Retrospective analysis of genetic diversity, clinical manifestations and risk factors, during outbreak of lumpy skin disease virus

Lumpy skin is a highly host-specific, contagious, transboundary, notifiable disease affecting cattle (Bos taurus and Bos indicus) and water buffalo (Bubalus bubalis), and also reported in some wild ruminants. The spread and reporting of Lumpy skin disease (LSD) in the past five years in disease-free countries, mainly in Pakistan, has highlighted the threat of its emergence and re-emergence in neighboring areas. Notably significant outbreaks of this disease have been reported in the neighboring countries of Pakistan during the last decades and are thought to be the reason for the first reported outbreak of LSD in Pakistan in the year 2021-22. This study targeted seven locations and collected samples and clinical data of LSD-suspected animals, focusing on clinical presentation, farm-level risk factors, and molecular characterization via PCR and subsequent phylogenetic relatedness of sequenced isolates. Out of the collected samples (n = 285), 117 cases were found positive for LSDV. The most frequent clinical signs included fever (83.7%), skin nodules (94.8%), emaciation (88.0%), and snoring (83.7%), all of which were statistically significant (p ≤ 0.05). Significant farm-level risk factors associated with LSDV positive cases included the use of shared water sources (64.9%), treatment by quack practitioners (79.4%), improper handling of manure (22.2%), and lack of disinfection (15.3%), with significant p-values ≤0.05. Molecular confirmation of LSDV was performed by PCR amplification of a 554-bp fragment of the RPO30 gene, a commonly used molecular marker for LSDV detection and characterization. The sequenced isolates showed close genetic similarity to strains reported from India, Bangladesh, and China, indicating a regional genetic relatedness among circulating LSDV strains. The study highlights that enhanced biosecurity, farmer education, vaccination, and veterinary guidance can prevent disease spread, improve livestock health, and reduce economic losses.