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

Abstract 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.