دورية أكاديمية

Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic

التفاصيل البيبلوغرافية
العنوان: Phylogenetic lineage dynamics of global parainfluenza virus type 3 post-COVID-19 pandemic
المؤلفون: Kihyun Lee, Kuenyoul Park, Heungsup Sung, Mi-Na Kim
المصدر: mSphere, Vol 9, Iss 4 (2024)
بيانات النشر: American Society for Microbiology, 2024.
سنة النشر: 2024
المجموعة: LCC:Microbiology
مصطلحات موضوعية: parainfluenza virus, molecular epidemiology, COVID-19, Microbiology, QR1-502
الوصف: ABSTRACTDuring the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of parainfluenza virus type 3 (PIV-3) decreased due to infection control measures. However, a post-pandemic resurgence of PIV-3 has recently been observed. Nonetheless, the role of viral genetic epidemiology, possibly influenced by a genetic bottleneck effect, remains unexplored. We investigated the phylogenetic structure of the publicly available PIV-3 whole-genome and hemagglutinin-neuraminidase (HN) gene sequences spanning the last 65 years, including the COVID-19 pandemic. Sequences were retrieved from the nucleotide database of the National Center for Biotechnology Information using the search term “Human respirovirus 3.” Sequence subsets covering all six genes of PIV-3 or the HN gene were designated as the whole-genome and HN surveillance data sets, respectively. Using these data sets, we constructed maximum-likelihood phylogenetic trees and performed a time-scaled analysis using a Bayesian SkyGrid coalescent prior. A total of 455 whole-genome and 1,139 HN gene sequences were extracted, revealing 10 and 11 distinct lineages, respectively, with >98% concurrence in lineage assignments. During the 2020 COVID-19 pandemic, only three single-lineage clusters were identified in Japan, Korea, and the USA. The inferred year of origin for PIV-3 was 1938 (1903–1963) for the whole-genome data set and 1955 (1930–1963) for the HN gene data set. Our study suggests that PIV-3 epidemics in the post-COVID era are likely influenced by a pandemic-driven bottleneck phenomenon and supports previous hypotheses suggesting s that PIV-3 originated during the early half of the 20th century.IMPORTANCEUsing publicly available parainfluenza virus type 3 (PIV-3) whole-genome sequences, we estimated that PIV-3 originated during the 1930s, consistent with previous hypotheses. Lineage typing and time-scaled phylogenetic analysis revealed that PIV-3 experienced a bottleneck phenomenon in Korea and the USA during the coronavirus disease 2019 pandemic. We identified the conservative hemagglutinin-neuraminidase gene as a viable alternative marker in long-term epidemiological studies of PIV-3 when whole-genome analysis is limited.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 2379-5042
العلاقة: https://doaj.org/toc/2379-5042Test
DOI: 10.1128/msphere.00624-23
الوصول الحر: https://doaj.org/article/e65dbd9711374ddfb06af339d6de6ed3Test
رقم الانضمام: edsdoj.65dbd9711374ddfb06af339d6de6ed3
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:23795042
DOI:10.1128/msphere.00624-23