Molecular Epidemiology and Phylogenetic Analysis of Peste des Petits Ruminants Virus Circulating in Sheep in Bangladesh

Abstract

Peste des petits ruminants (PPR) is a viral disease of small ruminants that is highly contagious, severe, reportable, and economically important. The present study was conducted to detect the PPR virus (PPRV) circulating in sheep in Bangladesh to determine its association with epidemiological risk factors and the degree of relationship between the F and H genes of the PPRV of sheep with those of other sheep and goat isolates. A cross-sectional study was conducted in five selected districts of Bangladesh to collect data on locations, ecological zones, breeds, age, sex, sources, time period, and farming systems using a structured questionnaire accompanied by face-to-face interviews. During sampling, 250 nasal swab samples were collected from live sheep with the typical clinical signs of PPR. Thereafter, a reverse-transcriptase polymerase chain reaction (RT-PCR) assay was employed to detect PPRV using the F and H genes. Risk factors were determined using bivariable and multivariable logistic regression analyses. Phylogenetic analysis of the detected PPRV was performed using MEGA software after sequencing both F and H genes. Using RT-PCR, 35.6% (89/250, 95% CI: 29.6%–41.6%) of the samples were found to be positive for PPRV. Locations, breeds, sources, and feeding systems were identified as potential molecular epidemiological risk factors for PPRV infection in a multivariate logistic regression model. Nucleotide sequencing and phylogenetic analysis showed that the PPRV strain was genetically related to the lineage IV virus isolates. For the F gene, the sequence divergence of our gene and other selected genes ranged from 0.01% to 0.018% within lineage IV, and the similarity ranged from 98.2% to 99.0%. In the case of the H gene, similar results were also observed in divergence, ranging from 0.017% to 0.083% among lineage IV and others, and similarity varied from 91.7% to 98.3%. To the best of our knowledge, this is the first study in Bangladesh conducted to determine the RT-PCR-based molecular epidemiology of PPRV in sheep. This study highlights the importance of establishing successful interventions for managing PPRV infections in small ruminants in Bangladesh.