猪流感病毒广东分离株遗传进化与致病性分析

Genetic evolution and pathogenicity of swine influenza viruses isolated from Guangdong Province

摘要:

【背景】 我国养猪业正面临猪流感病毒(swine influenza virus, SIV)的严峻挑战，流行毒株主要包括H1N1、H3N2和H1N2等，持续威胁养猪业的健康发展。【目的】 深入剖析广东地区猪流感病毒的流行毒株遗传进化特征，并对其致病性进行系统评估。【方法】 2021-2023年间，从广东省佛山、肇庆、清远、韶关等地级市的21个猪场采集疑似感染SIV的鼻拭子和肺脏病料样品共536份，其中45份样品经RT-qPCR测定为SIV阳性，采用犬肾上皮(Madin-Darby canine kidney, MDCK)细胞分离培养病毒，并进行全基因组测序分析。将所得序列与GenBank和GISAID收录的参考毒株序列进行比对，并构建进化树，揭示病毒的遗传进化特征。【结果】 本研究成功分离到4株SIV，其中2株EA H1N1亚型SIV (SWSG1/21, SWHRZ3/22)，其HA和NA基因源自EA分支，其他基因片段(PB2, PA, PB1, NP, M)源自Pdm/09分支，NS基因则源于TR H1N2分支。另分离到2株H1N2亚型重配毒株(SWLFT4/22, SWHH5/23)，其中SWLFT4/22由NA H1N2分支与Pdm/09 H1N1分支毒株重配而成，而SWHH5/23则涉及3个不同分支毒株的复杂重配。致病性试验结果表明，所有4株SIV均能导致小鼠死亡，尤其是SWSG1/21和SWLFT4/22表现出较强的致病性，死亡率高达100%。【结论】 本研究通过对广东地区猪群分离的4株SIV进行遗传进化和致病性分析，揭示了当地SIV复杂的基因重组背景及较强的致病性，为猪流感的防控策略制定提供了关键科学依据。

Abstract:

[Background] China's pig industry is facing severe challenges from swine influenza virus (SIV), and the epidemic strains mainly include H1N1, H3N2 and H1N2, which continue to threaten the healthy development of the pig industry. [Objective] The objective of this study was to analyze the genetic evolution characteristics and systematically evaluate the pathogenicity of the circulating strains of SIV in Guangdong Province. [Methods] From 2021 to 2023, a total of 536 nasal swabs and lung lesion samples suspected of SIV infection were collected from 21 pig farms in Foshan, Zhaoqing, Qingyuan, Shaoguan and other prefecture-level cities in Guangdong Province, of which 45 samples were tested positive for SIV by quantitative RT-qPCR. The virus strains were isolated by culture with MDCK cells and then whole genome sequencing was performed. The obtained sequences were compared with those of the reference strains in GenBank and GISAID, and a phylogenetic tree was constructed to reveal the genetic evolution characteristics of the virus. [Results] Two SIV strains (SWSG1/21 and SWHRZ3/22) of EA H1N1 subtype were isolated, with HA and NA genes derived from the EA clade, PB2, PA, PB1, NP, and M genes derived from the Pdm/09 clade, and the NS gene derived from the TR H1N2 clade. In addition, two H1N2 subtype reassortant strains (SWLFT4/22 and SWHH5/23) were isolated. SWLFT4/22 was reassorted from strains of the NA H1N2 clade and Pdm/09 H1N1 clade, while SWHH5/23 involved the complex reassortment of strains from three different clades. The results of the pathogenicity test showed that all the four strains of SIV caused death in mice. Particularly, SWSG1/21 and SWLFT4/22 showed strong pathogenicity, leading to a mortality rate of up to 100%. [Conclusion] We analyzed the genetic evolution and pathogenicity of four SIV strains isolated from pigs in Guangdong Province and revealed the complex genetic recombination background and strong pathogenicity of local SIV, which provided a scientific basis for the formulation of swine influenza prevention and control strategies.