{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T13:56:25Z","timestamp":1774533385603,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/gatesopenres.14155.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T00:00:00Z","timestamp":1679875200000}},{"DOI":"10.12688\/gatesopenres.14155.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T00:00:00Z","timestamp":1679875200000}}],"reference-count":17,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T00:00:00Z","timestamp":1679875200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-015823"],"award-info":[{"award-number":["INV-015823"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Global Challenge Research Fund award from The University of Sheffield","award":["MC_UP_A900\/1122"],"award-info":[{"award-number":["MC_UP_A900\/1122"]}]},{"name":"UK Research and Innovation grant","award":["MC_PC_19084"],"award-info":[{"award-number":["MC_PC_19084"]}]}],"content-domain":{"domain":["gatesopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Gates Open Res"],"abstract":"<ns4:p><ns4:bold>Background:<\/ns4:bold> In many countries,<ns4:italic> <\/ns4:italic>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.\u00a0<\/ns4:p><ns4:p> <ns4:bold>Methods<\/ns4:bold>: 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 \u00a0to 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.<\/ns4:p><ns4:p> <ns4:bold>Results:<\/ns4:bold> Overall virus positivity was 44.2%, with prevalence higher in children &lt;5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and &gt;50 years (39.9%), p&lt;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 &lt;5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and &gt;50 years (24.3%), p&lt;0.0001. In contrast, rhinoviruses were most prevalent in children &lt;5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and &gt;50 years (6.3%), p&lt;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.<\/ns4:p><ns4:p> <ns4:bold>Conclusion<\/ns4:bold>: 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.<\/ns4:p>","DOI":"10.12688\/gatesopenres.14155.3","type":"journal-article","created":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T10:40:21Z","timestamp":1679913621000},"page":"148","update-policy":"https:\/\/doi.org\/10.12688\/gatesopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia"],"prefix":"10.12688","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2621-8406","authenticated-orcid":false,"given":"Sheikh","family":"Jarju","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elina","family":"Senghore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helen","family":"Brotherton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lucy","family":"Affleck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alasana","family":"Saidykhan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samba","family":"Jallow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-2644-7330","authenticated-orcid":false,"given":"Ebrima","family":"Krubally","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edrisa","family":"Sinjanka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Morris Ngor","family":"Ndene","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fabakary","family":"Bajo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Musa M","family":"Sanyang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Binta","family":"Saidy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4489-4627","authenticated-orcid":false,"given":"Alasana","family":"Bah","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nuredin I","family":"Mohammed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9484-0830","authenticated-orcid":false,"given":"Karen","family":"Forrest","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ed","family":"Clarke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Umberto","family":"Dalessandro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdul K","family":"Sesay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Effua","family":"Usuf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7634-0955","authenticated-orcid":false,"given":"Carla","family":"Cerami","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Roca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beate","family":"Kampmann","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thushan I","family":"de Silva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2560","published-online":{"date-parts":[[2023,3,27]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"100015","DOI":"10.1016\/j.lana.2021.100015","article-title":"The impact of the COVID-19 pandemic on influenza, respiratory syncytial virus, and other seasonal respiratory virus circulation in Canada: A population-based study.","volume":"1","author":"H Groves","year":"2021","journal-title":"Lancet Reg Health Am."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/s41467-021-21157-9","article-title":"Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand.","volume":"12","author":"Q Huang","year":"2021","journal-title":"Nat Commun."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"2001847","DOI":"10.2807\/1560-7917.ES.2020.25.47.2001847","article-title":"Where has all the influenza gone? The impact of COVID-19 on the circulation of influenza and other respiratory viruses, Australia, March to September 2020.","volume":"25","author":"S Sullivan","year":"2020","journal-title":"Euro Surveill."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"2064-72","DOI":"10.3201\/eid2708.204954","article-title":"Intense and Mild First Epidemic Wave of Coronavirus Disease, The Gambia.","volume":"27","author":"B Abatan","year":"2021","journal-title":"Emerg Infect Dis."