1
|
Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
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.
Collapse
Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| |
Collapse
|
2
|
Mohammed NI, Mackenzie G, Ezeani E, Sidibeh M, Jammeh L, Sarwar G, Saine AKF, Sonko B, Gomez P, Dondeh BL, Hossain MJ, Jasseh M, Usuf E, Prentice AM, Jeffries D, Dalessandro U, Roca A. Quantifying excess mortality during the COVID-19 pandemic in 2020 in The Gambia: a time-series analysis of three health and demographic surveillance systems. Int J Infect Dis 2023; 128:61-68. [PMID: 36566776 PMCID: PMC9780021 DOI: 10.1016/j.ijid.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Estimates for COVID-19-related excess mortality for African populations using local data are needed to design and implement effective control policies. METHODS We applied time-series analysis using data from three health and demographic surveillance systems in The Gambia (Basse, Farafenni, and Keneba) to examine pandemic-related excess mortality during 2020, when the first SARS-CoV-2 wave was observed, compared to the pre-pandemic period (2016-2019). RESULTS Across the three sites, average mortality during the pre-pandemic period and the total deaths during 2020 were 1512 and 1634, respectively (Basse: 1099 vs 1179, Farafenni: 316 vs 351, Keneba: 98 vs 104). The overall annual crude mortality rates per 100,000 (95% CI) were 589 (559, 619) and 599 (571, 629) for the pre-pandemic and 2020 periods, respectively. The adjusted excess mortality rate was 8.8 (-34.3, 67.6) per 100,000 person-month with the adjusted rate ratio (aRR) = 1.01 (0.94,1.11). The age-stratified analysis showed excess mortality in Basse for infants (aRR = 1.22 [1.04, 1.46]) and in Farafenni for the 65+ years age group (aRR = 1.19 [1, 1.44]). CONCLUSION We did not find significant excess overall mortality in 2020 in The Gambia. However, some age groups may have been at risk of excess death. Public health response in countries with weak health systems needs to consider vulnerable age groups and the potential for collateral damage.
Collapse
Affiliation(s)
- Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
| | - Grant Mackenzie
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Murdoch Children's Research Institute, Melbourne, Australia
| | - Esu Ezeani
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mamadi Sidibeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Lamin Jammeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Aji Kumba Folawiyo Saine
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sonko
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Pierre Gomez
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bai Lamin Dondeh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Momodou Jasseh
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
| |
Collapse
|
3
|
Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2023; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
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.
Collapse
Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| |
Collapse
|
4
|
Jarju S, Senghore E, Brotherton H, Affleck L, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022; 6:148. [PMID: 36726685 PMCID: PMC9883272 DOI: 10.12688/gatesopenres.14155.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
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.
Collapse
Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Lucy Affleck
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ebrima Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| |
Collapse
|
5
|
Jarju S, Senghore E, Brotherton H, Saidykhan A, Jallow S, Krubally E, Sinjanka E, Ndene MN, Bajo F, Sanyang MM, Saidy B, Bah A, Mohammed NI, Forrest K, Clarke E, Dalessandro U, Sesay AK, Usuf E, Cerami C, Roca A, Kampmann B, de Silva TI. Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia. Gates Open Res 2022. [PMID: 36726685 DOI: 10.17605/osf.io/tsf78] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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.
Collapse
Affiliation(s)
- Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Elina Senghore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Helen Brotherton
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Saidykhan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Samba Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrissa Krubally
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Edrisa Sinjanka
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Morris Ngor Ndene
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Fabakary Bajo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Musa M Sanyang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Binta Saidy
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Alasana Bah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Nuredin I Mohammed
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Karen Forrest
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Umberto Dalessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Effua Usuf
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
| | - Anna Roca
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, P.O.BOX 273, The Gambia
- The Vaccine Centre, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- 4. Department of Infection, Immunity and Cardiovascular Disease, The Medical School, The University of Sheffield, Beech Hill Road, Sheffield, S10 2RX, UK
| |
Collapse
|
6
|
Kwambana-Adams B, Darboe S, Nabwera H, Foster-Nyarko E, Ikumapayi UN, Secka O, Betts M, Bradbury R, Wegmüller R, Lawal B, Saha D, Hossain MJ, Prentice AM, Kampmann B, Anderson S, Dalessandro U, Antonio M. Salmonella Infections in The Gambia, 2005-2015. Clin Infect Dis 2016; 61 Suppl 4:S354-62. [PMID: 26449952 DOI: 10.1093/cid/civ781] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There are large data gaps in the epidemiology of diseases caused by Salmonella enterica in West Africa. Regional surveillance of Salmonella infections is necessary, especially with the emergence and spread of multidrug-resistant clones. METHODS Data on Salmonella isolated from various clinical specimens from patients from across The Gambia were collected and analyzed retrospectively from 2005 to April 2015. Antibiotic sensitivity testing of Salmonella isolates was performed by disk diffusion method. Serotyping and serogrouping of Salmonella isolates was performed using standard microbiology techniques. RESULTS Two hundred three Salmonella isolates were isolated from 190 patients: 52% (106/203) from blood and 39% (79/203) from stool specimens. Salmonella was also isolated from urine, aspirates, cerebrospinal fluid, wounds, and abscesses. The prevalence of Salmonella in blood cultures was 0.8% (106/13,905). Of the serotyped salmonellae, 14% (21/152) were Salmonella enterica serovar Typhi, whereas 86% (131/152) were serovars other than Typhi (nontyphoidal Salmonella). Of the 102 typed NTS isolates, 40% (41) were Salmonella enterica serovar Typhimurium, 10% (10) were Salmonella enterica serovar Enteritidis, and 3% (3) were Salmonella enterica serovar Arizonae. Overall, 70% (142/203) of the salmonellae were pansusceptible. Multidrug resistance was found in 4% (9/203) of the isolates, 3 of which were Salmonella Enteritidis. CONCLUSIONS Salmonellae are associated with a wide spectrum of invasive and noninvasive infections across all ages in The Gambia. There is evidence of multidrug resistance in salmonellae that warrants vigilant monitoring and surveillance.
Collapse
Affiliation(s)
| | | | - Helen Nabwera
- Medical Research Council Unit, Fajara International Nutrition Group, Medical Research Council Unit, Banjul, The Gambia
| | | | | | | | | | - Richard Bradbury
- School of Medical and Applied Sciences, Central Queensland University, North Rockhampton, Australia
| | - Rita Wegmüller
- Medical Research Council Unit, Fajara International Nutrition Group, Medical Research Council Unit, Banjul, The Gambia
| | | | | | | | - Andrew M Prentice
- Medical Research Council Unit, Fajara International Nutrition Group, Medical Research Council Unit, Banjul, The Gambia
| | | | | | - Umberto Dalessandro
- Medical Research Council Unit, Fajara Institute of Tropical Medicine, Antwerp, Belgium Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine
| | - Martin Antonio
- Medical Research Council Unit, Fajara Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
7
|
Njai H, Shimakawa Y, Ferguson L, Sanneh B, Dalessandro U, Mendy M, Thursz M, Njie R, Lemoine M. Validation of hepatitis B surface antigen (HBsAg) rapid test to screen HBV infection in rural Gambia. Int J Infect Dis 2014. [DOI: 10.1016/j.ijid.2014.03.984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|