Phylogenetics and phylogeographic characteristics of coxsackievirus A16 in hand foot and mouth disease and herpangina cases collected in Beijing, China from 2019 to 2021

Genotyping and phylogeographic dynamics of coxsackievirus A16

Coxsackievirus A16 (CV-A16) is one of the major pathogens of Hand, Foot and Mouth disease. Here, we analyzed 287 full-length genome sequences of CV-A16 found worldwide from 1994 to 2019 to see the genomic evolution characteristics. Full-length genome-based phylogenetic tree divided the viruses into five different genotypes, G-a to G-e. The CV-A16 strains circulating in China dominate G-a and G-c, but can also be found in other genotypes including G-b and G-e. Phylogeographic analysis showed a high diversity of CV-A16 distribution. In addition, recombination was shown to drive the genomic evolution of CV-A16 during past decades. However, the structural proteins still remain relative conserved while there is extensive genomic recombination. This study updates the phylogenetic and phylogeographic information of CV-A16 and provides insights into the genetic characteristics of CV-A16.

First detection of multiple cases related to CV-A16 strain of B1c clade in Beijing in 2022

Coxsackievirus A16 (CV-A16) is a significant etiologic agent of hand, foot, and mouth disease (HFMD) and herpangina (HA), with the capacity to progress to severe complications, including encephalitis, aseptic meningitis, acute flaccid paralysis, myocarditis, and other critical conditions. Beijing's epidemiological surveillance system, established in 2008, encompasses 29 hospitals and 16 district disease control centers. From 2019 to 2021, the circulation of CV-A16 was characterized by the co-circulation of B1a and B1b clades. Multiple cases of HFMD linked to clade B1c has not been reported in Beijing until 2022. This study enrolled 400 HFMD and 493 HA cases. Employing real-time RT-PCR, 368 enterovirus-positive cases were identified, with 180 selected for sequencing. CV-A16 was detected in 18.89% (34/180) of the cases, second only to CV-A6, identified in 63.33% (114/180). Full-length VP1 gene sequences were successfully amplified and sequenced in 22 cases, revealing the presence of clades B1a, B1b, and B1c in 14, 3, and 5 cases, respectively. A cluster of five B1c clade cases occurred between June 29 and July 17, 2022, within a 7-km diameter region in Shunyi District. Phylogenetic analysis of five complete VP1 gene sequences and two full-genome sequences revealed close clustering with the 2018 Indian strain (GenBank accession: MH780757.1) within the B1c India branch, with NCBI BLAST results showing over 98% similarity. Comparative sequence analysis identified three unique amino acid variations (P3S, V25A, and I235V). The 2022 Shunyi District HFMD cases represent the first instances of spatiotemporally correlated CV-A16 B1c clade infections in Beijing, underscoring the necessity for heightened surveillance of B1c clade CV-A16 in HFMD and HA in this region.

Epidemiological and etiological investigations of hand, foot, and mouth disease in Jiashan, northeastern Zhejiang Province, China, during 2016 to 2022

Background

Hand, foot, and mouth disease (HFMD) is a common infectious disease in children. Enterovirus A71 (EV71) and coxsackievirus A16 (CA16) have been identified as the predominant pathogens for several decades. In recent years, coxsackievirus A6 (CA6) and coxsackievirus A10 (CA10) have played increasingly important roles in a series of HFMD outbreaks. We performed a retrospective analysis of the epidemiology of HFMD and the spectrum of different viral serotypes, to elucidate the genetic and phylogenetic characteristics of the main serotypes in the Jiashan area during 2016 to 2022.

Methods

Descriptive epidemiological methods were used to analyze the time and population distribution of HFMD in Jiashan during 2016 to 2022 based on surveillance data. Molecular diagnostic methods were performed to identify the viral serotypes and etiological characteristics of HFMD. Phylogenetic analyses was based on VP1 region of CA16 and CA6.

Results

The average annual incidence rate of HFMD fluctuated from 2016 to 2022. Children aged 1-5 years accounted for 81.65% of cases and boys were more frequently affected than girls. Except when HFMD was affected by the COVID-19 epidemic in 2020 and 2022, epidemics usually peak in June to July, followed by a small secondary peak from October to December and a decline in February. Urban areas had a high average incidence and rural areas had the lowest. Among 560 sample collected in Jiashan, 472 (84.29%) were positive for enterovirus. The most frequently identified serotypes were CA6 (296, 52.86%), CA16 (102, 18.21%), EV71 (16, 2.86%), CA10 (14, 2.50%) and other enteroviruses (44, 7.86%). There were 71 and 142 VP1 sequences from CA16 and CA6, respectively. Substitution of N218D, A220L and V251I was detected in CA16 and may have been related to viral infectivity. Phylogenetic analysis showed that CA16 could be assigned to two genogroups, B1a and B1b, while all the CA6 sequences belonged to the D3a genogroup.

Conclusion

CA6 and CA16 were the two major serotypes of enteroviruses circulating in the Jiashan area during 2016 to 2022. Continuous and comprehensive surveillance for HFMD is needed to better understand and evaluate the prevalence and evolution of the associated pathogens.

Circulating trends of hand, foot, and mouth disease in Hubei Province, China: Impact from the COVID-19 pandemic

Objectives

This study was performed to investigate the effect of non-pharmaceutical interventions on hand, foot, and mouth disease in Hubei Province China during the coronavirus disease 2019 pandemic.

Methods

Data and samples were collected from the hand, foot, and mouth disease surveillance laboratory network in Hubei Province between 2018 and 2022. The samples were identified as Enterovirus A71, Coxsackievirus A6or Coxsackievirus A16 via real-time polymerase chain reaction. Representative Coxsackievirus A6 and Coxsackievirus A16 samples were sequenced and subjected to phylogenetic analyses.

Results

A noticeable 3-fold reduction in the number of hand, foot, and mouth disease cases was observed from 2019 to 2020. The age and sex distributions of patients with hand, foot, and mouth disease were approximately the same from 2018 to 2022. The proportion of Coxsackievirus A6 accounted for 86 % in 2020 and 75 % in 2021 for hand, foot, and mouth disease compared with 48 % in 2018, 53 % in 2019, and 29 % in 2022. The proportions of Coxsackievirus A16 in 2020 and 2021 were 2 % and 17 %, respectively, showing a sharp decline in 2018 (37.8 %) and 2019 (35 %). In 2022, Coxsackievirus A16 was the dominant serotype (46 %). Only slight differences were found in the VP1 sequences across the different years.

Conclusions

Our study confirmed that a series of non-pharmaceutical interventions during the coronavirus disease 2019 period reduced the transmission of enteroviruses and that long-term restrictions could significantly change the prevalence of enterovirus serotypes causing hand, foot, and mouth disease.