dc.description.abstract | Enteroviruses (EV) are single-stranded, positive-sense RNA viruses in the Enterovirus genus of the Picornaviridae family. All enteroviruses have a similar genomic organization (7.2–8.5kb). The capsid proteins are coded on the 5’end of the ssRNA in a section called P1 (precursor 1). The nonstructural proteins are coded on the remaining sections of the genome, which are called P2 and P3. Changes in the structural protein genes of different enterovirus species reflect phylogenetic relationships. EV cause various clinical manifestations, including cutaneous, visceral, and neurological diseases. The Enterovirus genus consists of 12 species, including Enterovirus A (EV-A, 25 serotypes), Enterovirus B (EV-B, 63 serotypes), Enterovirus C (EV-C, 23 serotypes), Enterovirus D (EV-D, 5 serotypes), Enterovirus E (EV-E, 4 serotypes), Enterovirus F (EV-F, 6 serotypes), Enterovirus G (EV-G, 11 serotypes), Enterovirus H (EV-H, 1 serotype), Enterovirus J (EV-J, 6 serotypes), Rhinovirus A (80 serotypes), Rhinovirus B (32 serotypes), and Rhinovirus C (55 serotypes)
Chapter Two indicated that we successfully established a NGS platform to conduct genome sequencing for the serologically-untypable enterovirus isolates. Among 130 serologically-untypable isolates, 121(93%) of them were classified into 29 serotypes using CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer)-based RT-PCR to amplify VP1 genes (VP1-CODEHOP). We further selected 52 samples for NGS and identified 59 genome sequences from 51 samples, including 8 samples containing two virus genomes. We also detected 23 genome variants (nucleotide identity <90% comparing with genome sequences in public domain) with potential genetic recombination, including 9 inter-serotype recombinants and 14 strains with unknown sources of recombination.
Chapter Three indicated that we retrospectively detected EV-D68 from a child with Wilson’s disease in 2008 in Taiwan. After comparing this EV-D68/Taiwan/2008 strain with EV-D68 genomes obtained from the public domain, it was classified as genome type 1-B; it is phylogenetically related to the predominant EV-D68 viruses that circulated in 2009 in Vietnam.
In conclusion, we successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses, which could not only improve enterovirus surveillance but also provide genome sequences for evolution research.
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