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. 2024 Aug 19;16(8):1325.
doi: 10.3390/v16081325.

Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020-2021

Bhaveshan Reddy  1   2 , Andiswa Simane  2 , Hloniphile Mthiyane  1 , Bonolo Mashishi  1   2 , Nonhlanhla Mbenenge  1   2 , Florette K Treurnicht  1   2
Affiliations

Prevalence and Seasonal Patterns of 16 Common Viral Respiratory Pathogens during the COVID-19 Pandemic in Gauteng Province, South Africa, 2020-2021

Bhaveshan Reddy et al. Viruses. .

Abstract

Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The COVID-19 pandemic resulted in widespread morbidity and mortality, but generally, the diagnosis of other respiratory viruses was limited. This study aimed to assess the prevalence of other respiratory viruses during the 2020/2021 pandemic among patients of all ages who accessed care at public healthcare facilities in Gauteng Province, South Africa. Laboratory diagnosis for respiratory viruses, with or without SARS-CoV-2, was conducted via multiplex real-time polymerase chain reactions using respiratory specimens. A total of 1776 patients were included from 1 April 2020 to 31 March 2021, of which 766 (43.1%) were positive for respiratory viruses other than SARS-CoV-2. RV (368/1776; 20.7%) was the most prevalent, followed by RSV (304/1776; 17.1%), AdV (112/1776; 6.3%) and EV (105/1776; 5.9%). hCoV-OC43 (39/1776; 2.2%) was the most prevalent common coronavirus. SARS-CoV-2 co-infections were detected in 4.8% (24/500) of patients. Only 27.1% (482/1776) of patients were admitted to high-care or intensive care units. A decrease in respiratory virus detections was observed, except for RSV, EV and hCoV-OC43. RSV prevalence increased in 2021, while influenza A/B viruses remained undetected.

Keywords: COVID-19; SARS-CoV-2; prevalence; respiratory viruses; seasonal respiratory viruses.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Flow chart describing the total number of patients tested for RSV, influenza and other respiratory viruses via respiratory multiplex PCR (RVPCR) test and the proportion of respiratory virus-positive and -negative cases that were also tested for SARS-CoV-2.
Figure 2
Figure 2
Total number and percentage of all respiratory viruses detected according to age from April 2020 to March 2021, Johannesburg, South Africa. (a) Total number and percentage of respiratory viruses detected in all ages. (b) Total number and percentage of respiratory viruses detected in 0–2 years. (c) Total number and percentage of respiratory viruses detected in 3–5 years. (d) Total number and percentage of respiratory viruses detected in 6–18 years. (e) Total number and percentage of respiratory viruses detected in 19–64 years. (f) Total number and percentage of respiratory viruses detected in >65 years.
Figure 2
Figure 2
Total number and percentage of all respiratory viruses detected according to age from April 2020 to March 2021, Johannesburg, South Africa. (a) Total number and percentage of respiratory viruses detected in all ages. (b) Total number and percentage of respiratory viruses detected in 0–2 years. (c) Total number and percentage of respiratory viruses detected in 3–5 years. (d) Total number and percentage of respiratory viruses detected in 6–18 years. (e) Total number and percentage of respiratory viruses detected in 19–64 years. (f) Total number and percentage of respiratory viruses detected in >65 years.
Figure 3
Figure 3
Pattern of the seasonality of respiratory viruses from April 2020 to March 2021 in Johannesburg, South Africa. (a) Pattern of the seasonality of respiratory viruses in all ages. (b) Pattern of the seasonality of respiratory viruses in 0–2 years. (c) Pattern of the seasonality of respiratory viruses in 3–5 years. (d) Pattern of the seasonality of respiratory viruses in 6–18 years. (e) Pattern of the seasonality of respiratory viruses in 19–64 years. (f) Pattern of the seasonality of respiratory viruses in >65 years.
Figure 3
Figure 3
Pattern of the seasonality of respiratory viruses from April 2020 to March 2021 in Johannesburg, South Africa. (a) Pattern of the seasonality of respiratory viruses in all ages. (b) Pattern of the seasonality of respiratory viruses in 0–2 years. (c) Pattern of the seasonality of respiratory viruses in 3–5 years. (d) Pattern of the seasonality of respiratory viruses in 6–18 years. (e) Pattern of the seasonality of respiratory viruses in 19–64 years. (f) Pattern of the seasonality of respiratory viruses in >65 years.
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