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Arruda LB, Free HB, Simons D, Ansumana R, Elton L, Haider N, Honeyborne I, Asogun D, McHugh TD, Ntoumi F, Zumla A, Kock R. Current sampling and sequencing biases of Lassa mammarenavirus limit inference from phylogeography and molecular epidemiology in Lassa fever endemic regions. PLOS Glob Public Health 2023; 3:e0002159. [PMID: 37939051 PMCID: PMC10631635 DOI: 10.1371/journal.pgph.0002159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Lassa fever (LF) is a potentially lethal viral haemorrhagic infection of humans caused by Lassa mammarenavirus (LASV). It is an important endemic zoonotic disease in West Africa with growing evidence for increasing frequency and sizes of outbreaks. Phylogeographic and molecular epidemiology methods have projected expansion of the Lassa fever endemic zone in the context of future global change. The Natal multimammate mouse (Mastomys natalensis) is the predominant LASV reservoir, with few studies investigating the role of other animal species. To explore host sequencing biases, all LASV nucleotide sequences and associated metadata available on GenBank (n = 2,298) were retrieved. Most data originated from Nigeria (54%), Guinea (20%) and Sierra Leone (14%). Data from non-human hosts (n = 703) were limited and only 69 sequences encompassed complete genes. We found a strong positive correlation between the number of confirmed human cases and sequences at the country level (r = 0.93 (95% Confidence Interval = 0.71-0.98), p < 0.001) but no correlation exists between confirmed cases and the number of available rodent sequences (r = -0.019 (95% C.I. -0.71-0.69), p = 0.96). Spatial modelling of sequencing effort highlighted current biases in locations of available sequences, with increased sequencing effort observed in Southern Guinea and Southern Nigeria. Phylogenetic analyses showed geographic clustering of LASV lineages, suggestive of isolated events of human-to-rodent transmission and the emergence of currently circulating strains of LASV from the year 1498 in Nigeria. Overall, the current study highlights significant geographic limitations in LASV surveillance, particularly, in non-human hosts. Further investigation of the non-human reservoir of LASV, alongside expanded surveillance, are required for precise characterisation of the emergence and dispersal of LASV. Accurate surveillance of LASV circulation in non-human hosts is vital to guide early detection and initiation of public health interventions for future Lassa fever outbreaks.
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Affiliation(s)
- Liã Bárbara Arruda
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Hayley Beth Free
- The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - David Simons
- The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Rashid Ansumana
- School of Community Health Sciences, Njala University, Bo, Sierra Leone
| | - Linzy Elton
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Najmul Haider
- The Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Isobella Honeyborne
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Danny Asogun
- Ekpoma and Irrua Specialist Teaching Hospital, Ambrose Alli University, Irrua, Nigeria
| | - Timothy D. McHugh
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Francine Ntoumi
- Fondation Congolaise Pour la Recherche Médicale (FCRM), Brazzaville, Republic of Congo
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, London, United Kingdom
- NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, United Kingdom
| | - Richard Kock
- The Royal Veterinary College, University of London, Hatfield, United Kingdom
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Samuels RJ, Sumah I, Alhasan F, McHenry R, Short L, Chappell JD, Haddadin Z, Halasa NB, Valério ID, Amorim G, Grant DS, Schieffelin JS, Moon TD. Respiratory virus surveillance in hospitalized children less than two-years of age in Kenema, Sierra Leone during the COVID-19 pandemic (October 2020- October 2021). PLoS One 2023; 18:e0292652. [PMID: 37816008 PMCID: PMC10564235 DOI: 10.1371/journal.pone.0292652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Globally, viral pathogens are the leading cause of acute respiratory infection in children under-five years. We aim to describe the epidemiology of viral respiratory pathogens in hospitalized children under-two years of age in Eastern Province of Sierra Leone, during the second year of the SARS-CoV-2 pandemic. We conducted a prospective study of children hospitalized with respiratory symptoms between October 2020 and October 2021. We collected demographic and clinical characteristics and calculated each participant´s respiratory symptom severity. Nose and throat swabs were collected at enrollment. Total nucleic acid was purified and tested for multiple respiratory viruses. Statistical analysis was performed using R version 4.2.0 software. 502 children less than two-years of age were enrolled. 376 (74.9%) had at least one respiratory virus detected. The most common viruses isolated were HRV/EV (28.2%), RSV (19.5%) and PIV (13.1%). Influenza and SARS-CoV-2 were identified in only 9.2% and 3.9% of children, respectively. Viral co-detection was common. Human metapneumovirus and RSV had more than two-fold higher odds of requiring O2 therapy while hospitalized. Viral pathogen prevalence was high (74.9%) in our study population. Despite this, 100% of children received antibiotics, underscoring a need to expand laboratory diagnostic capacity and to revisit clinical guidelines implementation in these children. Continuous surveillance and serologic studies among more diverse age groups, with greater geographic breadth, are needed in Sierra Leone to better characterize the long-term impact of COVID-19 on respiratory virus prevalence and to better characterize the seasonality of respiratory viruses in Sierra Leone.
