Molecular typing of adenoviruses associated with respiratory illness among humans and poultry, Pakistan

Abstract Background Adenoviruses have caused epidemics among both humans and poultry in Pakistan. There is growing evidence that adenoviruses sometimes spillover to infect other species. In this pilot study, we sought to study the distribution of circulating adenovirus types among humans, poultry and other animals in several areas of Pakistan.Methods From February 2019 to March 2021, patients with influenza-like illness or pneumonia in seven hospitals near Islamabad were invited to participate in this study. Volunteers permitted the collection of an oropharyngeal or a nasopharyngeal swab and epidemiological data. Concomitantly, in Islamabad’s live bird markets and commercial or backyard farms, owners granted permission for oral or nasal swabs of their livestock with signs of respiratory illness to be studied. These specimens were screened with molecular assays for evidence of adenovirus infection.Results Among the 1705 samples collected, 96 (8.8%) of 1084 humans and 15 (4%) of 385 poultry had molecular evidence of adenovirus infection. The odds ratio (OR) of such molecular detections was greatest among participants with wheezing (OR = 10.9, 95% CI 6.0-19.7), coughing (OR = 3.3, 95% CI 1.8–5.8), fever (OR = 3.2, 95% CI1.8-5.7) or sore throat (OR = 3.2, 95% CI 1.8–5.6) compared to nasal congestion. Similarly, odds of positivity were greatest for participants from Sindh (OR = 6.4, 95% CI 2.3–18.0), Baluchistan (OR = 6.4, 95% CI2.3-18.0), Azad Jammu and Kashmir (OR = 4.8, 95% CI, 1.3–16.9), or Federal Capital regions (OR = 3.6, 95% CI, 1.4–9.6) compared to Punjab. Partial hexon gene sequencing identified co-circulation of HAdV-7 and HAdV-3 strains among humans. Further sequencing of adenoviral DNA polymerase identified HAdV-C1, HAdV-5, HAdV-89, HAdV-12, and HAdV-56. Notably, we detected molecular evidence of bovine adenovirus 2 in a sick human’s nasal swab. Additionally, FAdV-11 and FAdV-4 strains were identified among poultry swab specimens.Conclusion Compared to other studies, there was a relatively high prevalence of adenoviruses among sick humans and poultry, with the unusual discovery of molecular evidence of bovine adenovirus in a sick human’s airway. There was considerable diversity among detected adenovirus strains. As adenovirus epidemics have periodically occurred in Pakistan, assessing adenovirus prevalence and genotype distributions is prudent, especially among humans with respiratory illnesses.