Molecular characterization and phylogenetic analysis of porcine circovirus 2 from Kerala, India.

Porcine circovirus type 2 (PCV2), the causative agent of porcine circovirus-associated diseases (PCVADs), has a worldwide distribution, and is considered as one of the most important emerging viral pathogens of economic importance. In Kerala, a total of 62 tissue samples were collected during post mortem from pigs suspected to have died of PCV2 infection. The animals exhibited symptoms like respiratory illness, gradual wasting, rough hair coat, polypnoea, dyspnoea, pallor, diarrhoea, icterus, etc. PCV2 was detected in 36 (58.06%) samples by PCR. Phylogenetic analyses of complete ORF2, and complete genome sequences were carried out and genotypes 2d, 2 h and 2b were detected. The genotype predominant in Kerala was 2d. It was observed that genotypes 2 h and 2b have been recently introduced into North Kerala as it was not detected in the region prior to 2016. Close relationship of Kerala sequences with sequences from Tamil Nadu, Uttar Pradesh and Mizoram were noticed in the phylogenetic tree and also at the amino acid level. A unique K243N mutation was observed in one of the samples. It was also noticed that the most variable amino acid position in ORF2 was 169 where the occurrence of three possible amino acids were observed. The results of the study indicate that multiple genotypes of PCV2 are prevalent in pigs in Kerala and that the percent positivity is higher than that recorded in the State previously. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-023-00814-1.

Detection of Newcastle disease virus and assessment of associated relative risk in backyard and commercial poultry in Kerala, India.

BACKGROUND: Newcastle disease (ND) is an economically important viral disease affecting the poultry industry. In Kerala, a state in South India, incidences of ND in commercial and backyard poultry have been reported. But a systematic statewide study on the prevalence of the disease has not been carried out. OBJECTIVES: A cross-sectional survey was performed to detect the presence of Newcastle disease virus (NDV) in suspect cases and among apparently healthy commercial flocks and backyard poultry, in the state and to identify risk factors for NDV infection. METHODS: Real-time reverse transcription-PCR (RT-PCR) was used to detect the M gene of NDV in choanal swabs and tissue samples collected from live and dead birds, respectively and the results were statistically analysed. RESULTS: The predominant clinical signs of the examined birds included mild respiratory signs, huddling together and greenish diarrhoea. Nervous signs in the form of torticollis were noticed in birds in some of the affected flocks. On necropsy, many birds had haemorrhages in the proventriculus and caecal tonsils which were suggestive of ND. Of the 2079 samples tested, 167 (8.0%) were positive for the NDV M-gene by RT-PCR. Among 893 samples collected from diseased flocks, 129 (14.5%), were positive for M gene with pairwise relative risk (RR) of 15.6 as compared to apparently healthy flocks where 6 out of 650 (0.9%) samples were positive. All positive samples were from poultry; none of the ducks, pigeons, turkey and wild birds were positive. Commercial broilers were at higher risk of infection than commercial layers (RR: 4.5) and backyard poultry (RR: 4.9). Similarly, birds reared under intensive housing conditions were at a higher risk of being infected as compared to those reared under semi-intensive (RR: 6.7) or backyard housing (RR: 2.1). Multivariable analysis indicated that significantly higher risk of infection exists during migratory season and during ND outbreaks occurring nearby. Further, lower risk was observed with flock vaccination and backyard or semi-intensive housing when compared to intensive housing. When the M gene positive samples were tested by RT-PCR to determine whether the detected NDV were mesogenic/velogenic, 7 (4.2%) were positive. CONCLUSIONS: In Kerala, NDV is endemic in poultry with birds reared commercially under intensive rearing systems being affected the most. The outcome of this study also provides a link between epidemiologic knowledge and the development of successful disease control measures. Statistical analysis suggests that wild bird migration season and presence of migratory birds influences the prevalence of the virus in the State. Further studies are needed to genotype and sub-genotype the detected viruses and to generate baseline data on the prevalence of NDV strains, design better detection strategies, and determine patterns of NDV transmission across domestic poultry and wild bird populations in Kerala.

Complete Genome Sequences of Newcastle Disease Virus Isolates from Backyard Chickens in Northern India.

The molecular characterization of three Newcastle disease viruses (NDV) isolated from backyard chickens in the state of Haryana, India, was undertaken. Two genotype II strains and one genotype XIIIc class II isolate with genome sizes of 15,186 and 15,192 nucleotides (nt), respectively, were identified.