Respiratory viruses in rural Zambia before and during the COVID-19 pandemic

Abstract

Objectives: With the emergence of the COVID-19 pandemic, restrictions were implemented globally to control the virus. Data on respiratory pathogens in sub-Saharan Africa during the COVID-19 pandemic are scarce. This analysis was conducted to evaluate patterns of respiratory pathogens in rural Zambia before and during the first year of the pandemic.

Methods: Surveillance was established in December 2018 at Macha Hospital in southern Zambia. Patients with respiratory symptoms in the outpatient and inpatient clinics were recruited. Nasopharyngeal samples were collected and tested for respiratory pathogens. The prevalence of respiratory symptoms and pathogens was evaluated and compared in the first (December 10, 2018-December 9, 2019) and second (December 10, 2019-November 30, 2020) years of surveillance.

Results: Outpatient visits and admissions for respiratory illness significantly decreased from the first to second year, especially among children. SARS-CoV-2 was not detected from any participants in Year 2. Among outpatients and inpatients with respiratory symptoms, the prevalence of respiratory syncytial virus and influenza viruses decreased from the first to second year. In contrast, the prevalence of rhinovirus/enterovirus, metapneumovirus and parainfluenza virus increased.

Conclusions: The epidemiology of respiratory viruses in rural Zambia changed during the first year of the COVID-19 pandemic, suggesting that public health interventions may have had an impact on the introduction and circulation of respiratory pathogens in this area.

Keywords: Africa; COVID-19; influenza; respiratory syncytial virus; surveillance.

FIGURE 1

Respiratory illness among outpatients and inpatients in Macha, Zambia: December 2018–November 2020. (a) Weekly outpatient volume and proportion with influenza‐like illness. Grey shaded backgrounds delineate the introduction, duration and easing of COVID restrictions. R1 (March 18, 2020): Schools closed, mandatory masking in public, screening and isolation of travellers into Zambia, all airports outside of Lusaka closed to international flights, suspension of non‐essential travel outside of Zambia, restriction of public gathering, suspension of indoor dining, bars, nightclubs, cinemas, gyms, casinos closed. R2 (April 24, 2020): Resumption of congregation at places of worship, non‐contact sports and operation of salons and barbershops. R3 (May 8, 2020): Restaurants, cinemas, gyms and casinos reopened. Hotels, lodges, tour operators and other businesses that closed voluntarily advised to consider reopening. R4 (June 1, 2020): Primary and secondary schools reopened for examination classes only. June 8, 2020: colleges and universities began a phased reopening for final year students only. R5 (June 25, 2020): All international airports reopened. R6 (September 11, 2020): Reopening of all non‐examination classes in universities, colleges and schools. Partial reopening of bars, taverns and nightclubs. (b) Proportion of outpatients with influenza‐like illness (ILI) stratified by age. (c) Number of inpatient medical admissions and proportion admitted for acute respiratory infections (ARI). (d) Proportion of inpatients with a diagnosed acute respiratory illness at admission stratified by age. The red dashed line in all figures separates Year 1 (December 10, 2018–December 9, 2019) and Year 2 (December 10, 2019–November 30, 2020) of surveillance.

FIGURE 2

Prevalence of respiratory viruses among outpatients with ILI in Macha, Zambia from December 2018 to November 2020. Estimated prevalence of pathogens among outpatients with influenza‐like illness (ILI) from December 2018 to November 2020 for (a) influenza A virus, (b) influenza B virus, (c) respiratory syncytial virus (RSV), (d) rhinovirus/enterovirus, (e) parainfluenza virus, (f) human metapneumovirus, (g) non‐SARS‐CoV‐2 coronavirus, (h) adenovirus. Percentages for Year 1 (December 10, 2018–December 9, 2019) and Year 2 (December 10, 2019–November 30, 2020) represent estimated yearly pathogen prevalence overall among all outpatients with ILI. Lines represent estimated monthly prevalence, grey bands represent 95% confidence intervals. The vertical dashed line in all figures separates Year 1 and Year 2. The overall pathogen prevalence estimates for Year 1 differ from those previously published due to the different methodology used to account for sampling at recruitment and testing in this analysis.