The Emergence of Novel Variants of the Porcine Epidemic Diarrhea Virus Spike Gene from 2011 to 2023

IF 3.5 2区农林科学 Q2 INFECTIOUS DISEASES

Transboundary and Emerging Diseases Pub Date : 2024-07-16 DOI:10.1155/2024/2876278

Lin Zhang, Jian-Bo Liu, Hui-Zhen Liu, Yue-Xiao Lian, Yao-Wei Huang, Feng Cong

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Abstract

The porcine epidemic diarrhea virus (PEDV) has caused severe economic losses in the pig industry. Since its discovery, the virus has spread in pig herds for more than 50 years. Many new features have been found in the PEDV spike genes. In this study, 123 representative S genes were used to analyze their characteristics across strains. Phylogenetic analysis revealed that PEDV can be divided into nine groups: G1a, G1b, G1c, G1d, G2a, G2b, G2c, G2d, and G3. In addition, 21 different lengths of the S gene were found. Analysis of the amino acid insertion and deletion sites revealed that most deletions and insertions occurred in the loops of the spike quaternary structure, primarily in the D0 and N-terminal domains (NTDs). According to the above results, PEDV has undergone considerable evolution, possibly under the immune pressure of vaccination. These results are highly important for understanding the current epidemic situation of PEDV.

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2011 年至 2023 年猪流行性腹泻病毒尖峰基因新变异的出现

猪流行性腹泻病毒（PEDV）给养猪业造成了严重的经济损失。自发现以来，该病毒已在猪群中传播了 50 多年。在 PEDV 穗状基因中发现了许多新特征。本研究使用了 123 个具有代表性的 S 基因来分析不同毒株的特征。系统发育分析表明，PEDV 可分为九个组：G1a、G1b、G1c、G1d、G2a、G2b、G2c、G2d 和 G3。此外，还发现了 21 种不同长度的 S 基因。对氨基酸插入和缺失位点的分析表明，大多数缺失和插入发生在尖峰四元结构的环路中，主要是在 D0 和 N 端结构域（NTD）中。根据上述结果，PEDV 经历了相当大的进化，可能是在疫苗接种的免疫压力下发生的。这些结果对于了解 PEDV 目前的流行状况非常重要。

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来源期刊

Transboundary and Emerging Diseases 农林科学-传染病学

CiteScore

8.90

自引率

9.30%

发文量

350

审稿时长

1 months

期刊介绍： Transboundary and Emerging Diseases brings together in one place the latest research on infectious diseases considered to hold the greatest economic threat to animals and humans worldwide. The journal provides a venue for global research on their diagnosis, prevention and management, and for papers on public health, pathogenesis, epidemiology, statistical modeling, diagnostics, biosecurity issues, genomics, vaccine development and rapid communication of new outbreaks. Papers should include timely research approaches using state-of-the-art technologies. The editors encourage papers adopting a science-based approach on socio-economic and environmental factors influencing the management of the bio-security threat posed by these diseases, including risk analysis and disease spread modeling. Preference will be given to communications focusing on novel science-based approaches to controlling transboundary and emerging diseases. The following topics are generally considered out-of-scope, but decisions are made on a case-by-case basis (for example, studies on cryptic wildlife populations, and those on potential species extinctions): Pathogen discovery: a common pathogen newly recognised in a specific country, or a new pathogen or genetic sequence for which there is little context about — or insights regarding — its emergence or spread. Prevalence estimation surveys and risk factor studies based on survey (rather than longitudinal) methodology, except when such studies are unique. Surveys of knowledge, attitudes and practices are within scope. Diagnostic test development if not accompanied by robust sensitivity and specificity estimation from field studies. Studies focused only on laboratory methods in which relevance to disease emergence and spread is not obvious or can not be inferred (“pure research” type studies). Narrative literature reviews which do not generate new knowledge. Systematic and scoping reviews, and meta-analyses are within scope.