Phylogenetic and sequence analysis of Lumpy skin disease virus circulating in some governorates of Egypt during 2019/2020.

Abstract

Between July 2019 and September 2020, cases of lumpy skin disease (LSD) were reported in Egypt. 15 skin nodule samples, one blood sample and one nasal swab sample were collected from clinically infected cattle from eight governorates in Egypt in addition to one skin scab sample was collected from sheep clinically suspected for sheep pox virus (SPV) from El-Menia governorate. Samples were examined by real time polymerase chain reaction (PCR) where they were positive for lumpy skin disease virus (LSDV) and the SPV sample was positive. Then four samples were isolated for three passages on chorio-allantoic membrane (CAM) of specific pathogen free eggs (SPF-ECEs) and confirmed by presence of pock lesion. Finally, partial gene sequencing was applied for three strains based on GPCR gene. The results showed that the strains belong to the LSDV group. Two of the strains were identical, while one was almost the same with a 99.78% identity. The three strains had 12 nucleotides deletion in return for the Indian field strains of the 2019 outbreak in India, (NI-2490/Kenya) and (KSGP O-240, Kenyavac, KS-1) from Kenya. One strain was partially sequenced for three genes (P32, ORF 95 and ORF 103) to identify it more, and only ORF 103 was partially sequenced for the SPV sample for comparison. The ORF 103 comparison between LSDV strain and SPV sample showed 97.17% identity and 13 nucleotides dissimilarities. Results consequently points to a close relationship between the study strains and the circulating LSDV in Egypt, Africa, and the Middle East.