Proteomic analysis of differential expression of lung proteins in response to highly pathogenic avian influenza virus infection in chickens.

Elucidation of the molecular pathogenesis underlying virus-host interactions is important for the development of new diagnostic and therapeutic strategies against highly pathogenic avian influenza (HPAI) virus infection in chickens. However, the pathogenesis of HPAI virus in chickens is not completely understood. To identify the intracellular signaling pathways and critical host proteins associated with influenza pathogenesis, we analyzed the lung proteome of a chicken infected with HPAI H5N1 virus (A/duck/India/02CA10/2011/Agartala). Mass spectrometry data sets were searched against the chicken UniProt reference database. At the local false discovery rate level of 5%, a total of 3313 proteins with the presence of at least one unique peptide were identified in the chicken lung proteome datasets. Differential expression analysis of these proteins showed that 247 and 1754 proteins were downregulated at 12 h and 48 h postinfection, respectively. We observed expression of proteins of the predominant signaling pathways, including Toll-like receptors (TLRs), retinoic acid-inducible gene I-like receptors (RLRs), NOD-like receptors (NLRs), and JAK-STAT signaling. Activation of these pathways is associated with the cytokine storm effect and thus may be the cause of the severity of HPAI H5N1 infection in chickens. We also observed the expression of myeloid differentiation primary response protein (MyD88), inhibitor of nuclear factor kappa B kinase subunit beta (IKBKB), interleukin 1 receptor associated kinase 4 (IRAK4), RELA proto-oncogene NF-κB subunit (RELA), and mitochondrial antiviral signaling protein (MAVS), which are involved in critical signaling pathways, as well as other, less-commonly identified proteins such as hepatocyte nuclear factor 4 alpha (HNF4A), ELAV-like RNA binding protein 1 (ELAVL1), fibronectin 1 (FN1), COP9 signalosome subunit 5 (COPS5), cullin 1 (CUL1), breast cancer type 1 susceptibility protein (BRCA1), and the FYN proto-oncogene Src family tyrosine kinase (FYN) as main hub proteins that might play important roles in influenza pathogenesis in chickens. In summary, we identified the signaling pathways and the proteomic determinants associated with disease pathogenesis in chickens infected with HPAI H5N1 virus.

ESBL-producing Shiga-toxigenic E. coli (STEC) associated with piglet diarrhoea in India.

The present study was conducted to investigate the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli carrying other virulence genes associated with piglet diarrhoea. Faecal samples from the piglets with history of diarrhoea were processed for isolation of E. coli and were tested for their ability of ESBL production. ESBL encoding genes and other virulence genes were detected by specific PCR, and amplicons were sequenced. Ability of transferring the ESBL genes between the enteric bacteria was tested in in vitro HGT. A total of 170 E. coli was isolated, of which 43 (25.29 %) were confirmed as ESBL producer by double disc synergy test (DDST). Altogether, 6.47 and 2.94 % isolates were positive for bla TEM and bla CTX-M-15 genes, respectively, of which 2.35 % isolates were positive for both the genes and only 0.6 % isolate was positive for the bla CTX-M gene alone. The resistance traits could not be transferred to the recipient host. Based on PCR, 2 (1.18 %) and 1 (0.59 %) isolates were recorded as Shiga-toxin-producing E. coli (STEC) and enteropathogenic E. coli (EPEC), respectively. Both the STEC (one isolate positive for stx 2 and another positive for stx 2 and hlyA) isolates belonging to serogroup O2 and NT were also positive for the bla CTX-M-15 gene. This is the first report of ESBL-producing E. coli isolate possessing the STEC gene associated with piglet diarrhoea.

The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility.

