Sequencing and In Silico Multi-aspect Analysis of S1 Glycoprotein in 793/B Serotype of Infectious Bronchitis Virus Isolated From Iran in 2003 and 2011

Infectious bronchitis (IB) is an acute, highly contagious, and economically important viral disease of chickens. The S1 subunit from Spike (S) protein plays the major role in protective immunity and is involved in the host-virus interactions, as well as infectious bronchitis virus (IBV) serotyping. Aim of the present study was multi-aspect analysis of the molecular and immunological features of 5' part belonging to the S1 glycoprotein sequence of Iranian 793/B IBV strain isolates. This might ideally help in characterization, prevention, and vaccine development. The tissue samples were prepared, followed by virus isolation, reverse transcription polymerase chain reaction and restriction fragment length polymorphism analysis. In addition, sequencing and registration of the sequences in the National Center for Biotechnology Information were performed. Moreover, 12 sequences were retrieved from Fars province, Iran. The next steps included evaluation of conservation/variability along the sequences, phylogenetic analysis, estimation of the average evolutionary divergence over all the sequence pairs, predicting the phosphorylation/N-glycosylation/palmitoylation sites, and the final analysis of antigenicity. The findings of alignment, entropy plot, and pairwise similarity analysis revealed 17 hypervariable regions. The isolates belonging to Tehran were clustered in phylogenetic tree, and the most similar isolates to them were ADW11182 and ADW11183. Location of some of the N-glycosylation/phosphorylation/palmitoylation points indicated that these sites were conserved among the isolates. Furthermore, the frequency of epitopes and their scores reflect the high immunogenicity of S1 protein in 793/B serotype. Analysis of the primary and secondary structures demonstrated that their parameters had variable values and were different regarding the number and location of α-helix, β-strand, and coils. According to our findings, the Iranian isolates of 793/B serotype change their molecular characteristics during time and in different geographical regions. These alterations might account for failure in prevention programs and differences in virulence and pathogenicity

Detection of Avian Influenza Virus of H9 Subtype in the Faeces of Experimentally and Naturally Infected Chickens by Reverse Transcription-Polymerase Chain Reaction

Avian Influenza (AI) is a viral, highly contagious disease of domestic and wild birds. In an avian diagnostic laboratory, it is essential to have methods for rapid detection of respiratory viruses. In the present study, cloacal swabs collected from chickens experimentally and naturally infected with mild pathogenicity AI virus subtype H9, used in a reverse transcription-polymerase chain reaction (RTPCR) assay for detection of AI. On cloacal swabs collected from experimentally infected chickens, AI virus was detected most frequently between days 3 and 7 post infection (p.i.) and the relative sensitivity, specificity, correlation rate, positive predictive value and negative predictive value of the RT-PCR compared to virus isolation (VI) assay were 84%, 80%, 82%, 83% and 81%, respectively. On pooled cloacal swabs collected from flocks suspected of AI, these results were 96%, 100%, 97%, 83% and 100%, respectively. The results proved that the RT-PCR assay could be a reliable and rapid alternative to VI assay for detection of AI virus subtype H9 in faecal specimens

Biodiversity and epidemic potential of Chiropteran coronaviruses (<i>Nidovirales: Coronaviridae</i>)

Aim. The aim of this review is a comprehensive analysis of current literature data on coronaviruses identified in bats.Discussion. Coronaviruses (Coronaviridae) constitute the most extensive family of viruses of the order Nidovirales. Coronaviruses have a wide range of hosts, including mammals (Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus) and birds (Deltacoronavirus, Gammacoronavirus), amphibians (Alphaletovirus) and are pathogens of respiratory, intestinal, cardiovascular. Until the beginning of this century, only etiological agents of mild and moderate respiratory diseases were known among pathogenic coronaviruses for humans. In the 21st century, new highly pathogenic coronaviruses were discovered that caused outbreaks of severe pneumonia with high mortality: the severe acute respiratory syndrome coronavirus (Severe acute respiratory syndrome‐related coronavirus, SARS‐CoV; 2002‐2003, southern provinces of China), the Middle East respiratory coronavirus Syndrome (Middle East respiratory syndrome‐related coronavirus, MERS‐CoV; 2012, western part of Saudi Arabia) and type 2 acute respiratory syndrome coronavirus (Severe acute respiratory syndrome‐related coronavirus 2, SARS‐CoV‐2; 2019 ‐..., the eastern part of central China). The natural reservoirs of SARS‐CoV, SARS‐CoV‐2 and MERS‐CoV are bats (Chiroptera). Coronaviruses circulating in bat populations are not only phylogenetically close to the currently known especially dangerous human viruses but probably have epidemic potential that can be realized in the future.Conclusion. This review presents current data on coronaviruses of bats: taxonomic status, spectrum of potential hosts, distribution. The ecological features of coronaviruses of bats are considered in the context of their epidemiological significance. The origin of pathogenic human coronaviruses is discussed