31st International Dynamics & Evolution of Human Viruses

EVOLUTION AND TRANSMISSION DYNAMICS OF RESPIRATORY SYNCYTIAL VIRUS GROUP A IN THE PAKISTAN NEONATAL POPULATION DURING THE COVID-19 PANDEMIC

Not scheduled

20m

Squamish, BC, Canada

Poster Phylodynamics & phylogeography

Speaker

Dr Sana Tamim (Research Fellow, Fogarty International Centre, National Institute of Health, US)

Description

Background: In 2019, the National Influenza Centre at the National Institute of Health, Pakistan in collaboration with the World Health Organization implemented dedicated human respiratory syncytial virus (RSV) surveillance in children below the age of two years, which circulation overlaps with that of influenza and other respiratory viruses during the winter months.
Methods: Nasal swabs were collected weekly from five sentinel sites. In 2019-2022 seasons, RSV and influenza positivity were assessed through RT-PCR among patients with extended severe acute respiratory infection case definition. Type-specific primers were used to evaluate the fluctuation of groups A and B viruses. Multivariable logistic regression analysis was employed to investigate associations between patient demographic and clinical characteristics. A subset of sequenced samples was studied using phylodynamic modeling using the BEAST framework.
Results and Discussion: During the three years of study, 758 samples were collected. A total of 18.7 % (n=142) were positive for RSV, among which 93.6% (n=133) were positive for RSV-A and 6.3% (n=9) for RSV-B. The RSV positivity rate increased from 13% (17/130) in 2019-20 to 32.1% (64/199) in 2020-21. However, it decreased to 10.0% (13/129) in 2021-22 likely due to the preventive measures imposed for COVID-19. The statistical analysis showed RSV cases to have 1.76 times the odds of being admitted to the ICU than RSV negative patients (P = 0.04; 95% CI: 1.04 - 2.99). Phylodynamic modeling revealed that during this period five independent introductions occurred in 2017 and 2018 and three introductions in 2020, after which these viruses tended to persist for one year before replacement. TMRCA of the individual genes was estimated between 1968-1976.
Conclusion: The planned surveillance of RSV in concert with phylodynamic modeling is a valuable technique for predicting RSV diversity in subsequent seasons, while providing valuable insights for informed implementation of RSV vaccination and therapeutic efforts.