Genomic epidemiology of equine influenza virus in the United Kingdom

英国马流感病毒的基因组流行病学

• 批准号: BB/V002821/1
• 负责人: Pablo Murcia
• 金额: $ 50.56万
• 依托单位: University of Glasgow
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV002821%2F1
• 关键词: Genomic; epidemiology; equine; influenza; virus

The horse industry and its associated industries make a substantial contribution to the UK economy. Therefore, not only do equine infectious diseases pose a serious risk to horses, but also have the potential to significantly affect the National economy.Equine influenza (EI) is arguably the most important infectious disease of the horse (in economic terms). EI is endemic in the UK and many other countries around the world and is caused by equine influenza virus (EIV). As with other influenza viruses, EIV can acquire mutations in its genome and evade host immunity induced by vaccination. However, epidemiological information has shown that in the UK, EI affects mainly unvaccinated animals. Vaccination against EI is compulsory for competition horses.In 2019 the UK experienced one of the largest EI epidemics in history: over 200 outbreaks spread throughout all four Nations were reported. An important feature of this epidemic is that 26 of the outbreaks were reported among vaccinated horses. This led to a six-day closure of all horse competitions, causing significant economic losses. While the total losses incurred by the cancellation of equestrian events is currently unknown (but likely to have run into millions of pounds), the Horserace Betting Levy Board has confirmed that the betting levy alone (i.e. the tax raised on bets) that was lost was £1.5M over the 6 days. As the 2019 EIV epidemic was finally contained, we can use it to learn valuable insight to prevent and control future epidemics. Current advances in sequencing technologies allow us to characterise the entire EIV genome directly from a nasal swab obtained from a sick horse. In turn, virus genetic information, if linked with epidemiological data, can be used to track the spread of viral diseases in time and space.We propose to combine genetic information with epidemiological data to reconstruct the spread of EIV during the 2019 epidemic, identify the most likely origin of the epizootic virus, and determine the patterns of genetic change of EIV during the epidemic. To this end, we will sequence nearly 400 virus genomes, most of them from the 2019 UK epidemic, as well as viruses from other countries to put the epidemic in a global context. This is a joint project between the Centre for Virus Research (CVR) and the Animal Health Trust (AHT). The CVR is a National Centre for Virology and has extensive expertise in virus sequencing and sequence analyses. The AHT is the reference laboratory for EI and hosts Equiflunet, a UK-wide equine surveillance network specifically designed to monitor EI.Results from this project will help inform the design of improved intervention measures to prevent and control future EIV epidemics.

马产业及其相关产业为英国经济做出了巨大贡献。因此，马传染病不仅对马匹构成严重风险，而且有可能显著影响国民经济。马流感（EI）可以说是马最重要的传染病（从经济角度来看）。EI在英国和世界上许多其他国家流行，由马流感病毒（EIV）引起。与其他流感病毒一样，EIV可以在其基因组中获得突变并逃避疫苗接种诱导的宿主免疫。然而，流行病学信息表明，在英国，EI主要影响未接种疫苗的动物。2019年，英国经历了历史上最大的EI疫情之一：据报道，在所有四个国家中爆发了200多起疫情。这一流行病的一个重要特征是，26起疫情是在接种疫苗的马中报告的。这导致所有赛马比赛关闭六天，造成重大经济损失。虽然取消马术赛事所造成的总损失目前尚不清楚（但可能已经达到数百万英镑），但Horserace Betting Levy Board已经确认，仅博彩税（即对投注征收的税）在6天内就损失了150万英镑。随着2019年EIV疫情最终得到控制，我们可以利用它来学习预防和控制未来流行病的宝贵见解。目前测序技术的进步使我们能够直接从病马的鼻拭子中扩增整个EIV基因组。反过来，病毒遗传信息如果与流行病学数据联系起来，可以用于追踪病毒性疾病在时间和空间上的传播，我们建议将遗传信息与流行病学数据联合收割机结合，重建2019年疫情期间EIV的传播情况，确定兽疫病毒最可能的起源，并确定疫情期间EIV的基因变化模式。为此，我们将对近400个病毒基因组进行测序，其中大部分来自2019年英国疫情，以及来自其他国家的病毒，将疫情置于全球背景下。这是病毒研究中心（CVR）和动物健康信托基金（AHT）之间的一个联合项目。CVR是一个国家病毒学中心，在病毒测序和序列分析方面拥有广泛的专业知识。AHT是EI和主机Equiflunet的参考实验室，Equiflunet是一个专门用于监测EI的英国范围内的马监测网络。该项目的结果将有助于为改进干预措施的设计提供信息，以预防和控制未来的EIV流行。

项目成果

Equine flu after the jump.

• DOI: 10.1038/s41579-022-00688-y
• 发表时间: 2022-03-01
• 期刊: Nature reviews. Microbiology
• 作者: Hofer, Ursula

Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage.

甲型流感病毒宿主转移后的长期适应导致宿主内病毒适应性增强，这是由于复制率更高、呼吸道上皮内更广泛传播和组织损伤减少。

• DOI: 10.1371/journal.ppat.1010174
• 发表时间: 2021-12
• 期刊: PLoS pathogens
• 影响因子: 6.7
• 作者: Amat JAR;Patton V;Chauché C;Goldfarb D;Crispell J;Gu Q;Coburn AM;Gonzalez G;Mair D;Tong L;Martinez-Sobrido L;Marshall JF;Marchesi F;Murcia PR
• 通讯作者: Murcia PR

A Review on Equine Influenza from a Human Influenza Perspective.

• DOI: 10.3390/v14061312
• 发表时间: 2022-06-15
• 期刊: Viruses

Capturing variation in metagenomic assembly graphs with MetaCortex.

• DOI: 10.1093/bioinformatics/btad020
• 发表时间: 2023-01-01
• 期刊: Bioinformatics (Oxford, England)