},{"key":"ref-6","article-title":"Gambia Demographics.","author":"G Demographics","year":"2020"},{"key":"ref-7","article-title":"Gambia Climate.","year":"2021"},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"925-30","DOI":"10.1097\/INF.0000000000002761","article-title":"Viral Etiology, Clinical Features and Antibiotic Use in Children <5 Years of Age in the Gambia Presenting With Influenza-like Illness.","volume":"39","author":"S Jarju","year":"2020","journal-title":"Pediatr Infect Dis J."},{"key":"ref-9","article-title":"The Republic of the Gambia national deployment and vaccination plan for COVID-19.","year":"2020"},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"S129-35","DOI":"10.1093\/infdis\/jis576","article-title":"Sentinel surveillance for influenza in Senegal, 1996\u20132009.","volume":"206 Suppl 1","author":"M Niang","year":"2012","journal-title":"J Infect Dis."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"2001600","DOI":"10.2807\/1560-7917.ES.2021.26.29.2001600","article-title":"Decline of influenza and respiratory syncytial virus detection in facility-based surveillance during the COVID-19 pandemic, South Africa, January to October 2020.","volume":"26","author":"S Tempia","year":"2021","journal-title":"Euro Surveill."},{"key":"ref-14","doi-asserted-by":"publisher","first-page":"647-54","DOI":"10.1111\/tmi.13781","article-title":"Respiratory viruses in rural Zambia before and during the COVID-19 pandemic.","volume":"27","author":"G Loevinsohn","year":"2022","journal-title":"Trop Med Int Health."},{"key":"ref-15","doi-asserted-by":"publisher","first-page":"1553266","DOI":"10.1155\/2022\/1553266","article-title":"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.","volume":"2022","author":"P Ntagereka","year":"2022","journal-title":"Can J Infect Dis Med Microbiol."},{"key":"ref-16","doi-asserted-by":"publisher","first-page":"10-15","DOI":"10.1111\/1753-6405.13168","article-title":"Respiratory virus detection during the COVID-19 pandemic in Queensland, Australia.","volume":"46","author":"A El-Heneidy","year":"2022","journal-title":"Aust N Z J Public Health."},{"key":"ref-17","doi-asserted-by":"publisher","first-page":"e20210583","DOI":"10.1084\/jem.20210583","article-title":"Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics.","volume":"218","author":"N Cheemarla","year":"2021","journal-title":"J Exp Med."},{"key":"ref-18","doi-asserted-by":"publisher","first-page":"31-8","DOI":"10.1093\/infdis\/jiab147","article-title":"Human Rhinovirus Infection Blocks Severe Acute Respiratory Syndrome Coronavirus 2 Replication Within the Respiratory Epithelium: Implications for COVID-19 Epidemiology.","volume":"224","author":"K Dee","year":"2021","journal-title":"J Infect Dis."},{"key":"ref-19","doi-asserted-by":"publisher","first-page":"27142-27150","DOI":"10.1073\/pnas.1911083116","article-title":"Virus-virus interactions impact the population dynamics of influenza and the common cold.","volume":"116","author":"S Nickbakhsh","year":"2019","journal-title":"Proc Natl Acad Sci U S A."},{"key":"ref-20","doi-asserted-by":"publisher","first-page":"e254-e62","DOI":"10.1016\/s2666-5247(20)30114-2","article-title":"Interference between rhinovirus and influenza A virus: a clinical data analysis and experimental infection study.","volume":"1","author":"A Wu","year":"2020","journal-title":"Lancet Microbe."}],"container-title":["Gates Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,27]],"date-time":"2023-03-27T15:20:31Z","timestamp":1679930431000},"score":1,"resource":{"primary":{"URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,27]]},"references-count":17,"URL":"https:\/\/doi.org\/10.12688\/gatesopenres.14155.3","relation":{},"ISSN":["2572-4754"],"issn-type":[{"value":"2572-4754","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,27]]},"assertion":[{"value":"Indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/gatesopenres.15460.r32800, Ivy A. Asante, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, 18 Jan 2023, version 1, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v1#referee-response-32800","order":0,"name":"referee-response-32800","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Sheikh Jarju<\/b>; \n<i>Posted: 08 Feb 2023<\/i>; Comments: \n<b>1. From Figure 1, it looks like the authors looked at some selected sites in The Gambia, as<\/b>&nbsp;\n<b>opposed to the whole country. Even if sites were few and distributed throughout the<\/b>&nbsp;\n<b>country, it would be said to represent the country. For consideration, the authors could<\/b>&nbsp;\n<b>include \u2018selected sites in The Gambia\u2019 in their title.<\/b>  We appreciate the reviewer\u2019s point that the study only included data from limited sites. The sites selected represented both an urban and rural settlement of the country and many people seek medical care in the urban clinics we have included from different part of the country. We have discussed these limitations but feel that we do not need to change the title of the manuscript.  \n<b>2. The authors used a multiplex RT-PCR assay that detected a panel of respiratory&nbsp;pathogens. This&nbsp;detection however did not distinguish,&nbsp;or sub-type viruses seen. E.g.,&nbsp;for influenza B,&nbsp;lineage determination was not reported, same for influenza A and the&nbsp;human.<\/b> \n<b>coronaviruses. If this data is available, it should be included.<\/b>  We agree with the suggestion that lineage information, for example influenza virus, would have added an additional information. Unfortunately, we do not have this data as all seasonal coronaviruses were detected on one probe. We do, however, have a specific H1N1 assay and what we report are influenza A data stratified by whether they were positive in the influenza A assay alone (which would pick up both H3N2 and H1N1) or in both this assay and the H1N1 specific assay. This is stated in the table legends.  \n<b>3. Specify what UTM was used. What is the volume of the Universal transport medium? Why<\/b> \n<b>did the researchers choose to collect only NP swabs and not a combined OP\/NP swab?