Emerging recombination of the C2 sub-genotype of HFMD-associated CV-A4 is persistently and extensively circulating in China

Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting

Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.

An outbreak of a novel recombinant Coxsackievirus A4 in a kindergarten, Shandong Province, China, 2021

In 2021, twenty children exhibiting influenza-like illnesses were reported from a kindergarten in Shandong Province, China. Eleven genomes of Coxsackievirus A4 (CV-A4) were obtained from the pediatric cases, sharing <93% genome sequence identities with known CV-A4 strains. Further analyses suggested potential genetic recombination in the P3 region of the novel strains.

The Structure, Function, and Mechanisms of Action of Enterovirus Non-structural Protein 2C

Enteroviruses are a group of RNA viruses belonging to the family Picornaviridae. They include human enterovirus groups A, B, C, and D as well as non-human enteroviruses. Enterovirus infections can lead to hand, foot, and mouth disease and herpangina, whose clinical manifestations are often mild, although some strains can result in severe neurological complications such as encephalitis, myocarditis, meningitis, and poliomyelitis. To date, research on enterovirus non-structural proteins has mainly focused on the 2A and 3C proteases and 3D polymerase. However, another non-structural protein, 2C, is the most highly conserved protein, and plays a vital role in the enterovirus life cycle. There are relatively few studies on this protein. Previous studies have demonstrated that enterovirus 2C is involved in virus uncoating, host cell membrane rearrangements, RNA replication, encapsidation, morphogenesis, ATPase, helicase, and chaperoning activities. Despite ongoing research, little is known about the pathogenesis of enterovirus 2C proteins in viral replication or in the host innate immune system. In this review, we discuss and summarize the current understanding of the structure, function, and mechanism of the enterovirus 2C proteins, focusing on the key mutations and motifs involved in viral infection, replication, and immune regulation. We also focus on recent progress in research into the role of 2C proteins in regulating the pattern recognition receptors and type I interferon signaling pathway to facilitate viral replication. Given these functions and mechanisms, the potential application of the 2C proteins as a target for anti-viral drug development is also discussed. Future studies will focus on the determination of more crystal structures of enterovirus 2C proteins, which might provide more potential targets for anti-viral drug development against enterovirus infections.

Genomic epidemiology of coxsackievirus A16 in mainland of China, 2000-18

Hand, foot, and mouth disease (HFMD), which is a frequently reported and concerning disease worldwide, is a severe burden on societies globally, especially in the countries of East and Southeast Asia. Coxsackievirus A16 (CV-A16) is one of the most important causes of HFMD and a severe threat to human health, especially in children under 5 years of age. To investigate the epidemiological characteristics, spread dynamics, recombinant forms (RFs), and other features of CV-A16, we leveraged the continuous surveillance data of CV-A16-related HFMD cases collected over an 18-year period. With the advent of the EV-A71 vaccine since 2016, which targeted the EV-A71-related HFMD cases, EV-A71-related HFMD cases decreased dramatically, whereas the CV-A16-related HFMD cases showed an upward trend from 2017 to October 2019. The CV-A16 strains observed in this study were genetically related and widely distributed in the mainland of China. Our results show that three clusters (B1a-B1c) existed in the mainland of China and that the cluster of B1b dominates the diffusion of CV-A16 in China. We found that eastern China played a decisive role in seeding the diffusion of CV-A16 in China, with a more complex and variant transmission trend. Although EV-A71 vaccine was launched in China in 2016, it did not affect the genetic diversity of CV-A16, and its genetic diversity did not decline, which confirmed the epidemiological surveillance trend of CV-A16. Two discontinuous clusters (2000-13 and 2014-18) were observed in the full-length genome and arranged along the time gradient, which revealed the reason why the relative genetic diversity of CV-A16 increased and experienced more complex fluctuation model after 2014. In addition, the switch from RFs B (RF-B) and RF-C co-circulation to RF-D contributes to the prevalence of B1b cluster in China after 2008. The correlation between genotype and RFs partially explained the current prevalence of B1b. This study provides unprecedented full-length genomic sequences of CV-A16 in China, with a wider geographic distribution and a long-term time scale. The study presents valuable information about CV-A16, aimed at developing effective control strategies, as well as a call for a more robust surveillance system, especially in the Asia-Pacific region.

Molecular epidemiology and clinical characteristics of herpangina children in Beijing, China: a surveillance study

Background

Herpangina is a highly infectious disease, which is usually prevalent in preschool children.

Methods

This study analyzed the clinical and pathogenic characteristics of herpangina children to demonstrate the epidemiology of herpangina. Clinical manifestations, laboratory indicators and pharyngeal swabs were collected from children with herpangina who were monitored by Tongzhou Center for Disease Control and Prevention in Beijing, 2008. Utilizing pharyngeal swabs, virus extraction and amplification were performed for nucleotide identification and sequencing. The phylogenetic analysis was conducted based on all sequences amplified in this study and strains retrieved from GenBank.

Results

Among 190 children with herpangina, 69.0% (131/190) were positive for enterovirus. Eight genotypes were identified, mainly including CV-A6 (39/131), CV-A4 (25/131), CV-A10 (24/131). The phylogenetic analysis showed one CV-A6 strain of Tongzhou was imported from Japan. CV-A10 strains were clustered into five groups (A-E). The dominant cluster of CV-A10 was Group E6 between 2009 and 2013, and converted to Group E5 after 2013. CV-A6 was the predominant pathogen causing herpangina in Tongzhou in 2018, followed by CV-A4 and CV-A10.

Conclusions

The circulation of coxsackievirus had spatiotemporal cluster. In controlling the transmission of herpangina, the surveillance and reporting system should be enhanced.