Introduction: Highly pathogenic avian influenza (HPAI) viruses, such as H5N1, continue to pose a serious threat to animal agriculture, wildlife and to public health. Controlling and mitigating this disease in domestic birds requires a better understanding of what makes some species highly susceptible (such as turkey and chicken) while others are highly resistant (such as pigeon and goose). Susceptibility to H5N1 varies both with species and strain; for example, species that are tolerant of most H5N1 strains, such as crows and ducks, have shown high mortality to emerging strains in recent years. Therefore, in this study we aimed to examine and compare the response of these six species, to low pathogenic avian influenza (H9N2) and two strains of H5N1 with differing virulence (clade 2.2 and clade 2.3.2.1) to determine how susceptible and tolerant species respond to HPAI challenge. Methods: Birds were challenged in infection trials and samples (brain, ileum and lung) were collected at three time points post infection. The transcriptomic response of birds was examined using a comparative approach, revealing several important discoveries. Results: We found that susceptible birds had high viral loads and strong neuro-inflammatory response in the brain, which may explain the neurological symptoms and high mortality rates exhibited following H5N1 infection. We discovered differential regulation of genes associated with nerve function in the lung and ileum, with stronger differential regulation in resistant species. This has intriguing implications for the transmission of the virus to the central nervous system (CNS) and may also indicate neuro-immune involvement at the mucosal surfaces. Additionally, we identified delayed timing of the immune response in ducks and crows following infection with the more deadly H5N1 strain, which may account for the higher mortality in these species caused by this strain. Lastly, we identified candidate genes with potential roles in susceptibility/resistance which provide excellent targets for future research. Discussion: This study has helped elucidate the responses underlying susceptibility to H5N1 influenza in avian species, which will be critical in developing sustainable strategies for future control of HPAI in domestic poultry.

Corrigendum: The molecular basis of differential host responses to avian influenza viruses in avian species with differing susceptibility.

[This corrects the article DOI: 10.3389/fcimb.2023.1067993.].

Understanding the Demographic, Clinical, and Real-Time Polymerase Chain Reaction Profiles of COVID-19 Patients in a Tertiary Care Hospital in Northeast India.

Introduction and aims The demographic and clinical profile and dynamics of real-time polymerase chain reaction (RT-PCR) in coronavirus disease 2019 (COVID-19) patients are not well understood. The study aimed to analyze the demographic, clinical, and RT-PCR profiles of COVID-19 patients. Methodology The study was a retrospective, observational study conducted at a COVID-19 care facility, and the study period was from April 2020 to March 2021. Patients with laboratory-confirmed COVID-19 by real-time polymerase chain reaction (RT-PCR) were enrolled in the study. Patients with incomplete details or with only single PCR tests were excluded. Demographic and clinical details and the results of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR collected at different time points were retrieved from the records. The statistical software Minitab version 17.1.0 package (Minitab, LLC, State College, PA, USA) and Rstudio version 1.3.959 (Rstudio, Boston, MA, USA) were used for the statistical analysis. Results The mean duration from symptom onset to the last positive RT-PCR was 14.2 ± 4.2 days. The proportions of positive RT-PCR tests were 100%, 40.6%, 7.5%, and 0% at the end of the first, second, third, and fourth weeks of illness. The median duration of days to first negative RT-PCR in the asymptomatic patients was 8 ± 4 days, and 88.2% of asymptomatic patients were RT-PCR-negative within 14 days. A total of 16 symptomatic patients had prolonged positive test results even after three weeks of symptom onset. Older patients were associated with prolonged RT-PCR positivity. Conclusion This study revealed that the average period of RT-PCR positivity from the onset of symptoms is >2 weeks in symptomatic COVID-19 patients. Prolonged observation in the elderly population and repeat RT-PCR before discharge or discontinuation of quarantine is required.

Detection of coinfection of a divergent subgroup of genotype I Japanese encephalitis virus in multiple classical swine fever virus outbreaks in pigs of Assam, India.

A retrospective investigation of pig tissue samples from different classical swine fever virus (CSFV) outbreaks was undertaken employing RT-PCR for possible coinfection with other swine viruses. Four samples from three different outbreaks were found to be coinfected with Japanese encephalitis virus (JEV). Phylogenetic analysis was done based on complete E gene sequenced from all four coinfected samples. This revealed a new introduction of a divergent subgroup of JEV genotype I in India. This is the first report of detection of coinfection of JEV and CSFV in pigs and the first incidence of JEV genotype I in pigs in India.