Hand, foot, and mouth disease (HFMD) is a common infectious disease in children, primarily caused by human enteroviruses (EVs). This study describes the epidemiological characteristics of HFMD in Taiyuan, China (2017-2024), also the genetic features of Coxsackievirus A6 (CVA6). The incidence of HFMD showed significant variations during this period. Male cases outnumbered females, with children aged 0-6 years accounting for 81.88% of all cases and exhibiting a distinct seasonal distribution pattern. Real-time reverse transcription polymerase chain reaction was performed on 4389 clinical specimens, identifying 1,920 human EVs-positive specimens. Positive cases included 690 CVA6, 530 CVA16, 65 CVA10, 152 Enterovirus A71, and 483 other human EVs. Pathogen spectrum analysis revealed that CVA6 maintained high prevalence from 2017 to 2023 but declined in 2024. Phylogenetic analysis of 194 complete VP1 sequences revealed all strains belonged to sub-genotype D3 within genotype D. Nucleic acid homology ranged from 91.4% to 100%, and amino acid similarity from 97.0% to 100%. A persistent, continuously circulating lineage existed within the D3a branch. The GH loop within VP1 revealed high sequence conservation and structural stability, confirming its suitability as a vaccine target. These findings enhance genetic data on CVA6, thereby providing crucial scientific basis for prevention and vaccine development.

The increased circulation of enteroviruses (EVs) from July to December 2024 necessitated a retrospective analysis of hospitalized children with acute respiratory infections in Beijing, China, during 2017-2024. Among the 155 cases confirmed as EVs (0.67%, 155/23,245), with peaks in a triennial pattern and predominance between July and October, 114 were EV-D68, with 82 (71.93%) detected between July and October 2024. Among the 79 VP1 gene sequences of EV-D68 classified into subclades B3 (50.63%, 40/79) and D1 (49.37%, 39/79) through phylogenetic analysis, 31 (77.50%, 31/40) were B3 from 2024, and 34 (87.18%, 34/39) were D1 from 2024. More patients infected with B3 required oxygen supplementation than those infected with D1 (p = 0.042). Therefore, an epidemic of EV-D68 with the co-circulation of B3 and D1 was observed in 2024, with more severe disease caused by B3 than by D1, which underscores the urgent need for surveillance of EV-D68.

Coxsackievirus A4 (CVA4) is an enterovirus associated with diverse clinical syndromes, yet its global evolution and transmission dynamics remain poorly defined. This study aimed to characterize the molecular epidemiology, evolutionary history, and phylodynamic patterns of CVA4 at both local and global scales. In 2024, 34 CVA4 infections were identified during a localized herpangina outbreak in Beijing, primarily affecting children under 5 years of age, with a pronounced peak in July. High detection and isolation rates, together with temporal clustering in mid-2024, indicate a genuine short-term expansion rather than sporadic detection. Phylogenetic analysis of global VP1 sequences resolved six genotypes (A-F), with Beijing strains clustering within genotype E and subgenotype F2, reflecting ongoing worldwide circulation. Bayesian phylodynamic analysis estimated a VP1 evolutionary rate of 1.626 × 10-3 substitutions per site per year (95% highest probability density [HPD], 1.428-1.827 × 10-3) and dated the CVA4 time to the most recent common ancestor back to March 1917 (95% HPD, June 1908-April 1926). Demographic reconstruction revealed fluctuating genetic diversity, with notable expansions in 2013 and 2016, as well as a modest increase in 2023 preceding the outbreak. Phylogeographic analyses identified France and China as key seeding regions. Recombination in the P2 and P3 regions, including evidence of CVA2-related donors, highlights recombination as a major contributor to CVA4 diversity. These findings improve our understanding of CVA4 evolution and transmission and underscore the need for enhanced genomic surveillance.

