differences s in nucleotides and amino acids between branches were 17.0%-22.3% and 4.2%-4.9%, respectively. According to the above molecular genotyping criteria, CVB5 worldwide could be divided into four genotypes: A, B, C and D. Genotypes A and C might have disappeared during the evolution and were no longer prevalent. Genotypes B and D of CVB5 presented a co-epidemic trend worldwide. The predominant genotype of CVB5 in the Chinese mainland was genotype D with a small proportion of genotype B.Conclusions:In this study, the criteria for molecular typing of CVB5 was established and the CVB5 strains worldwide were classified into four genotypes accordingly. This is of important value for further understanding of the genetic variation and transition of CVB5 as well as for molecular traceability.

血清型别鉴定及基因分型分析是开展肠道病毒(Enterovirus,EV)分子进化特征研究的重要内容.目前为止,国内外对柯萨奇病毒A组9型(Coxsackievirus A9,CVA9)的研究主要集中在衣壳蛋白区的细胞受体结合位点及其基因特性分析,而基于全长VP1序列的基因型划分结果尚未明确.本研究依托国家手足口病监测网络,对2010-2019年全国31个省级行政区(省、自治区、直辖市)上送的18238份手足口病样本中分离出的24株CVA9进行全长VP1区序列测定,并与GenBank中所有全长VP1区序列一起进行基因型划分研究.测序结果显示24株CVA9分离株VP1全长为906bp,编码302个氨基酸,与CVA9原型株(Griggs)核苷酸和氨基酸相似性分别为80.5％～97.6％和92.3％～99.6％.结合系统进化树和同一血清型内不同基因型的核苷酸差异界值为15％～25％,将全球CVA9划分为A-H八个基因型.进化树显示B、C和D基因型在病毒进化过程中已消失,而E、F和G基因型呈现共循环的趋势,其中G基因型包含了亚洲、北美洲、大洋洲和欧洲等9个国家的毒株,是CVA9的优势基因型.大部分中国株属于G基因型,与世界流行趋势一致.但在2018年新疆一例手足口病患儿体内分离到的CVA9毒株却与俄罗斯有很近的亲缘关系,被划分为F基因型,推测该毒株为俄罗斯输入株.CVA9虽具有明显的地理聚性,但G基因型中包含的多国家和多时间段的毒株也提示CVA9病毒可能存在远距离的传播和流行.

Coxsackievirus A12 (CVA12) is an enterovirus that has been isolated in many countries in recent years. However, studies on CVA12 are limited, and its effective population size, evolutionary dynamics and recombination patterns have not been clarified now. In this study, we described the phylogenetic characteristics of 16 CVA12 strains isolated from pediatric HFMD patients in mainland China from 2010 to 2019. Comparison of the nucleotide sequences and amino acid sequences with the CVA12 prototype strain revealed that the 16 CVA12 strains are identical in 78.8–79% and 94–94.2%, respectively. A phylodynamic analysis based on the 16 full-length VP1 sequences from this study and 21 sequences obtained from GenBank revealed a mean substitution rate of 6.61 × 10−3 substitutions/site/year (95% HPD: 5.16–8.20 × 10−3), dating the time to most recent common ancestor (tMRCA) of CVA12 back to 1946 (95% HPD: 1942–1947). The Bayesian skyline plot showed that the effective population size has experienced twice dynamic fluctuations since 2007. Phylogeographic analysis identified two significant migration pathways, indicating the existence of cross-provincial transmission of CVA12 in mainland China. Recombination analysis revealed two recombination patterns between 16 CVA12 strains and other EV-A, suggesting that there may be extensive genetic exchange between CVA12 and other enteroviruses. In summary, a total of 16 full-length CVA12 strains were reported in this study, providing valuable references for further studies of CVA12 worldwide.

Echovirus 30 (E30), a member of species B enterovirus, is associated with outbreaks of aseptic meningitis and has become a global health emergency. However, the pathogenesis of E30 remains poorly understood due to the lack of appropriate animal models. In this study, we established a mouse infection model to explore the pathogenicity of E30. The 2-day-old IFNAR-/- mice infected with E30 strain WZ16 showed lethargy and paralysis, and some died. Obvious pathological changes were observed in the skeletal muscle, brain tissue, and other tissues, with the highest viral load in the skeletal muscles. Transcriptome analysis of brain and skeletal muscle tissues from infected mice showed that significant differentially expressed genes were enriched in complement response and neuropathy-related pathways. Using immunofluorescence assay, we found that the viral double-stranded RNA (dsRNA) was detected in the mouse brain region and could infect human glioma (U251) cells. These results indicated that E30 affects the nervous system, and they provide a theoretical basis for understanding its pathogenesis. IMPORTANCE Echovirus 30 (E30) infection causes a wide spectrum of diseases with mild symptoms, such as hand, foot, and mouth disease (HFMD), acute flaccid paralysis, and aseptic meningitis and other diseases, especially one of the most common pathogens causing aseptic meningitis outbreaks. We established a novel mouse model of E30 infection by inoculating neonatal mice with clinical isolates of E30 and observed the pathological changes induced by E30. Using the E30 infection model, we found complement responses and neuropathy-related genes in the mice tissues at the transcriptome level. Moreover, we found that the viral dsRNA localized in the mouse brain and could replicate in human glioma cell line U251 rather than in the neuroblastoma cell line, SK-N-SH.