Hassan Ayah M, El-Mayet Fouad S, El-Habbaa Ayman S, Shahein Momtaz A, El Zowalaty Mohamed E, Hagag Naglaa M, Sharawi Saad S A
Genome Research Unit, Animal Health Research Institute, Agricultural Research Center, 12618 Giza, Egypt.
Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, 13736, Kaliobia, Egypt.
Virus Res. 2022 Apr 2;311:198651. doi: 10.1016/j.virusres.2021.198651. Epub 2021 Dec 5.
An outbreak of foot-and-mouth disease virus (FMDV) serotype SAT 2 occurred in Egypt in 2018, which affected cattle and water buffalo. Previous phylogenetic studies on FMDV circulating in Egypt have mainly focused on genomic regions encoding structural proteins which determine FMDV serotype. So far, none of these studies have analyzed the open reading frame (ORF) sequence of Egyptian SAT 2/Lib-12 lineage. The present study aimed to analyze and identify the ORF genome sequence of Lib-12 lineage which belongs to FMDV serotype SAT 2 topotype VII in Egypt. The protocol workflow was optimized and tested using a representative field isolate of FMDV/SAT 2/Lib-12 from a bovine tongue sample collected in 2018 from Ismailia governorate (SAT2/EGY/Ismailia/2018). The protocol was based on reverse transcription polymerase chain reaction with multiple overlapping primers, amplicons sequencing, and assembly to complete the ORF consensus sequence. Alignments of the sequence fragments formed consensus genome sequence of 7219 nucleotides in length. The complete nucleotide sequence of the Egyptian isolate was related to Ethiopian, Nigerian, and Ghanaian strains, with identity not exceeding 95%. The divergence in the genetic identity of the Egyptian SAT 2/Lib-12 lineage from other Egyptian strains and Libyan isolates was 7%, and this may be attributed to the absence of the Lib-12 lineage ORF sequence from Egypt and Libya in the database. The present study significantly advances knowledge of the molecular analysis of FMDV SAT 2 and the design of vaccine selection for FMDV SAT 2 in Egypt. The study protocol could be applied to other FMDV serotypes.
2018年埃及爆发了口蹄疫病毒（FMDV）SAT 2血清型疫情，疫情影响了牛和水牛。此前对埃及流行的FMDV进行的系统发育研究主要集中在编码决定FMDV血清型的结构蛋白的基因组区域。到目前为止，这些研究均未分析埃及SAT 2/Lib-12谱系的开放阅读框（ORF）序列。本研究旨在分析和鉴定属于埃及FMDV血清型SAT 2 VII型的Lib-12谱系的ORF基因组序列。使用2018年从伊斯梅利亚省采集的一份牛舌样本中分离得到的具有代表性的FMDV/SAT 2/Lib-12田间毒株，对实验方案流程进行了优化和测试（SAT2/EGY/Ismailia/2018）。该方案基于逆转录聚合酶链反应，使用多个重叠引物、扩增子测序和组装来完成ORF共有序列。序列片段比对形成了长度为7219个核苷酸的共有基因组序列。埃及分离株的完整核苷酸序列与埃塞俄比亚、尼日利亚和加纳的毒株相关，同一性不超过95%。埃及SAT 2/Lib-12谱系与其他埃及毒株和利比亚分离株在遗传同一性上的差异为7%，这可能归因于数据库中缺少埃及和利比亚的Lib-12谱系ORF序列。本研究显著推进了对FMDV SAT 2分子分析的认识以及埃及FMDV SAT 2疫苗选择的设计。该研究方案可应用于其他FMDV血清型。