It has been reported that chronic infection of human norovirus (HuNoV) may potentially serve as a reservoir for viral variants with the possibility to evade population immunity or alter the binding sites of HBGA receptors. In this study, a child diagnosed with Burkitt lymphoma and positive for HuNoV determined by real-time PCR (qPCR) firstly in 15 August 2016, was followed up until 20 March 2018, and 26 fecal specimens and one vomitus were collected to trace the evolutionary characteristics of HuNoV by phylogenetic analysis, meta-genomics next-generation sequencing (mNGS), and temporal evolutionary analysis of VP1 among 23 specimens positive for HuNoV. There were 15 specimens with partial RdRp gene sequences forming an independent cluster with sequences of GII.P31, 14 with the region C sequences and 11 with P domain sequences of VP1 gene clustered together with HuNoV GII.4 Sydney_2012. All these sequences showed that mutations accumulated nearly in a time order, and more mutations were shown in the key epitopes A-E or near the binding sites for HBGA in subdomain P2 with higher evolutionary rates. Analysis of NGS data identified intra-host viral quasi-species, and two genome sequences of the same length from mNGS were assembled from N705, with mutations located in the region of subdomain P2 (1171 nt-1202 nt) which led to five amino acid mutations. In conclusion, the accumulated mutations of HuNoV, especially in subdomain P2, were explored in a child with Burkitt lymphoma, and the sequencing of HuNoV from immunocompromised individuals was proven critical for monitoring intra-host quasi-species evolution and potential variant emergence, providing basic data for clinical infection control.

Background Human bocavirus 1 (HBoV1) causes acute respiratory infections (ARIs) in children, but its diagnosis is complicated by prolonged viral shedding. There are indications that the detection of a circular genome in a clinical specimens may be associated with acute infection. Methods Respiratory specimens collected from pediatric patients with ARIs during January 2021 to July 2024 were screened by a duplex qPCR, which was developed to distinguish circular genome from total viral genomes and evaluated by nested PCR and antigen test. Clinical data were collected from patients with single HBoV1 infection to reveal the association of circular genome with ARIs and the severity of pneumonia. Results Among 520 specimens positive for HBoV1 DNA, 206 (39.61%) were positive for circular genomes as determined by duplex qPCR, with the median load of total genomes 1010.08 (IQR 109.26, 1010.62) copies/mL significantly higher than 107.81 (IQR 106.88, 108.60) copies/mL in the circular genome negative group (p < 0.0001). In the antigen-positive group, the positive rate for circular genomes was 78.57% (44/56), significantly higher than 34.29% (108/315) observed in the antigen-negative group. Among patients single positive for HBoV1, the circular genome-positive group (n=106) showed more severe clinical manifestations and required more intensive treatment. Logistic regression analysis identified the circular genome as a strong independent risk factor for severe pneumonia (OR = 6.38, AUC = 0.82). Conclusion Circular genome of HBoV1 associated with high load of viral DNA, positive antigen and severe pneumonia in children may serve as a biomarker for acute HBoV1 infection and severe pneumonia.

Introduction:Coxsackievirus A12 (CVA12) is a serotype of Enterovirus A. Its evolutionary and molecular characteristics remain poorly understood. Methods:The metagenomic Next-Generation Sequencing (mNGS) strategy were used to investigate the viral diversity. The viral isolation, proliferation assays, phylogenetic relationships and recombination events were analyzed. Results:In this study, nine clinical specimens collected in Beijing, China, during March 2010 to October 2019 were identified as CVA12 positive, among which five were confirmed by mNGS. Then five CVA12 strains were isolated, and the proliferation assays demonstrated the preferential replication of CVA12 in rhabdomyosarcoma (RD) cells, with rapid intracellular replication before being released extracellularly, over Hep-2 cells. Transcriptomic profiling of infected RD cells revealed that the significant up-regulated genes were involved in inflammatory responses and transcriptional regulation (e.g., JUN, FOS), suggesting robust host immune activation. Phylogenetic analysis identified that four strains were clustered into genogroup E, indicating a lineage undergoing active transmission in Beijing, China, the other one into genogroups B. Recombination analysis revealed that strain s7275 exhibited recombination with CVA5 (strain 3,490, GenBank access number OK334538) at the breakpoint position 3,373-6,634, while the others showed recombination with EV-A71 (strain EV71/P1034/2013/China, GenBank access number KP289419) at breakpoint position 3,370-6,645. Discussion:These findings underscored the genetic diversity and recombination dynamics which provided insights into the evolutionary implications of CVA12, and its proliferation features in RD cells of CVA12. Further research is needed to elucidate the functional mechanisms of CVA12 infection and its role for disease.

Objective:Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control. Methods:Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes. Results:Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16. Conclusion:A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.

