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Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea

Authors
Kim, Ha NuiYoon, Soo-YoungLim, Chae SeungLee, Chang KyuYoon, Jung
Issue Date
Aug-2022
Publisher
Elsevier BV
Keywords
Human parainfluenza virus 3; Phylogenetic analysis; Emerging lineages
Citation
Journal of Clinical Virology, v.153
Indexed
SCIE
SCOPUS
Journal Title
Journal of Clinical Virology
Volume
153
URI
https://scholarworks.korea.ac.kr/kumedicine/handle/2021.sw.kumedicine/61127
DOI
10.1016/j.jcv.2022.105213
ISSN
1386-6532
Abstract
Background Human parainfluenza virus 3 (HPIV3) is a major respiratory pathogen that causes acute respiratory infections in infants and children. Since September 2021, an out-of-season HPIV3 rebound has been noted in Korea. The objective of this study was to analyze the molecular characteristics of the HPIV3 strains responsible for the outbreak in Seoul, South Korea. Methods A total of 61 HPIV3-positive nasopharyngeal swab specimens were collected between October and November 2021. Using 33 HPIV3-positive specimens, partial nucleotide sequences of the HPIV3 hemagglutinin-neuraminidase (HN) gene were aligned with previously published HN gene sequences for phylogenetic and genetic distance (p-distance) analyses. Results Phylogenetic tree revealed that all Seoul HPIV3 strains grouped within the phylogenetic subcluster C3. However, these strains formed a unique cluster that branched separately from the C3a lineage. This cluster showed 99% bootstrap support with a p-distance < 0.001. Genetic distances within the other C3 lineages ranged from 0.013 (C3a) to 0.023 (C3c). Deduced amino acid sequences of the HN gene revealed four protein substitutions in Seoul HPIV3 strains that have rarely been observed in other reference strains: A22T, K31N, G387S, and E514K. Conclusions Phylogenetic analysis of Seoul HPIV3 strains revealed that the strain belonged to a separate cluster within subcluster C3. Genetic distances among strains within subcluster C3 suggest the emergence of a new genetic lineage. The emergence of a new genetic lineage could pose a potential risk of a new epidemic. Further monitoring of the circulating HPIV3 strains is needed to understand the importance of newly discovered mutations.
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Lim, Chae Seung
Guro Hospital (Department of Laboratory Medicine, Guro Hospital)
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