Genetic characterization and evolution of emerging non-polio enteroviruses in Hong Kong

Abstract

Enteroviruses (EVs) are highly contagious and responsible for a spectrum of human diseases. EV outbreaks occur every year with occasional serious epidemics in Hong Kong and nearby areas in Asia. Recombinant strains of EV-A71, coxsackievirus A2 (CV-A2) and CV-A22 have been previously reported in Hong Kong. However, molecular typing of EVs other than EV-A71 is not routinely performed in most clinical or even public health laboratories, let alone analyses of the comprehensive circulating pattern, epidemiology, recombination, and evolution of different EVs. To understand the genetic diversity and evolution of enterovirus circulating, and potentially novel or emerging in Hong Kong, nasopharyngeal aspirates (NPAs) from hospitalized patients from 2010 to 2017 were subject to EV identifications by partial 5’UTR and VP1 sequencing. 2C and 3D genes were sequenced to detect any potential recombination. Interest strains were selected for genome and recombination analysis. EVs were identified in 101 (0.97%) NPAs, including 43 EV-A, 10 EV-B, 2 EV-C, and 46 EV-D. In this study, EV-D68 was the most frequently detected EVs, followed by CV-A6, and then CV-A4. EV-D68 infections peaked from late spring to summer. Phylogenetic analysis of VP1, 2C and 3D genes showed four distinct clades (A-D) while clades B and D were subdivided into B1-B3 and D1-D2, respectively. EV-D68 subclades B1, B3 and D1 have been circulating in Hong Kong since 2010. The subclade B3 might be originated from strains of subclade B1 and cause more severe diseases. The subclade D1 might cause severe infections in adults/elderlies with underlying co-morbidities. CV-A6 infections peaked during mid-summer and mid-autumn. Phylogenetic analysis of VP1 gene showed four distinct genotypes (A-D) while genotype D were subdivided into D1-D5. CV-A6 genotype D5 was mainly circulating in Hong Kong and mainland China. Four novel CV-A6 recombinant strains were discovered. HK459455/2013 belonged to CV-A6 recombination group RJ; HK458288/2015 and HK446377/2015 represented a novel group RL arisen from CV-A6/CV-A4; and HK463069/2015 represented a novel group RM arisen from CV-A6/EV-A71. Recombination breakpoints were commonly detected in 3D region. CV-A4 infections were found from late spring to summer. Analysis of VP1 gene suggested that a previously recognized genotype III should be subdivided into two distinct subgenotypes III and IV. Five novel CV-A4 recombinant strains were discovered. Genome analyses demonstrated that recombination of HK436180/2012 was arisen between CV-A4/CV-A6, HK436203/2012 was arisen from CV-A4, CV-A2 and undistinguished “donor”, while HK421778/2014, HK452775/2016, and HK458564/2016 were arisen between CV-A4/CV-A2. Recombination breakpoints were commonly detected in P2 region. Other non-polio EVs, including some novel recombinant strains of EV-B, are potentially emerging in Hong Kong. Commercial intravenous immunoglobulin can neutralize different EVs, suggesting it as a promising treatment for the infections of emerging and novel EV strains. In conclusion, EV-D68 and CV-A6 were the most frequently detected EVs circulating in Hong Kong while CV-A4 was potentially emerging. The novel/emerging strains of EV-D68 and CV-A6 might cause more severe diseases in our population. Commercial intravenous immunoglobulin is an effective early treatment for infections of emerging EVs and an optional therapy for novel recombinant strains.