ABSTRACT Human bocavirus (HBoVs) is an emerging virus globally, and its prevalence, diversity, and evolution in children with acute gastroenteritis require further study. Fecal specimens collected from outpatients with acute gastroenteritis in Beijing, China, from April 2014 to December 2023, were tested for HBoVs by PCR targeting the NS1 gene. Genotyping was based on the NP1/VP1 boundary region, and nearly full-length HBoV2 sequences were analyzed phylogenetically. A total of 79 HBoVs-positive specimens (2.5%, 79/3,116, 95% CI: 2.0%–3.1%) were detected, with HBoV2 (65.8%, 52/79, 95% CI: 55.4%–76.3%) as the dominant genotype, followed by HBoV1 (25.3%, 20/79, 95% CI: 15.7%–34.9%) and HBoV3 (8.9%, 7/79, 95% CI: 2.6%–15.1%). HBoVs were distributed throughout the year, with higher positive rates observed from August to December 2018–2021. They predominantly infected children younger than 5 years, especially those aged 6–24 months (3.3%, 52/1,591, 95% CI: 2.4%–4.1%). HBoV2C was the prevalent sub-genotype in Beijing. Novel recombination events were detected between HBoV2 sub-genotypes, with breakpoints in the NS1 and VP3 gene regions. Evolutionary analysis estimated the time to the most recent common ancestor (tMRCA) for HBoV2 dating back to 1845, with a mean nucleotide substitution rate of 1.4 × 10−4 substitutions/site/year, and that HBoV2A evolved faster than HBoV2C. The evolutionary rates decreased in the following order: NP1, VP3, VP1, and NS1. A purifying selection was observed on HBoV2 genes, with one positively selected site in the NS1 gene. In conclusion, HBoV2 was the dominant genotype in children with acute gastroenteritis in Beijing, China, with higher susceptibility in those under 2 years old. Novel recombination events between HBoV2 sub-genotypes occurred frequently.IMPORTANCEAcute gastroenteritis remains a leading cause of morbidity and mortality in children, with viral infections being the primary causative agents. In this study, we investigated the prevalence of human bocavirus (HBoVs) in children with acute gastroenteritis in Beijing from 2014 to 2023, identifying HBoV2C as the predominant sub-genotype. Additionally, this study reported the first estimate of the evolutionary rate for global HBoV2 (1.4 × 10−4 substitutions/site/year) and identified novel intra-genotype recombination events in HBoV2. The results not only filled a gap in the evolutionary studies of global HBoV2 but also offered valuable data for the development of effective surveillance and prevention strategies for controlling acute gastroenteritis in children.

Enterovirus D68 (EV-D68), a serotype of the enterovirus species D, has garnered significant attention due to outbreaks reported in 2014, 2016, and 2018. In this study, 36 Chinese EV-D68 strains were isolated, sequenced, and combined with all EV-D68 VP1 sequences from GenBank to form a data set of 1679 sequences. This data set served as the basis for phylogenetic, evolutionary dynamics, phylogeographic, and key amino acid site mutation analyses of EV-D68. Based on the VP1 region, EV-D68 is classified into four genotypes (A-D), and seven subgenotypes (B1-B3, D1-D4), with B3 and D3 being the predominant subgenotypes. Bayesian skyline plots indicated that genotypes B and D experienced multiple population expansions, aligning with reported EV-D68 outbreaks. Phylogeographic analyses of the B3 subgenotypes revealed sequences from Europe and North America clustering into a single evolutionary branch, suggesting significant transmission between these regions. Additionally, mutation analysis identified VP1-98 as a high-frequency mutation site, differing significantly between the previously prevalent A and C genotypes and the currently prevalent B and D genotypes. However, the functional implications of this mutation require further investigation. This study provides a solid theoretical basis for epidemiological research, disease surveillance, and prevention efforts related to EV-D68.

