Molecular characterization of a novel variant of infectious bronchitis virus from field outbreaks in backyard chicken population of North East India

Infectious bronchitis virus (IBV) causes considerable economic impacts on global poultry production. Since its emergence in early 1930, IBV continues to evolve and now exists in a wide range of antigenically and genetically distinct variants, that makes the prevention and the control of the disease both complex and challenging. Although IBV has been reported regularly from different corner of India, information about the molecular epidemiology of circulating strain in relation to clinical form of the disease is not available. We have studied the clinico-pathology and confirmed eight distinct field outbreaks of the disease from poultry population of Mizoram, India. The clinical disease in affected birds resulted sever pathological lesions involving respiratory, gastrointestinal, and urinary system together. The complete S1 nucleotide sequences and protein analyses have revealed a distinct variant of genotype I-IBV (GI), designated as GI-24 circulating in India. The S1 protein of the field strains displayed unique additional eighteen amino acids at C terminal end when compared with M41strain. Comparison of the S1 protein among all the 27 lineages of GI revealed five mutations that are exclusive to only the Indian strains. All the field strains have also possessed the amino acid mutations at highly variable region 2 (HVR2) of S1 receptor-binding domain (RBD) that are considered characteristic of nephropathogenic strains. The circulating GI-24 strains displayed potency for a wide range of tropism from respiratory epithelium to GIT and urinary system. This study provides insight on recently emerging IBV outbreaks in NER, India, which might be causing huge economic losses to the poultry farmers in the region.

Emergence of a novel genotype of class II New Castle Disease virus in North Eastern States of India

Outbreaks of New Castle Disease from three north eastern states of India were confirmed by clinico-pathological examination followed by reverse transcription-PCR detection of F gene of ND Virus (NDV). Irrespective of vaccination, the outbreaks resulted 90-100% mortality in the affected flocks. The analysis of fusion protein sequences from ten field isolates revealed them as the velogenic or highly virulent strain. Phylogenetic analyses based on the complete F gene nucleotide sequences of the isolates have characterized only one of the isolate (OK149201) in the genotype XIII.2.2. The rest of the nine isolates are depicted in a distinct monophyletic group with average nucleotide distances from the other 20 genotypes ranged from 10.90 - 20.70. The nine isolates were further divided into two sub branches with the bootstrap support value of 100% at the nodes that define the two subgroups with an average evolutionary nucleotide distance of 6.00between the isolates in the two subgroups. As per the recommendation put forth in recently updated unified phylogenetic classification system for NDV, our findings clearly indicates emergence of a novel genotype of class II NDV in the biodiversity hot spot region of NER, India. The isolates in the newly identified genotype is designated with next available Roman numerals XXII. Further, the two subgroups within the genotype are designated as XXII.1 and XXII.2.

Indian porcine reproductive and respiratory syndrome virus bears discontinuous deletion of 30 amino acids in nonstructural protein 2

Since its first outbreak in 2013, porcine reproductive and respiratory syndrome (PRRS) has established as an enzootic disease in pig population of Mizoram state, India. Our previous studies based on phylogenetic analysis of ORF5 and ORF7 gene sequences revealed close relationship of Indian PRRSV with the highly pathogenic variant of PRRSV (HP-PRRSV) of Chinese origin. Despite the control measures, second major outbreak of the disease was recorded in Aizawl district of Mizoram in 2015. The objective of the present study was to examine the origin of PRRSV isolates of 2015 outbreak, identification of deleted region in Nsp2 gene and determination of any genetic variation between 2013 and 2015 isolates of PRRSV. The outbreak was confirmed by the detection of PRRSV-specific antibodies in 57 out of 92 serum samples (61.96 %) and also by RT-PCR in 42 out of 42 necropsy samples (100 %). Nucleotide sequence analysis of Nsp2 coding region of Indian isolates and comparison with reference sequences revealed 90 nucleotides discontinuous deletion further establishes the closeness of Indian PRRSV to Chinese HP-PRRSV. Further, sequence and phylogenetic analysis of ORF5, ORF7 and Nsp2 genes of Indian PRRSV from both 2013 and 2015 revealed that the outbreaks were caused by two different strains of HP-PRRSV closely associated with the Chinese 10 HEB-3 isolate and 07QN isolates of Vietnam origin respectively. The present study confirms that the Indian PRRSV is a highly pathogenic variant of PRRSV and this study serves as the basis for developing practical and effective control measures against this disease.

Porcine reproductive and respiratory syndrome virus (PRRSV) from the first outbreak of India shows close relationship with the highly pathogenic variant of China

BACKGROUND

Porcine reproductive and respiratory syndrome (PRRS) is an economically important viral disease of pigs worldwide. India has reported the first outbreak of PRRS in the pig population of Mizoram state to the Office International des Epizooties on the 26 June 2013.

HYPOTHESIS/OBJECTIVES

The aim of the present study was to determine the genotype and origin of porcine reproductive and respiratory syndrome virus (PRRSV) from the first outbreak in the pig population of Mizoram state, India, in 2013.

ANIMALS AND METHODS

A total of 880 affected pigs from the outbreak were clinically examined, 51 animals were necropsied and tested by reverse transcription polymerase chain reaction (RT-PCR) to detect PRRSV and 148 serum samples were tested to detect PRRSV-specific antibodies. The full open reading frame 5 (ORF5) gene sequences from 12 and ORF7 gene sequences from three clinical cases were sequenced and analysed for genomic characterization, respectively.

RESULTS

The outbreak was confirmed by the detection of PRRSV-specific antibodies in 109 out of 148 serum samples (74%) and also by RT-PCR in 46 out of 51 necropsy samples (90%). Notably, ORF5 and ORF7 genes of Indian strain shares the same nucleotide positions i.e. 13,698-14,300 and 14,799-15,170, respectively, with the highly pathogenic (HP) strain of China and were grouped together in a phylogenetic tree.

CONCLUSIONS AND CLINICAL IMPORTANCE

Sequence and phylogenetic analysis of ORF5 and ORF7 confirmed that the Indian strain has a close link with the HP-PRRSV of China. The current study forms an essential step for better understanding of the epidemiology as well as the movement and spread of the disease in India.