<\/b>  We did use UTM Copan 360C with 1ml medium. This has been added to the methods. We used nasopharyngeal swabs as the method of choice due to the extensive experience in our field teams in NPS collection during many studies of viral and bacterial carriage.  \n<b>4. or the ILI surveillance system, is there a systematic approach to sample collection? E.g. A specific number expected each week.&nbsp;This could explain the number of samples tested during each of the months; what accounted for the high number of samples in one month and a low number in another?<\/b> We have included a statement about this in response to a comment from reviewer 1 in the methods. We attempted to recruit everyone who fulfilled the case definition and was willing to participate in the study.  \n<b>5.&nbsp;Is the SARS-CoV-2 data observed in this study comparable to national data? It is not very<\/b>&nbsp;\n<b>clear.<\/b>  Yes, the SARS-CoV-2 data observed in our study is comparable with the national data. We have stated this and added a reference.  \n<b>6. Was there any correlation between detection of SARS-CoV-2 and other respiratory viruses?<\/b>  No clear correlations are present. We have reported the number of co-infections and also highlighted the potential viral interference observed between SARS-CoV-2, influenza and human rhinoviruses in terms of the peaks observed. This is included in the discussion already.","URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3#referee-comment-3592","order":1,"name":"referee-comment-3592","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/gatesopenres.15460.r32799, Antonia Ho, Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, 27 Jan 2023, version 1, indexed","URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v1#referee-response-32799","order":2,"name":"referee-response-32799","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Sheikh Jarju<\/b>; \n<i>Posted: 08 Feb 2023<\/i>; \n<b>Comments:<\/b> \n<b>1. Local SARS-CoV-2 and influenza vaccination policy should be stated in the Methods.<\/b>  We agree that it is important to highlight the local SARS-CoV-2 and influenza vaccination policy. In the Gambia Government national deployment and vaccination plan for COVID-19 vaccines, priority groups are highlighted that includes health personnel, community workers, older people of age 65 years and above and people with pre-existing conditions would be considered for vaccination first, in that order (\n<b>The Gambia Government, 2020; The Republic of the Gambia national deployment and vaccination plan for COVID-19; Banjul<\/b>). We have now referenced this document. However, there is no influenza vaccine policy in The Gambia, which we state in the methods.  \n<b>More detail on the PaTS trial should be included. It is an RCT comparing Ivermectin vs.<\/b> \n<b>aspirin vs. placebo. Were samples included from participants from both cohorts 1 and 2? <\/b>  The samples from PaTS included in this study were those initially screened to qualify for subsequent recruitment into cohort 1 or 2. This was at the initial stage of the study. Following successful screening and 2\n<sup>nd<\/sup> consenting to join the study, samples were then followed up and as per severity of conditions, they were then distributed into cohort 1 or 2. &nbsp;We only stopped at the screening level and didn\u2019t include samples that were already in cohort 1 or 2. We have tried to make this clearer in the methods.  2. \n<b>The sampling strategy of ILI surveillance (study 1) should be included; age criteria, target<\/b> \n<b>numbers per day\/week, as number of included samples seems to vary greatly according to<\/b> \n<b>Figure 2.<\/b>  The ILI surveillance (study 1) recruited all age groups. We recruited all participants that fulfilled the case definition in a day\/week and were willing to participate in the study. We have added some text to the methods to make this clearer. The fluctuation in numbers could be due to a number of reasons, but most likely due to the number of patients presenting with ILI.  3. \n<b>Limited demographic\/clinical data are included, presumably not collected by ILI<\/b> \n<b>surveillance. Co-morbidities and vaccination status would have been useful.<\/b>  We agree that these aspects would be interesting. Unfortunately, we do not have extensive and systematically collected data on these variables from all the various data sources included in this ILI study.  4. \n<b>The manuscript highlights scarce data on respiratory viral circulation from Africa - and<\/b>\n<b> mentions data from South Africa (Tempia Eurosurveillance 2021) and Ntagereka (Infect Dis<\/b>\n<b> med Micro 2022), but should also include Loevinsohn et al. (20221), which was&nbsp;published <\/b>\n<b>prior to this manuscript. This surveillance study in Zambia found a substantial decline in the<\/b>\n<b> prevalence of RSV and influenza in the first year of the pandemic, while an increase in the<\/b>\n<b> prevalence of rhino\/enteroviruses and non-SARS-CoV-2 coronaviruses was observed&nbsp;after<\/b>\n<b> March 2020 (when SARS-CoV-2 emerged in Zambia), compared to 2019.<\/b>  We agree that the Zambia paper is an important publication to reference in our manuscript and have discussed this paper.","URL":"https:\/\/gatesopenresearch.org\/articles\/6-148\/v3#referee-comment-3593","order":3,"name":"referee-comment-3593","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The study was funded by the Bill and Melinda Gates Foundation (INV-015823), a Global Challenge Research Fund award from The University of Sheffield, UK, MRCG Vaccines and Immunity core funding (MC_UP_A900\/1122), and PaTS trial funding from a UK Research and Innovation grant (MC_PC_19084). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}