Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Abstract

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Results: Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion: Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.

Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020–2021

“…As previously described, in Cameroon, HRSV detection peaked in December 2020 and June 2021 [35]. This temporal distribution of HRSV differs from other Cameroonian research studies reporting viruses other than SARS-CoV-2 [34,51], but it is consistent with that described in The Gambia [52] during the epidemic period. This could be the result of the public health efforts put in place to stop the COVID-19 pandemic having a suppressive effect on HRSV cases, which decreased the total number of cases and threw off previously noted seasonal trends in various nations [53,54].…”

Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2

“…Among the torque teno viruses (TTV), the most prevalent genogroups were TTV-1-25 and 27-29. This was followed by torque teno midi viruses (TTMDV) (1,2,4,(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) and torque teno mini viruses (TTMV) (1-12, 16, 18, and 27). The relative abundance of these commensal viruses in nasopharyngeal swabs collected from pediatric patients is presented in Figure 3A,B.…”

“…Moreover, the observed decrease or absence of activity in expected viral waves, such as Respiratory Syncytial Virus (RSV) [2], can be attributed to the closure of schools during the pandemic lockdown. Previous studies have highlighted the co-circulation of multiple viruses during SARS-CoV-2 waves, particularly enteroviruses, rhinoviruses, and influenza A [3,4]. However, respiratory symptoms can be caused by specific viruses that may not be detectable using conventional respiratory virus panels.…”