Hand, foot, and mouth disease (HFMD) represents a globally prevalent infectious disease that is caused by enteroviruses. Enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), and coxsackievirus A6 (CVA6) are recognized as the predominant causative agents of HFMD. CVA16 is a member of the genus Enterovirus within the family Picornaviridae. B1a and B1b are the most prevalent subgenotypes, whereas the B1c subgenotype is relatively scarce. In this study, a comprehensive analysis was conducted on 15 of CVA16 B1c strains isolated from samples of patients diagnosed with HFMD in Jixi (Heilongjiang Province, China) in 2022. Subsequently, whole genome sequencing of these strains was carried out. Phylogenetic origin and potential recombination events were analyzed by aligning sequences of isolated of CVA16 B1c strains with related sequences deposited in GenBank. The CVA16 B1c isolates examined in this study exhibited a high degree of similarities. Specifically, the nucleotide similarity within the VP1 region ranged from 99.6 to 100%. The average nucleotide substitution rate of CVA16 B1c viruses worldwide was estimated to be 5.14 × 10−3 (4.13–6.27 × 10−3) substitution/site/year, and the most recent common ancestor could be traced back to 2003. The earliest CVA16 B1c strain isolated in China was traced back to 2011. Transmission pathway analysis suggested that Chinese strains may have originated in India. Recombination analysis showed that CVA16 B1c strains likely undergone recombination events with EV-A71 and CVA4. In conclusion, the analysis of a cluster of CVA16 B1c cases detected for the first time in Heilongjiang Province not only expanded the gene sequence library of CVA16 B1c strains in China but also offered an epidemiological basis for further investigations into the antigen–antibody interactions and pathogenicity of CVA16 B1c.

With the cancellation of non-pharmaceutical interventions (NPIs) since December 26, 2022, in Beijing, it is essential to update the endemic pattern of respiratory syncytial virus (RSV) in pediatric patients. Respiratory specimens were collected from hospitalized children with acute respiratory infections (ARIs) from January 2022 to December 2023 in Beijing for multiple pathogen screening. Then, specimens positive for RSV were subtyped by PCR and genotyped by G gene sequencing and phylogenetic analysis with Mega X. The clinical data of children only positive for RSV were compared using SPSS 22.0 software. Among 7131 specimens enrolled, there were 9.21% (203/2205) and 10.74% (529/4926) positive for RSV before and after the cancellation of NPIs, respectively. The expected RSV endemic season from November 2022 to March 2023 disappeared, and the RSV positive rates kept in 0.00% in January and February 2023, which were then increased rapidly to 14.81% in April and 24.60% in May, and to 14.35% and 18.18% again in November and December 2023, with the dominant subtype of RSV transferred from A to B in November 2023. Phylogenetic analysis revealed that clusters ON1.2 and BA9.3, especially, a new variant RSV-B-BA9-954bp, only showed in specimens collected after the cancellation of NPIs. Higher proportion of children aged 3-6 years and over 6 years which increased from 10.56% to 21.41%, and from 3.33% to 7.59%, respectively, and less severe pneumonia cases which decreased from 50.00% to 17.86%, were observed after the cancellation of NPIs. With the cancellation of NPIs, a delayed endemic season of RSV was shown in April and May 2023, with new clusters of ON1.2 and BA9.3, especially a new variant (RSV-B-BA9-954bp), a high proportion of children aged 3-6 years and over 6 years, and less severe pneumonia cases.

Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1,663 sequences were collected, forming a 442-sequences dataset for VP1 coding region analysis and a 345-sequences dataset for RF identification. Based on the VP1 coding region used for serotyping, three genotypes (A, B, and D), two subgenotypes of genotype B (B1 and B2), and three clusters of subgenotype B1 (B1a, B1b, and B1c) were identified. Cluster B1b has dominated the global epidemics, B2 disappeared in 2000, and D is an emerging genotype dating back to August 2002. Globally, four oscillation phases of CVA16 evolution, with a peak in 2013, and three migration pathways were identified. Europe, China, and Japan have served as the seeds for the global transmission of CVA16. Based on the 3D coding region of the RFs, five clusters of RFs (RF-A to -E) were identified. The shift in RFs from RF-B and RF-C to RF-D was accompanied by a change in genotype from B2 to B1a and B1c and then to B1b. In conclusion, the evolution and population dynamics of CVA16, especially the coevolution of 3D and VP1 genes, revealed that genotype evolution and RF replacement were synergistic rather than stochastic.

