Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023

TL;DR

This study identifies common and novel respiratory viruses in Jilin, China, using sequencing to guide local health surveillance.

Contribution

The first documented detection of picobirnavirus in respiratory specimens from China.

Findings

Common respiratory pathogens included SARS-CoV-2, RSV B, and influenza B in both pediatric and adult populations.

A novel picobirnavirus was identified in adult sputum samples, closely related to human-associated strains.

Phylogenetic analyses showed high sequence similarity with epidemic strains from other regions of China.

Abstract

Respiratory viral infections impose a significant global health burden, necessitating continuous regional surveillance to understand pathogen circulation. This study aimed to characterize the spectrum of respiratory pathogens and identify potential causative agents in Jilin Province, northeast China, during 2023.

Using metagenomic next-generation sequencing, we analyzed 250 respiratory samples and 195 blood samples, sequencing of all samples yielded 399,256 viral reads. Bioinformatic and phylogenetic analyses were conducted to identify and characterize the detected viruses.

Severe acute respiratory syndrome coronavirus 2 (lineage BA.2), human respiratory syncytial virus B (lineage GB5.0.5a), and influenza B virus (lineage V1A.3a.2) were identified as common respiratory pathogens across both pediatric and adult populations. Influenza A virus (lineage 3C.2a1b.2a.2a.3a.1), rhinovirus (subtype C), human respiratory syncytial virus A (lineage GA2.3.5), human respiratory syncytial virus B (lineage GB5.0.5a), and human metapneumovirus (lineage A2c) were detected in pediatric or adult respiratory samples. Human Pegivirus (genotype 3) was detected exclusively in adult blood samples. Strikingly, a novel picobirnavirus was identified in adult sputum samples, sequence and structural analyses consistently indicate that this picobirnavirus is closely related to human-associated strains, exhibiting ≥70% amino acid identity and an RdRP structure nearly identical to that of picobirnaviruses previously identified in human upper respiratory swabs from Cambodia. This finding was validated by nested RT-PCR, representing the first documented detection of picobirnavirus in respiratory specimens from China. As most identified strains were first reported in northeast China, we also conducted comprehensive phylogenetic analyses of representative viruses, revealing high sequence similarity with epidemic strains from other regions of China.

These findings delineate the respiratory viruses of northeast China, providing data for region-specific surveillance to mitigate future public health risks.

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