Genetic Characterization of Highly Similar H9N2 Viruses Isolated from Swine and Poultry in China.

Tianqi Hong¹ Wei Zhang¹ Chenlu Xia^2,3 Yuzhong Zhao^4,5

Affiliations 5 institutions

Jining Polytechnic, Jining, Shandong 272007, China.
College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, China
Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, Shandong 271018, China.
Jining Polytechnic, Jining, Shandong 272007, China
College of Veterinary Medicine, Shandong Agricultural University, Tai'an, Shandong 271018, China. Electronic address: [email protected].

PMID42849636 DOI10.1016/j.micpath.2026.108868 Year2026 Journal Microbial pathogenesis Microb Pathog Languageeng Publication statusActive

Active Last checked 2026-10-10 03:30:25 Source: NCBI PubMed

Abstract

H9N2 avian influenza viruses (AIVs) are widely distributed in poultry and have attracted continued attention because of their high reassortment potential and ability to cross species barriers. In March 2019, two H9N2 viruses were isolated from a pig and a chicken, respectively, in Shandong Province, China. In this study, we characterized the whole-genome features, phylogenetic relationships, molecular characteristics, and pathogenicity of the two viruses in mice. Whole-genome sequence analysis showed that the eight gene segments of the two isolates shared 99.9%-100% nucleotide sequence identity. Phylogenetic analysis showed that the two viruses had the same reassortant genomic composition, with the HA and NA genes related to the Y280-like lineage, the PB2 and M genes related to the G1-like lineage, and the PB1, PA, NP, and NS genes related to the SH/F98-like lineage. According to the historical H9N2 genotype nomenclature, both viruses were classified as G57 and were genetically closely related to H9N2 viruses previously detected in environmental samples in Jiangsu Province, China. Several amino acid substitutions previously associated with mammalian adaptation, receptor binding, viral replication, and antigenic variation were identified in both isolates; however, their biological effects were not experimentally evaluated in this study. In mice, both viruses replicated in the lungs and nasal turbinates and caused interstitial pneumonia, but neither virus caused significant body weight loss or death, and no virus was detected in the liver, spleen, kidney, or brain. Overall, the two H9N2 viruses isolated from a pig and a chicken showed highly similar whole-genome characteristics and shared several molecular features previously associated with mammalian adaptation. However, given the limited number of isolates and the lack of direct epidemiological and transmission evidence, the present study does not provide sufficient evidence to establish direct poultry-to-swine transmission, the direction of transmission, or sustained cross-species transmission.

Supporting text Virus Host Location

avian influenza virus 64 H9N2 29 mammalian adaptation 6 poultry 134 reassortment 40 swine 271

Evidence records

6 total

Zoonotic Surveillance

2 records · 1 evidence types

Evidence type Virus Isolation

2 records

OVE12333 Virus Isolation

Key finding

An H9N2 avian influenza virus was isolated from a pig in Shandong Province, China, in March 2019.

Virus

Host

Location

Supporting text

In March 2019, two H9N2 viruses were isolated from a pig and a chicken, respectively, in Shandong Province, China.

OVE12334 Virus Isolation

Key finding

An H9N2 avian influenza virus was isolated from a chicken in Shandong Province, China, in March 2019.

Virus

Host

Location

Supporting text

In March 2019, two H9N2 viruses were isolated from a pig and a chicken, respectively, in Shandong Province, China.

Experimental Infection

1 records · 1 evidence types

Evidence type Pathogenicity Experiment

1 records

OVE12338 Pathogenicity Experiment

Key finding

Two H9N2 viruses caused interstitial pneumonia and replicated in lungs and nasal turbinates of mice without significant weight loss or death and without detectable dissemination to other organs.

Virus

Host

Location

Supporting text

In mice, both viruses replicated in the lungs and nasal turbinates and caused interstitial pneumonia, but neither virus caused significant body weight loss or death, and no virus was detected in the liver, spleen, kidney, or brain.

Method: in vivo mouse infection | virus detection in organs | clinical observation of weight loss and mortality | histopathology (interstitial pneumonia)
Experimental system: mouse model

Functional Mechanism

1 records · 1 evidence types

Evidence type Molecular Adaptation

1 records

OVE12337 Molecular Adaptation

Key finding

Both H9N2 isolates carried amino acid substitutions previously linked to mammalian adaptation, receptor binding, viral replication, and antigenic variation.

Virus

Host

Location

Supporting text

Several amino acid substitutions previously associated with mammalian adaptation, receptor binding, viral replication, and antigenic variation were identified in both isolates; however, their biological effects were not experimentally evaluated in this study.

Mechanism types: host-range expansion | receptor binding | replication adaptation | immune escape

Genomic Evolution

2 records · 2 evidence types

Evidence type Recombination or Reassortment

1 records

OVE12335 Recombination or Reassortment

Key finding

Two H9N2 viruses shared an identical reassortant genome: HA/NA from Y280-like, PB2/M from G1-like, and PB1/PA/NP/NS from SH/F98-like lineages.

Virus

Host

Location

Supporting text

Phylogenetic analysis showed that the two viruses had the same reassortant genomic composition, with the HA and NA genes related to the Y280-like lineage, the PB2 and M genes related to the G1-like lineage, and the PB1, PA, NP, and NS genes related to the SH/F98-like lineage.

Event type: reassortment
Genes or segments: HA (Y280-like) | NA (Y280-like) | PB2 (G1-like) | M (G1-like) | PB1 (SH/F98-like) | PA (SH/F98-like) | NP (SH/F98-like) | NS (SH/F98-like)

Evidence type Phylogenetic Evolution

1 records

OVE12336 Phylogenetic Evolution

Key finding

Both H9N2 isolates were classified as genotype G57 and closely related to H9N2 viruses previously detected in environmental samples in Jiangsu Province.

Virus

Host

Location

Supporting text

In March 2019, two H9N2 viruses were isolated from a pig and a chicken, respectively, in Shandong Province, China. According to the historical H9N2 genotype nomenclature, both viruses were classified as G57 and were genetically closely related to H9N2 viruses previously detected in environmental samples in Jiangsu Province, China.