Recombination events in human adenovirus (HAdV) have led to some new highly pathogenic or infectious types. It is vital to monitor recombinant HAdVs, especially in children with acute respiratory tract infections (ARIs). In the retrospective study, HAdV positive specimens were collected from pediatric patients with ARIs during 2015 to 2021, then typed by sequence analysis of the penton base, hexon and fiber gene sequence. For those with inconsistent typing results, a modified method with species-specific primer sets of a fiber gene sequence was developed to distinguish co-infections of different types from recombinant HAdV infections. Then, plaque assays combined with meta-genomic next-generation sequencing (mNGS) were used to reveal the HAdV genomic characteristics. There were 466 cases positive for HAdV DNA (2.89%, 466/16,097) and 350 (75.11%, 350/466) successfully typed with the most prevalent types HAdV-B3 (56.57%, 198/350) and HAdV-B7 (32.00%, 112/350), followed by HAdV-C1 (6.00%, 21/350). Among 35 cases (7.51%, 35/466) with inconsistent typing results, nine cases were confirmed as co-infections by different types of HAdVs, and 26 cases as recombinant HAdVs in six genetic patterns primarily clustered to species C (25 cases) in pattern 1–5, or species D (1 case) in pattern 6. The novel recombinant HAdV of species D was identified with multiple recombinant events among HAdV-D53, HAdV-D64, and HAdV-D8, and officially named as HAdV-D115. High-frequency recombination of HAdVs in six genetic recombination patterns were identified among children with ARIs in Beijing. Specifically, there is a novel Adenovirus D human/CHN/S8130/2023/115[P22H8F8] designed as HAdV D115.

Background: The increasing incidence of hand, foot, and mouth disease (HFMD) associated with Coxsackievirus A6 (CVA6) has become a very significant public health problem. The aim of this study is to investigate the recombination, geographic transmission, and evolutionary characteristics of the global CVA6. Methods: From 2019 to 2022, 73 full-length CVA6 sequences were obtained from HFMD patients in China and analyzed in combination with 1032 published whole genome sequences. Based on this dataset, the phylogenetic features, recombinant diversity, Bayesian phylodynamic characteristics, and key amino acid variations in CVA6 were analyzed. Results: The four genotypes of CVA6, A, D, E, and F, are divided into 24 recombinant forms (RFs, RF -A - RF -X) based on differences in the P3 coding region. The eastern China region plays a key role in the dissemination of CVA6 in China. VP1 -137 and VP1 -138 are located in the DE loop on the surface of the CVA6 VP1 protein, with the former being a highly variable site and the latter having more non-synonymous substitutions. Conclusions: Based on whole genome sequences, this study contributes to the CVA6 monitoring, early warning, and the pathogenic mechanism by studying recombination diversity, geographical transmission characteristics, and the variation of important amino acid sites.

Background: Variations in the fusion (F) protein of respiratory syncytial virus (RSV) with main antigenic sites I–V and Ø may affect the development of RSV vaccines and therapies. Methods: In the study, 30 respiratory specimens positive for RSV were randomly selected from children with acute lower respiratory infections (ALRI) in Beijing every year from 2012 to 2021 for F gene sequencing. Then, 300 F gene sequences and 508 uploaded to GenBank from China were subjected to phylogenetic analysis. Results: The results indicated the nucleotide identities were 95.4–100% among 446 sequences of RSV A, and 96.3–100% among 362 of RSV B. The most common variant loci were N80K (100.00%) and R213S (97.76%) for site Ø, and V384I/T (98.43%) for site I among sequences of RSV A, and M152I (100.00%), I185V (100.00%), and L172Q/H (94.48%) for site V, and R202Q (99.45%) for site Ø among sequences of RSV B. N276S appears in 95.29% sequences of RSV A, while S276N and N262 I/S appear in 1.38% and 0.55% sequences of RSV B, respectively. No variation was found in all sequences at the binding sites of 14N4 and motavizumab. Conclusions: There were cumulative variations of the RSV F gene, especially at some binding sites of antigenic sites.

