Changes in prevalence and seasonality of pathogens identified in acute respiratory tract infections in hospitalised individuals in rural and urban settings in South Africa; 2018–2022

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Authors

Davids, Michaela
Johnstone, Siobhan
Mendes, Adriano
Brecht, Gadean
Avenant, Theunis Johannes
Du Plessis, Nicolette Marie
De Villiers, Maryke
Page, N.A. (Nicola)
Venter, Marietjie

Journal Title

Journal ISSN

Volume Title

Publisher

MDPI

Abstract

Severe acute respiratory tract infections (SARIs) has been well described in South Africa with seasonal patterns described for influenza and respiratory syncytial virus (RSV), while others occur year-round (rhinovirus and adenovirus). This prospective syndromic hospital-based surveillance study describes the prevalence and impact of public interventions on the seasonality of other respiratory pathogens during the coronavirus disease-19 (COVID-19) pandemic. This occurred from August 2018 to April 2022, with 2595 patients who met the SARS case definition and 442 controls, from three sentinel urban and rural hospital sites in South Africa. Naso/oro-pharyngeal (NP/OP) swabs were tested using the FastTrack Diagnostics® Respiratory pathogens 33 (RUO) kit. Descriptive statistics, odds ratios, and univariate/multivariate analyses were used. Rhinovirus (14.80%, 228/1540) and Streptococcus pneumoniae (28.50%, 439/1540) were most frequently detected in NP/OP swabs and in children <1 years old (35%, 648/1876). Among others, pathogens associated with SARI cases causing disease were influenza A&B, HRV, RSV, hCoV 229e, Haemophilus influenzae, Staphylococcus aureus, and Streptococcus pneumoniae. Pre-COVID-19, seasonal trends of these pathogens correlated with previous years, with RSV and influenza A seasons only resuming after the national lockdown (2021). It is evident that stringent lockdown conditions have severe impacts on the prevalence of respiratory tract infections.

Description

DATA AVAILABILITY STATEMENT : No new data were created.

Keywords

Severe acute respiratory illness (SARI), South Africa (SA), Influenza, Respiratory syncytial virus (RSV), Respiratory tract infections, Multiplex real-time PCR, Polymerase chain reaction (PCR), Hospitalised cases, Seasonality, COVID-19 pandemic, Coronavirus disease 2019 (COVID-19), South Africa (SA), SDG-03: Good health and well-being

Sustainable Development Goals

SDG-03:Good heatlh and well-being

Citation

Davids, M.; Johnstone, S.; Mendes, A.; Brecht, G.; Avenant, T.; du Plessis, N.; de Villiers, M.; Page, N.; Venter, M. Changes in Prevalence and Seasonality of Pathogens Identified in Acute Respiratory Tract Infections in Hospitalised Individuals in Rural and Urban Settings in South Africa; 2018–2022. Viruses 2024, 16, 404. https://doi.org/10.3390/v16030404.