Molecular Evidence of Coinfection with Acute Respiratory Viruses and High Prevalence of SARS-CoV-2 among Patients Presenting Flu-Like Illness in Bukavu City, Democratic Republic of Congo

Bisimwa, Patrick N.; Basengere, Rodrigue Ayagirwe; Baharanyi, Tshass Chasinga; Kashosi, Théophile Mitima; Buhendwa, Jean-Paul Chikwanine; Bisimwa, Parvine Basimane; Kusinza, Aline Byabene; Mugumaarhahama, Yannick; Shukuru, Dieudonne Wasso; Simon, Patrick Baenyi; Tonui, Ronald; Birindwa, Ahadi Bwihangane; Mukwege, Denis

doi:10.1155/2022/1553266

“…This study captures a snapshot of the fifth wave which coincided with the emergence and rapid spread of the Omicron variant of SARS‐CoV‐2. SARS‐CoV‐2 positivity is similar to another study conducted in a geographically analogous region in the Democratic Republic of Congo 19 …”

Section: Discussionsupporting

confidence: 83%

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co‐infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

Ruttoh,

Symekher,

Majanja

et al. 2023

Influenza Resp Viruses

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2

0

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BackgroundThe emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has been the most significant public health challenge in over a century. SARS‐CoV‐2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS‐CoV‐2 and monitor the co‐circulation of SARS‐CoV‐2 with other acute respiratory pathogens in Rift Valley, Kenya.MethodsWe conducted a cross‐sectional active sentinel surveillance for the SARS‐CoV‐2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy‐one patients aged between 3 years and 98 years presenting with influenza‐like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) for SARS‐CoV‐2, influenza A, influenza B and respiratory syncytial virus (RSV).ResultsThe samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS‐CoV‐2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS‐CoV‐2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A‐H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co‐infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS‐CoV‐2 positive samples.ConclusionsAugmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence‐based clinical and public health interventions.

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“…In Canada, the average weekly positivity rate for influenza A in 2020-2021 was 0.012% compared to 10.40% in prepandemic years, and 0.006% for influenza B compared to 2.60% in pre-pandemic years 1 . Data from other African countries are scarce, with influenza and RSV reductions observed in South Africa and Zambia 13,14 , but not in the Democratic Republic of the Congo (5.6% influenza A positivity and 0.9% influenza B positivity Dec 2020 -March 2021) 15 . Interestingly, the reduction in RSV and influenza in Zambia during the first year of the COVID-19 pandemic was accompanied by increases in rhino/enteroviruses, seasonal coronaviruses, parainfluenza viruses and human metapneumovirus 14 .…”

Section: Resultsmentioning

confidence: 99%

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

Jarju

¹

,

Senghore

²

,

Brotherton

³

et al. 2023

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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.

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“…Only 2.9% (41/1397) of recruited participants were hospitalized for their illness, although details of the clinical reasons for admission were not available. 15 Total numbers are shown with % in brackets. The denominators for age and sex percentages are the total recruited numbers at each site or all participants combined.…”

Section: Resultsmentioning

confidence: 99%

“…In Canada, the average weekly positivity rate for influenza A in 2020-2021 was 0.012% compared to 10.40% in pre-pandemic years, and 0.006% for influenza B compared to 2.60% in pre-pandemic years 1 . Data from other African countries are scarce, with influenza and RSV reductions observed in South Africa and Zambia 13,14 , but not in the Democratic Republic of the Congo (5.6% influenza A positivity and 0.9% influenza B positivity Dec 2020 -March 2021) 15 . Interestingly, the reduction in RSV and influenza in Zambia during the first year of the COVID-19 pandemic was accompanied by increases in rhino/enteroviruses, seasonal coronaviruses, parainfluenza viruses and human metapneumovirus 14 .…”

Section: Discussionmentioning

confidence: 99%

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

Jarju

¹

,

Senghore²,

Brotherton³

et al. 2023

Gates Open Res

0

View full text Add to dashboard Cite

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.

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Molecular Evidence of Coinfection with Acute Respiratory Viruses and High Prevalence of SARS-CoV-2 among Patients Presenting Flu-Like Illness in Bukavu City, Democratic Republic of Congo

Cited by 8 publications

References 28 publications

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co‐infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

Tracking severe acute respiratory syndrome coronavirus 2 transmission and co‐infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya

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

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

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