Molecular characterization of pathogenic 4/91-like and QX-like infectious bronchitis virus infecting commercial poultry farms in Indonesia

Abstract

Background and Aim: Existing data on the characteristics of infectious bronchitis virus (IBV) gathered throughout Indonesia have been recognized to indicate variants similar to globally distributed vaccine strains. Despite past and current intensive vaccination programs, IBV infections in the country's poultry industry have not been effectively controlled. Therefore, this study aimed to investigate the genotype of several isolates based on partial S1 gene sequences. In particular, the investigation is directed to focus on layer chickens in actively vaccinated farms indicating IBV symptoms. Materials and Methods: Samples were isolated from ten different layer chicken flocks experiencing respiratory problem, drops in egg production, and a "penguin-like" stance, which were collected from commercial poultry farms in Central Java and Yogyakarta regions, Indonesia, within the periods of 2012-2018. Fragment of the S1 gene of IBV sampled from actively vaccinated commercial poultry farms was amplified using primer 5'-aca tgg taa ttt ttc aga tgg-3' (forward) and 5'-cag att gct tac aac cac c-3' (reverse) with the length of polymerase chain reaction (PCR) product at 383 bp. The sequence of samples was then compared with the sequence of reference S1 gene nucleotides of IBV from NCBI GenBank database. The amino acid analysis and multiple alignment sequence were conducted using Mega X. Results: During necropsy, enlargement of the oviduct and swollen kidney were observed. Reverse transcription-PCR diagnosis of their 383 bp S1 gene showed that all samples were IBV positive. Phylogenetic analysis of the S1 gene discovered seven samples to be clustered as 4/91-like strains. Meanwhile, the remaining three samples were grouped in QX-like strain cluster. Conclusion: This study is a pioneering report providing molecular evidence of pathogenic QX-like and 4/91-like strains circulating in Indonesia. Findings discovered, in this study, strongly suggested the importance of improving protections by available IBV vaccines through updated circulating strain clusters. It is critical to ensure the delivery of an effective control measurement of and vaccination protocols against IBV infections in the country's commercial poultry industry in particular and worldwide in general.

Isolation and characterization of avian coronavirus from healthy Eclectus parrots (Eclectus roratus) from Indonesia

“…Wibowo et al [17] and Setiawaty et al [22] showed the presence of a circulating infectious 4/91 strain in Indonesia. Sequences obtained from Wibowo et al [17] were 4/91-like IBV originating from Indonesia in 2017 to 2018.…”

“…Wibowo et al [17] and Setiawaty et al [22] showed the presence of a circulating infectious 4/91 strain in Indonesia. Sequences obtained from Wibowo et al [17] were 4/91-like IBV originating from Indonesia in 2017 to 2018. These sequences were included in our phylogenetic analysis but appeared to be slightly different from our isolated virus in each of the nucleotides numbered: 55, 80, 98, 175, 211, 223, and 225.…”

“…The resulting nucleotide sequences were aligned and compared with the S1 gene available from GenBank. Nucleotides taken from GenBank were used for alignment and tree construction, including genes that represent each IBV lineage according to Valastro et al [16], Indonesian isolates from Wibowo et al [17], and LX4 (AY189157) and Israel variant 1 (AF0937940), to illustrate well-used QX and 4/91 variant sequences. The genes used in the analysis are listed in Table-2.…”

“…The study by Setiawaty et al [22] showed that the 4/91 gene recovered from an outbreak may show sequence homology to the live vaccine. The study by Wibowo et al [17] was conducted in East Java, while the study by Setiawaty et al [22] was conducted in West Java, which is in close proximity to the place that this research was conducted. This might explain why, in our study, we were able to isolate an IB-like virus that was close in homology to the IBV 4/91 strain.…”

“…This has mostly contributed to the widespread usage of vaccinations [16]. However, in Indonesia, vaccines commonly used in poultry are from the GI-1 lineage, which consists of Masstype IBV such as M41, H52, or H120 strains [17,22]. Information dating back to 1977 and 1985 states that at that time, circulating IBV in Indonesia was close to the IBV Massachusetts, IBV Connecticut, and Australian strains [23].…”