Enterovirus C116 (EV-C116) is a new member of the enterovirus C group which is closely associated with several infectious diseases. Although sporadic studies have detected EV-C116 in clinical samples worldwide, there is currently limited information available. In this study, two EV-C-positive fecal specimens were detected in apparently healthy children, which harbored low abundance, through meta-transcriptome sequencing. Based on the prototypes of several EV-Cs, two lineages were observed. Lineage 1 included many types that could not cause EV-like cytopathic effect in cell culture. Three genogroups of EV-C116 were divided in the maximum likelihood tree, and the two strains in this study (XZ2 and XZ113) formed two different lineages, suggesting that EV-C116 still diffuses worldwide. Obvious inter-type recombination events were observed in the XZ2 strain, with CVA22 identified as a minor donor. However, another strain (XZ113) underwent different recombination situations, highlighting the importance of recombination in the formation of EV-Cs biodiversity. The EV-C116 strains could propagate in rhabdomyosarcoma cell cultures at low titer; however, EV-like cytopathic effects were not observed. HEp-2, L20B, VERO, and 293T cell lines did not provide an appropriate environment for EV-C116 growth. These results challenge the traditional recognition of the uncultured nature of EV-C116 strains and explain the difficulty of clinical detection.

Head-to-tail sequences have been reported in human bocavirus (HBoV) 1-4. To reveal their features and functions, HBoV DNA was screened among respiratory specimens from pediatric patients with an acute respiratory infection (ARI) between April 2020 and December 2022, followed by HBoV genotyping. Head-to-tail sequences were detected using nested PCR, TA cloning, and Sanger sequencing, and these findings were confirmed by mNGS and amplicon sequencing. The secondary structure was predicted using the Mfold web server. The results indicated that head-to-tail sequences were detected in 42 specimens through TA cloning from 351 specimens positive for HBoV1 DNA, yielding 92 sequences into 32 types and 2 categories. Additionally, head-to-tail sequences were detected in 16 specimens by amplicon sequencing, yielding 60 sequences categorized into 23 types. The 374nt type, detected in 13 specimens, contains variants 374a and 374b, which differ in the unpaired loop regions of the palindrome or complementary reverse sequences, implying a switch of template chains during the replication process. The mNGS results in three specimens confirmed the presence of circular genome in copies below 1%. In conclusion, head-to-tail sequences of HBoV1 were common in children with ARI and were highly diverse in length and sequences. The variants may be generated by the switch of the template chain in the rolling-circle replication model.

The aim of this study was to determine the global genetic diversity and transmission dynamics of coxsackievirus B4 (CVB4) and to propose future directions for disease surveillance. Next-generation sequencing was performed to obtain the complete genome sequence of CVB4, and the genetic diversity and transmission dynamics of CVB4 worldwide were analyzed using bioinformatics methods such as phylogenetic analysis, evolutionary dynamics, and phylogeographic analysis. Forty complete genomes of CVB4 were identified from asymptomatic infected individuals and hand, foot, and mouth disease (HFMD) patients. Frequent recombination between CVB4 and EV-B multiple serotypes in the 3Dpol region was found and formed 12 recombinant patterns (A-L). Among these, the CVB4 isolated from asymptomatic infected persons and HFMD patients belonged to lineages H and I, respectively. Transmission dynamics analysis based on the VP1 region revealed that CVB4 epidemics in countries outside China were dominated by the D genotype, whereas the E genotype was dominant in China, and both genotypes evolved at a rate of > 6.50 × 10−3 substitutions/site/year. CVB4 spreads through the population unseen, with the risk of disease outbreaks persisting as susceptible individuals accumulate. Our findings add to publicly available CVB4 genomic sequence data and deepen our understanding of CVB4 molecular epidemiology.

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.

柯萨奇病毒B组3型（Coxsackievirus B3,CVB3）是肠道病毒中流行较为广泛的血清型之一,在全球多个国家和地区曾报道儿童急性心肌炎、无菌性脑膜炎、手足口病等的暴发流行,严重威胁儿童健康和公共卫生安全。本研究对广东省2020年手足口病患者标本中分离到的8株CVB3进行基因特征和进化分析,结果显示分离到的8株CVB3 VP1区核苷酸序列相似性为98.2%～99.5%,与原型株Nancy的核苷酸序列相似性在77.9%～78.5%之间,与其他CVB3中国大陆流行株的核苷酸序列相似性为79.6%～82.2%。8株CVB3均为E基因型,为广东省首次报道。8株CVB3分离株在进化树上聚集,提示病毒发生了局部传播。全基因组序列分析提示2株广东CVB3分离株在非结构蛋白区有重组现象的发生。本研究为E基因型CVB3在我国的流行传播和疾病防控提供基础资料。