Genetic characteristics of human parainfluenza viruses 1–4 associated with acute lower respiratory tract infection in Chinese children, during 2015–2021

Yun Zhu; Yun Sun; Changchong Li; Gen Lu; Rong Jin; Baoping Xu; Yunxiao Shang; Junhong Ai; Ran Wang; Yali Duan; Xiangpeng Chen; Zhengde Xie

doi:10.1128/spectrum.03432-23

Microbiology Spectrum (Oct 2024)

Genetic characteristics of human parainfluenza viruses 1–4 associated with acute lower respiratory tract infection in Chinese children, during 2015–2021

Yun Zhu,
Yun Sun,
Changchong Li,
Gen Lu,
Rong Jin,
Baoping Xu,
Yunxiao Shang,
Junhong Ai,
Ran Wang,
Yali Duan,
Xiangpeng Chen,
Zhengde Xie

Affiliations

Yun Zhu: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Yun Sun: The Division of General Pediatrics, Yinchuan Women and Children Healthcare Hospital, Yinchuan, China
Changchong Li: Department of Pediatric of Pulmonology, The 2nd Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
Gen Lu: The Respiratory Department, Guangzhou Women and Children’s Medical Center, Guangzhou, China
Rong Jin: The Respiratory Department, Guizhou Maternal and Child Health Care Hospital, Guiyang Children’s Hospital, Guiyang, China
Baoping Xu: Department of Respiratory Diseases I, Beijing Children’s Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Yunxiao Shang: The Division of Pediatric Respiratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
Junhong Ai: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Ran Wang: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Yali Duan: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Xiangpeng Chen: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
Zhengde Xie: Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China

DOI: https://doi.org/10.1128/spectrum.03432-23
Journal volume & issue: Vol. 12, no. 10

Abstract

Read online

ABSTRACT Human parainfluenza viruses (HPIVs) are a significant cause of acute lower respiratory tract infections (ALRTIs) among young children and elderly individuals worldwide. The four types of HPIVs (HPIV1–4) can cause recurrent infections and pose a significant economic burden on health care systems globally. However, owing to the limited availability of complete genome sequences, the genetic evolution of these viruses and the development of vaccines and antiviral treatments are hampered. To address this issue, this study utilized next-generation sequencing to obtain 156 complete genome sequences of HPIV1–4, which were isolated from hospitalized children with ALRTIs in six regions of China between 2015 and 2021. This study revealed multiple clades, lineages, or sublineages of HPIVs circulating in mainland China, with a novel clade D of HPIV1 identified as geographically restricted to China. Moreover, this study identified the endemic dominant genotype of HPIV3, lineage C3, which has widely spread and continuously circulated in China. Bioinformatic analysis of the genome sequences revealed that the proteins of HPIV3 possessed the most variable sites, with the P protein showing more diversity than the other proteins among all types of HPIVs. The HN proteins of HPIV1–3 are all under negative/purifying selection, and two amino acid substitutions in the HN proteins correspond to known mAb neutralizing sites in the two HPIV3 strains. These findings provide crucial insights into the genetic diversity and evolutionary dynamics of HPIVs circulating among children in China and may facilitate research on the molecular diagnosis, vaccine development, and surveillance of HPIVs.IMPORTANCEPhylogenetic analysis revealed the prevalence of multiple clades, lineages, or sublineages of human parainfluenza viruses (HPIVs) circulating in mainland China. Notably, a unique evolutionary branch of HPIV1 containing only Chinese strains was identified and designated clade D. Furthermore, in 2023, HPIV3 strains from Pakistan and Russia formed a new lineage within clade C, named C6. The first HPIV4b sequence obtained in this study from China belongs to lineage C2. Evolutionary rate assessments revealed that both the HN and whole-genome sequences of HPIV3 presented the lowest evolutionary rates compared with those of the other HPIV types, with rates of 6.98E−04 substitutions/site/year (95% HPD: 5.87E−04 to 8.25E−03) and 5.85E−04 substitutions/site/year (95% HPD: 5.12E−04 to 6.62E−04), respectively. Recombination analysis revealed a potential recombination event in the F gene of an HPIV1 strain in this study. Additionally, all the newly obtained HPIV1–3 strains exhibited negative selection pressure, and two mutations were identified in the HN protein of two HPIV3 strains at monoclonal antibody-binding sites.

Published in Microbiology Spectrum

ISSN: 2165-0497 (Online)
Publisher: American Society for Microbiology
Country of publisher: United States
LCC subjects: Science: Microbiology
Website: https://journals.asm.org/journal/spectrum

About the journal

Abstract

Keywords