Title : Respiratory Virus Surveillance among Outpatients in Rural Zambia in 2021
Abstract:
Background: Respiratory infections are a major cause of morbidity and mortality globally but are relatively understudied in sub-Saharan Africa.To assess the diversity, prevalence and pathogen composition of circulating respiratory viruses amongst symptomatic outpatients in rural Zambia, we analyzed samples from an existing influenza-like illness (ILI), influenza virus (IV) and respiratory syncytial virus (RSV) surveillance program established in 2018 at Macha Hospital in Zambia.
Methods: Nasopharyngeal (NP) samples were collected year-round from outpatients with ILI and tested onsite for Influenza A and B viruses (IAV and IBV), RSV, and SARS-CoV-2 using Xpert Xpress SARS-CoV-2/Flu/RSV (Cepheid, Sunnyvale, CA). Samples were additionally tested for the presence of other respiratory viruses by ePlex RP 2.0 (Genmark Diagnostics, Carlsbad, CA) using a novel capture and concentration sample processing methodology.
Results: IAV was detected from March to December (overall prevalence: 9.4%), with a peak (36.7%) in June. IBV was detected from June to December (overall prevalence: 12.5%), with a peak (54.3%) in September. RSV was detected from January to April (overall prevalence: 18.7%), with a peak (66.0%) in February. SARS-CoV-2 was detected throughout the year (overall prevalence: 4.1%), with a peak (16.5%) in December. The overall Rhinovirus/enterovirus (Rhv/Ev) was detected throughout the year (overall prevalence: 23.6%), with multiple peaks in March, April and October. Parainfluenza (PiV) had an overall prevalence of 9.8% with a peak in July (27.1%). Adenovirus (AdV) had an overall prevalence of 6.6% with a peak in June (28.8%), while non-SARS-CoV-2 seasonal coronaviruses (CoV, 229E, HKU1, OC43, NL63) had an overall prevalence of 4.3% with a peak in November (23.8%). Lastly, metapneumovirus (hMpV) had an overall prevalence of 2.5% with a peak in November (10.1%). Among participants tested with ePlex, a virus was identified in 76.5% of samples, including 11.5% where ≥2 viruses were identified. The most common coinfections were Rhv/Ev with either AdV (20.7%) or PiV (20.7%).
Conclusion: We found a broad diversity of viruses in addition to those detected by routine surveillance (IVs, RSV, SARS-CoV-2) in this population. The burden of respiratory viruses in this population can be significant, and depending on the time of year, may be contributed by multiple organisms.
