Yadav Priya, Kumar Ankeet, Nath Sujith S, Devasurmutt Yashas, Shashidhar Geetha, Joshi Madhvi, Puvar Apurvasinh, Sharma Sonal, Raval Janvi, Pandit Rameshchandra, Chavda Priyank, Nagaraj Sudeep, Revanaiah Yogisharadhya, Patil Deepak, Raval S K, Raval Jigar, Kanani Amit, Thakar Falguni, Kumar Naveen, Reddy Gundallahalli Bayyappa Manjunatha, Joshi Chaitanya, Gulati Baldev Raj, Tatu Utpal
Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
Central Research Laboratory, KIMS, Bangalore, 560070, India.
BMC Genomics. 2024 Feb 19;25(1):196. doi: 10.1186/s12864-024-10061-3.
Lumpy skin disease virus (LSDV) belongs to the genus Capripoxvirus and family Poxviridae. LSDV was endemic in most of Africa, the Middle East and Turkey, but since 2015, several outbreaks have been reported in other countries. In this study, we used whole genome sequencing approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations compared to the Reference Neethling strain sequence and the previous field strains. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. Thirty-eight genes have more than 2 variations per gene, and these genes belong to viral-core proteins, viral binding proteins, replication, and RNA polymerase proteins. We highlight the importance of several SNPs in various genes, which may play an essential role in the pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues.
结节性皮肤病病毒（LSDV）属于痘病毒科山羊痘病毒属。LSDV在非洲大部分地区、中东和土耳其呈地方流行性，但自2015年以来，其他国家也报告了几起疫情。在本研究中，我们使用全基因组测序方法来调查疫情的起源并了解该病毒的基因组概况。我们的研究表明，与参考尼斯林毒株序列和先前的田间毒株相比，2022年疫情的LSDV毒株表现出许多遗传变异。在22个基因组序列中总共发现了1819个变异，其中包括399个基因外突变、153个插入移码突变、234个缺失移码突变、271个单核苷酸多态性（SNP）和762个沉默SNP。38个基因每个基因有超过2个变异，这些基因属于病毒核心蛋白、病毒结合蛋白、复制蛋白和RNA聚合酶蛋白。我们强调了各种基因中几个SNP的重要性，它们可能在LSDV的发病机制中起重要作用。对LSDV的所有全基因组序列进行的系统发育分析表明，印度存在两种类型的变体。发现一组突变较少的变体更接近来自兰契的2019年LSDV毒株，而另一组与2015年俄罗斯以前的疫情聚集在一起。我们的研究强调了病毒疫情基因组特征的重要性，不仅要监测突变频率，还要在疫情持续时研究其在LSDV发病机制中的作用。
