Dataset Information

PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018.

ABSTRACT: This study applied a molecular-based method to detect parainfluenza virus 5 (PIV5) collected from 2016 to 2018 in nine provinces of Republic of Korea. We demonstrated that PIV5 was detectable in both serum and pooled organs at an average positive rate of 1.78% (99/5566). Among these, the complete genome sequence of 15,246 nucleotides was obtained for 12 field strains. Three out of the 12 strains had the lowest genetic identity (96.20-96.68%) among the 21 porcine PIV5 genomes collected in Germany, China, India, and Republic of Korea from 1998 to 2017. By analyzing a large collection of complete genome sequences of the structural protein-coding F and HN genes, this study proposed a classification of PIV5 into two lineages, 1 and 2, and identified that group 2.2.2 within sub-lineage 2.2 was substantially divergent. The evolution of two structural protein-coding genes was largely under purifying selection. A few codons (6/9 for the F gene, 7/8 for the HN gene) had elevated dN/dS values, which were loaded on internal branches and were predicted to be related to beneficial trait(s) of the virus.

SUBMITTER: Truong HT

PROVIDER: S-EPMC10384901 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018.

Truong Ha-Thai HT Nguyen Van-Giap VG Pham Le-Bich-Hang LB Huynh Thi-My-Le TM Lee Jasper J Hwang Su-Jin SJ Lee Jae-Myun JM Chung Hee-Chun HC

Veterinary sciences 20230625 7

This study applied a molecular-based method to detect parainfluenza virus 5 (PIV5) collected from 2016 to 2018 in nine provinces of Republic of Korea. We demonstrated that PIV5 was detectable in both serum and pooled organs at an average positive rate of 1.78% (99/5566). Among these, the complete genome sequence of 15,246 nucleotides was obtained for 12 field strains. Three out of the 12 strains had the lowest genetic identity (96.20-96.68%) among the 21 porcine PIV5 genomes collected in Germany ...[more]

PMID: 37505820

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Project description:BackgroundSince the onset of the coronavirus disease-2019 (COVID-19) pandemic, the prevalence of respiratory infectious diseases, particularly, the flu epidemic, has considerably decreased. The low detection rate and decreased number of specimens have hindered the implementation of the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS), a sentinel surveillance system. Most patients with influenza-like illness visit the COVID-19 screening clinic; therefore, the number of samples collected in sentinel surveillance has decreased by more than 50%. Thus, the Korea Disease Control and Prevention Agency supplemented sentinel surveillance with non-sentinel surveillance by private medical diagnostic centers. We report here a delayed and unprecedented high detection of human parainfluenza virus (hPIV) in the Republic of Korea during the COVID-19 pandemic through sentinel and non-sentinel surveillance. We also examined the causes and implications of the changes in prevalence of hPIV.l METHODS: We collected data for 56,984 and 257,217 samples obtained through sentinel and non-sentinel surveillance, respectively. Eight viruses were confirmed using real-time reverse transcription-polymerase chain reaction (PCR) or real-time PCR. Some specimens from the sentinel surveillance were used for genetic characterization of hPIV type 3.ResultsIn 2020, hPIV was rarely detected; however, it was detected in August 2021. The detection rate continued to increase considerably in September and reached over 70% in October, 2021. The detection rate of hPIV3 was significantly higher in infants and preschoolers aged 0-6 years in both sentinel and non-sentinel surveillance. Detection of hPIV was delayed in metropolitan areas compared to that in suburban regions. The hemagglutinin-neuraminidase sequences of hPIV3 generated in 2021 were not distinct from those detected prior to the COVID-19 pandemic.ConclusionsThe operation of non-sentinel and sentinel surveillance to monitor respiratory viruses could sensitively detect an unprecedented revival of hPIV in the Republic of Korea during the COVID-19 pandemic.

Dataset Information

PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018.

Publications

PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018.

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