Molecular characterization of lumpy skin disease virus (LSDV) emerged in Bangladesh reveals unique genetic features compared to contemporary field strains

Abstract

Background: Lumpy skin disease (LSD) is a contagious viral disease of cattle caused by lumpy skin disease virus (LSDV). LSD has recently spread in Asia following outbreaks in the Middle East and Europe. The disease emerged in Bangladesh in July 2019 in the Chattogram district, then rapidly spread throughout the entire country. We investigated six LSD outbreaks in Bangladesh to record the clinical signs and collect samples for diagnostic confirmation. Furthermore, we performed the molecular characterization of Bangladesh isolates, analyzing the full RPO30 and GPCR genes and the partial EEV glycoprotein gene.

Results: Clinical observations revealed common LSD clinical signs in the affected cattle. PCR and real-time PCR, showed the presence of the LSDV genome in samples from all six districts. Phylogenetic analysis and detailed inspection of multiple sequence alignments revealed that Bangladesh isolates differ from common LSDV field isolates encountered in Africa, the Middle East, and Europe, as well as newly emerged LSDV variants in Russia and China. Instead, they were closely related to LSDV KSGP-0240, LSDV NI2490, and LSDV Kenya.

Conclusions: These results show the importance of continuous monitoring and characterization of circulating strains and the need to continually refine the strategies for differentiating vaccine strains from field viruses.

Keywords: Bangladesh; EEV glycoprotein; GPCR; Lumpy skin disease virus;Capripoxvirus;RPO30.

Fig. 1

Skin lesions characteristics of lumpy skin disease in 3 animals in Bangladesh. The generalized circumscribed active nodular skin lesions covering the entire body are visible. Source: own

Fig. 2

Map of Bangladesh showing the sample collection area. The map is an own creation using Arc GIS software version 13.2

Fig. 3

Agarose gel electrophoresis showing the 390 bp amplicon of P32 gene for selected samples of Bangladesh. Lane M: 100 bp DNA ladder, Lane 1–5: LSDV field samples, Lane PC: positive control, lane NC: negative control

Fig. 4

Maximum clade credibility (MCC) tree based on the complete RPO30 complete gene sequences of capripoxviruses. The posterior probabilities are plotted as respective nodes labels. LSDVs from Bangladesh are highlighted in red and reference sequences are represented with their accession numbers

Fig. 5

Maximum clade credibility (MCC) tree based on the complete GPCR gene sequences of Capripoxviruses, plotted together with multiple sequence alignment. Only the portion of the alignment between positions 80 and 120 is shown. The posterior probabilities are plotted as respective nodes labels. LSDVs from Bangladesh are highlighted in red and reference sequences are represented with their accession numbers

Fig. 6

Multiple sequence alignments of the partial nucleotide sequences of the of EEV glycoprotein gene. LSDVs from Bangladesh were aligned with representative LSDVs’ sequences retrieved from GenBank. A unique sequence signature of 27-nucleotide only in LSDV Neethling like viruses is highlighted in the box. Identical nucleotides are indicated with dots