Molecular characterisation of pigeon paramyxovirus and other viruses identified by deep sequencing in pigeons and doves in South Africa

Abstract

Pigeons, whether feral or bred for meat or sport like pigeon racing, are susceptible to a variety of diseases, many of which are caused by viral infections. Newcastle disease (ND) caused by Orthoavulavirus javaense, an avian paramyxovirus 1 (APMV1) virus is an example of a viral infection. Pigeon paramyxovirus (PPMV), a pigeon-specific variant of NDV that causes pigeon epidemics, is one of the most serious infectious illnesses within this host. The focus of the first part of the study was dedicated to investigating the molecular epidemiology of PPMVs in South Africa from 2012 onwards. A total of thirty-six field samples and isolated viruses were initially examined using real-time reverse transcriptase-polymerase chain reaction (RT-PCR) targeting a partial fragment of the M and F gene. Among these, it was observed that the kidneys from recent clinical cases exhibited the highest viral loads. Conventional RT-PCR, Sanger DNA sequencing, virus isolation in QH9/2-1 quail cells and Ion Torrent Next-Generation Sequencing (NGS) were applied, and the complete or partial genomes of twenty-one PPMVs were obtained for further analysis. Phylogenetic analysis grouped the recent South African viruses into subgenotypes VI.2.1.1.2.1 (VIj) and VI.2.1.1.2.2 (Vik). Based on a partial phylogenetic analysis of the fusion gene, these South African viruses displayed a close genetic relationship to PPMV strains sampled from pigeons in Switzerland and Belgium in 2005, 2007 and 2022. However, a phylogenetic analysis based on the complete fusion gene sequence revealed that the South Africa viruses were closely related to PPMV strains sampled from pigeons in Australia and Belgium in 2005, 2007 and 2011. South Africa PPMVs and other African PPMV strains included in a blast results analysis indicated no relatedness between each other, suggesting no intra-continental spread. The Ion Torrent reads obtained in the previous section were investigated further for the presence of other viruses by utilising a de novo assembly approach and BLAST analysis. Additional viruses detected included Autographacalifornica nucleopolyhedrovirus, Avian coronavirus (Pigeon coronavirus), Avian endogenous virus, Avian leukosis virus, Avian myeloblastosis virus, Avian orthoavula virus 1 (Pigeon v paramyxovirus), Avian sarcoma virus (Rous sarcoma virus), Bovine viral diarrhea virus, pigeon circovirus (PiCV), Human Gammaherpesvirus, Infectious bronchitis virus, porcine rotavirus, Semliki Forest virus, Tasmanian devil retrovirus, Torque teno virus (pigeon torque teno virus) and white spot syndrome virus. A phylogenetic analysis was performed with the three pigeon circovirus genomes discovered in a previous section through a metagenomic approach, plus eleven additional pigeon circovirus genome sequences previously detected during research at the University of Pretoria in recent years. The analysis of genotype classification yielded intriguing results, with 10 samples falling under the G genotype, two in the H genotype, and the final two in genotypes E and D, respectively. These samples displayed strong genetic association with PiCV strains obtained from pigeons in different countries, such as Belgium, Brazil, China, Germany, Italy, and Poland, from 2000 to 2021. This finding underscores the widespread distribution and genetic diversity of PiCV strains across international pigeon populations over the past two decades.