Molecular evolutionary #dynamics of #coxsackievirus A16 in #Shenzhen, #China, 2012–2022

 

Highlights

    • A decade of CV-A16 molecular epidemiology in Shenzhen was analyzed.

    • Bayesian methods estimated the molecular evolutionary rate of CV-A16.

    • Transmission risk and evolutionary dynamics of CV-A16 in Shenzhen were assessed.

Abstract

Objectives

To investigate the epidemiological and genetic characteristics of coxsackievirus A16 (CVA16) associated with hand, foot and mouth disease (HFMD) in Shenzhen, China.

Methods

CVA16 was examined by a real-time RT-PCR method. Complete VP1 gene sequences of CVA16 strains were determined, and sequence analyses were performed using a series of bioinformatics programs.

Results

Of 6436 mild HFMD specimens collected between 2012 and 2022, 1395 (21.7%) were CVA16-positive, with annual detection rates ranging from 4.1% to 45.4% and peaking in 2018. Molecular phylogenetic analysis revealed the circulation of three CVA16 sub-genotypes (B1a, B1b and B3) in Shenzhen, China. The major sub-genotype was B1b from 2013 to 2019, while the sub-genotype B1a predominated in 2020-2022. Phylogenetic and sequence homology analyses suggested that re-emerging CVA16 B1a strains in Shenzhen originated from Vietnam and Thailand. The mean evolutionary rate of CVA16 strains circulating in Shenzhen was estimated at 3.604×10-3 substitutions per site per year. Distinct amino acid mutations in VP1 correlated with temporal shifts in Shenzhen's dominant CVA16 sub-genotypes: N14S/L23M for B1b, and T164K/V251I for the 2017–2022 re-emergent B1a.

Conclusion

In the post-EV-A71 vaccine era, CVA16 remains one of the major pathogens of HFMD in Shenzhen. Over the study period, the CVA16 sub-genotype in Shenzhen underwent a B1a→B1b→B1a turnover, which was associated with both imported lineages and local adaptive evolution. This study underscores the critical importance of continuous molecular surveillance for CVA16.

Source: 

Link: https://doi.org/10.1016/j.jcv.2026.105998

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Return of the Biennial #Circulation of #Enterovirus D68 in #Colorado #Children in 2024 Following the Large 2022 #Outbreak

Abstract

Enterovirus D68 (EV-D68) caused large biennial cyclical outbreaks of respiratory disease and cases of acute flaccid myelitis from 2014 to 2018 in the USA. An anticipated outbreak did not occur in 2020, likely due to non-pharmaceutical interventions targeting the COVID-19 pandemic. A large respiratory disease outbreak occurred again in 2022, but uncertainty remained regarding if circulation of EV-D68 would return to the pre-pandemic patterns. We conducted prospective active surveillance of clinical respiratory specimens from Colorado children for EV-D68 in 2023 and 2024. A subset of residual specimens positive for rhinovirus/enterovirus (RV/EV) were tested for EV-D68 via a validated in-house EV-D68 reverse transcription–PCR assay. During epi weeks 18–44 in 2023, 525 residual specimens positive for RV/EV all tested negative for EV-D68. In 2024, during epi weeks 18–44, 10 (1.8%) of the 546 RV/EV-positive specimens were EV-D68-positive. The EV-D68-positive cases were predominantly young children (median age 4.8 years) receiving treatment with asthma medications. Following the 2022 EV-D68 outbreak, an anticipated outbreak did not occur in 2023. While EV-D68 was detected in 2024, the number of cases was not as significant as in prior outbreak years. Continued surveillance for EV-D68 will be important to understand the future dynamics of EV-D68 circulation and prepare for future outbreaks.

Source: Viruses, https://www.mdpi.com/1999-4915/17/5/673

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The Emergence of #Coxsackievirus A16 Subgenotype B1c: A Key Driver of the #HFMD #Epidemic in #Guangdong, #China

Abstract

Background: 

In 2024, mainland China witnessed a significant upsurge in Hand, Foot, and Mouth Disease (HFMD) cases. Coxsackievirus A16 (CVA16) is one of the primary causative agents of HFMD. Long-term monitoring of theCVA16 infection rate and genotype changes is crucial for the prevention and control of HFMD. 

Methods: 

A total of 40,673 clinical specimens were collected from suspected HFMD cases in Guangdong province from 2018 to 2024, including rectal swabs (n = 27,954), throat swabs (n = 6791), stool (n = 5923), cerebrospinal fluid (n = 3), and herpes fluid (n = 2). A total of 24,410 samples were detected as EV-positive and further typed by RT-PCR. A total of 872 CVA16-positive samples were isolated and further sequenced to obtain the full-length VP1 sequence. Phylogenetic analysis was performed based on viral protein 1 gene (VP1). 

Results: 

In the first 25 weeks of 2024, reported cases of HFMD were 1.36 times higher than the mean rates of 2023. In 2024, CVA16 predominated at 75.42%, contrasting with the past etiological pattern in which the CVA6 was predominant with the detection rate ranging from 32.85 to 77.61% from 2019 to 2023. Phylogenetic analysis based on the VP1 gene revealed that the B1a and B1b subtypes co-circulated in Guangdong from 2018 to 2022. The B1c outbreak clade, detected in Guangdong in 2023, constituted 68.24% of the 148 strains of CVA16 collected in 2024, suggesting a subtype shift in the CVA16 virus. There were three specific amino acid variations (P3S, I235V, and T240A) in the VP1 sequence of B1c. 

Conclusions: 

The new emergence of the CVA16 B1c outbreak clade in Guangdong during 2023–2024 highlights the necessity for the enhanced surveillance of the virus evolution epidemiological dynamic in this region. Furthermore, it is imperative to closely monitor the etiological pattern changes in Hand, Foot, and Mouth Disease (HFMD) in other regions as well. Such vigilance will be instrumental in guiding future vaccination strategies for HFMD.

Source: Viruses, https://www.mdpi.com/1999-4915/17/2/219

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