Introduction
Hand, foot and mouth disease (HFMD) is a widespread infectious disease characterized by rashes on the hands, feet, mouth, and occasionally buttocks with or without fever. Children under 5 years of age are the most susceptible population. In the past few decades, HFMD has been reported worldwide. HFMD has a significant disease burden in China and attracted considerable attention. From 2009 to 2019, 21.97 million HFMD cases, resulting in 3,561 deaths, were reported to the national surveillance system in China [
1].
HFMD is caused by a human enterovirus, among which human enterovirus 71 (EV71), Coxsackievirus A16 (CVA16), and Coxsackievirus A6 (CVA6) were the most prevalent pathogens [
2]. Illness caused by CVA16 and CVA6 infection is usually mild, whereas EV71 is responsible for severe central nervous system complications and even death [
2].
According to the VP1 region, EV71 is classified into genotypes A, B, C, D, E, and F. Genotypes B and C are further divided into subgenotypes B1–B5 and C1–C5 [
3‐
5]. Since the first reported detection of EV71 in 1998, subgenotype C4 has been the predominant agent circulating in mainland China.
In recent years, the etiology surveillance system in Beijing, and some other provinces in China found that the positive proportion of EV71-associated HFMD decreased dramatically. This phenomenon has attracted considerable attention. However, limited studies were carried out to investigate the molecular epidemiology characteristics of EV71. In this study, we described the epidemiology features and pathogen spectrum of HFMD. We conducted genetic analyses to investigate the phylogenetic characteristics, geographic diffusion pathway, and phylodynamic features of EV71 strains in Beijing from 2009 to 2019.
Discussion
EV71 was the leading pathogen responsible for severe HFMD cases, especially death. During 2009–2019, EV71-associated HFMD decreased greatly in Beijing and in many other provinces and cities [
21]. For our consideration, there were two reasons for this declination. The first one was that the pathogen spectrum of HFMD has changed since 2013. Non-CVA16 non-EV71 EV became the major pathogen of HFMD, and EV71-associated HFMD decreased greatly, resulting in less severe cases and fatal cases. Beijing municipality began vaccinating children between 0.5 and 5 years with the EV71 vaccine (self-paid, not compulsory) in August 2016. By the end of 2018, almost 30% of children had received a two-dose vaccine (not published), which was proven highly effective in preventing children from infection [
22]. Many children under 5 years of age receiving this vaccine could have reduced the EV71 infection greatly.
Genomic characteristics of EV71 showed that each gene segment shared a high homology among the EV71 sequences in this study, which implied that EV71 prevalent in Beijing shared a common source. 3D region of enterovirus is more susceptible to recombination than any other part [
20]. ML phylogenetic trees based on EV71 3D region in Beijing showed that all the 3D sequences clustered together only with lineage I, which was regarded as the dominant type and has never been replaced in China [
23]. This result suggested that no recombination events happened in the 3D region from 2009 to 2019 in Beijing.
The relative genetic diversity of the EV71 VP1 sequences first increased and peaked in 2012, which corresponded with the high positive proportion of EV71-associated HFMD in Beijing. With the non-EV71, non-CVA16 EV became the dominant agent, and EV71 genetic diversity declined with fluctuations from 2013 to 2016. After the EV71 vaccine was introduced in China in 2016, genetic diversity declined again. We speculated that it was the vaccine inoculation that prevented children from infection and as a consequence, reduced genetic diversity.
Natural selection pressure analysis showed that the dN/dS value of VP1 and P1 from 2017 to 2019 was smaller than 2009–2016, which implied that both VP1 and P1 had evolved into a relatively stable condition marked by low dN/dS value. Two positive selection sites were obtained from both VP1 and P1 by MEME. VP1-145 is a surface-exposed residue that is located within the DE loop. It has been confirmed that VP1-145 influenced the use of attachment receptors and the three-dimensional structure of the whole virion [
24]. Although amino acid residue changed from Ala to Ser on the VP1-293 site has been reported previously [
25], further study must confirm whether this correlates with viral pathogenicity.
In this study, the phylogeographic results revealed east China being the primary source sink for the EV71 dispersion all over the country. This is consistent with Zhang’s result [
23]. East China is the frontier of reform and opening up and contains many well-developed large cities. They are characterized by frequent international exchanges, active population mobility, and humid and warm climate suitable for the virus survival, which contributes to forming the source of EV71 and plays an important role in disseminating EV71. While for Beijing, the capital of China, a huge migratory population traveling between Beijing and other provinces intensified the spread of the EV71. Therefore, strengthening surveillance of EV71 in Beijing and east China plays an important role in preventing and controlling EV71-associated HFMD.
The epidemic spread of EV71 displayed low Re estimates during the sampling period time, which was close to some previous research [
26,
27], suggesting that the introduction of effective prevention and control measures limited viral spread within the sampled populations. The average infectious period in this study agreed with a previous follow-up investigation [
28], in which the mild case group turned EV71 negative with a median shedding duration of 18 days, and some cases had a duration of shedding longer than 30 days.
There are limitations to this study. Owing to the severe impact on the surveillance system by the COVID-19 pandemic, the EV71 surveillance result from 2020 to 2022 was not included in this study, which could have provided more information about epidemic characteristics. Not enough EV71 sequences in Beijing or some regions in China of some years might bias the analysis result to a certain extent. Mainly analyzing of VP1 might not be able to clarify the overall epidemic characteristics of EV71, but still help us understand the epidemiological characteristics, phylogenetic features, and bayesian phylodynamics of EV71.
Conclusion
In conclusion, EV71 was not the major causative agent of HFMD in Beijing in recent years. EV71 prevalent in Beijing from 2009 to 2019, shared high homology in each gene, and were mainly transmitted from east China around 2003. Beijing played an important role in disseminating EV71 to central China. Low Re estimate of EV71 in Beijing implied strategies of prevention and control of HFMD were performed effectively in Beijing.
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