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Affiliation(s)
- Robert J. Samuels
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Sumah
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Rendie McHenry
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Laura Short
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - James D. Chappell
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Zaid Haddadin
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Natasha B. Halasa
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Inaê D. Valério
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Gustavo Amorim
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Donald S. Grant
- Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - John S. Schieffelin
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Tulane University, New Orleans, Louisiana, United States of America
| | - Troy D. Moon
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Tulane University, New Orleans, Louisiana, United States of America
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
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Moon TD, Sumah I, Amorim G, Alhasan F, Howard LM, Myers H, Green AF, Grant DS, Schieffelin JS, Samuels RJ. Antibiotic prescribing practices for acute respiratory illness in children less than 24 months of age in Kenema, Sierra Leone: is it time to move beyond algorithm driven decision making? BMC Infect Dis 2023; 23:626. [PMID: 37749485 PMCID: PMC10519098 DOI: 10.1186/s12879-023-08606-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Lower respiratory tract infections are the leading cause of mortality in young children globally. In many resource-limited settings clinicians rely on guidelines such as IMCI or ETAT + that promote empiric antibiotic utilization for management of acute respiratory illness (ARI). Numerous evaluations of both guidelines have shown an overall positive response however, several challenges have also been reported, including the potential for over-prescribing of unnecessary antibiotics. The aims of this study were to describe the antibiotic prescribing practices for children less than 24 months of age with symptoms of ARI, that were admitted to Kenema Government Hospital (KGH) in the Eastern Province of Sierra Leone, and to identify the number of children empirically prescribed antibiotics who were admitted to hospital with ARI, as well as their clinical signs, symptoms, and outcomes. METHODS We conducted a prospective study of children < 24 months of age admitted to the KGH pediatric ward with respiratory symptoms between October 1, 2020 and May 31, 2022. Study nurses collected data on demographic information, medical and medication history, and information on clinical course while hospitalized. RESULTS A total of 777 children were enrolled. Prior to arrival at the hospital, 224 children (28.8%) reported taking an antibiotic for this illness without improvement. Only 15 (1.9%) children received a chest radiograph to aid in diagnosis and 100% of patients were placed on antibiotics during their hospital stay. CONCLUSIONS Despite the lives saved, reliance on clinical decision-support tools such as IMCI and ETAT + for pediatric ARI, is resulting in the likely over-prescribing of antibiotics. Greater uptake of implementation research is needed to develop strategies and tools designed to optimize antibiotic use for ARI in LMIC settings. Additionally, much greater priority needs to be given to ensuring clinicians have the basic tools for clinical diagnosis, as well as greater investments in essential laboratory and radiographic diagnostics that help LMIC clinicians move beyond the sole reliance on algorithm based clinical decision making.
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Affiliation(s)
- Troy D Moon
- Department of Tropical Medicine and Infectious Diseases, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, Suite 2300, New Orleans, Louisiana, 70112, USA.
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Tulane University School of Medicine, 1440 Canal Street, Suite 1600, New Orleans, Louisiana, 70112, USA.
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 750, Nashville, TN, 37203, USA.
| | - Ibrahim Sumah
- Kenema Government Hospital, Ministry of Health and Sanitation, 1 Combema Road, Kenema, Sierra Leone, Sierra Leone
| | - Gustavo Amorim
- Department of Biostatistics, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 1000, Nashville, TN, 37203, USA
| | - Foday Alhasan
- Kenema Government Hospital, Ministry of Health and Sanitation, 1 Combema Road, Kenema, Sierra Leone, Sierra Leone
| | - Leigh M Howard
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 750, Nashville, TN, 37203, USA
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, D-7235 Medical Center North, 1161 21st Avenue South, Nashville, TN, 37232, USA
| | - Harriett Myers
- Department of Tropical Medicine and Infectious Diseases, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, Suite 2300, New Orleans, Louisiana, 70112, USA
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 750, Nashville, TN, 37203, USA
| | - Ann F Green
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 750, Nashville, TN, 37203, USA
| | - Donald S Grant
- Kenema Government Hospital, Ministry of Health and Sanitation, 1 Combema Road, Kenema, Sierra Leone, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, New England Ville, Freetown, Sierra Leone
| | - John S Schieffelin
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Tulane University School of Medicine, 1440 Canal Street, Suite 1600, New Orleans, Louisiana, 70112, USA
| | - Robert J Samuels
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 750, Nashville, TN, 37203, USA
- Kenema Government Hospital, Ministry of Health and Sanitation, 1 Combema Road, Kenema, Sierra Leone, Sierra Leone
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Grant DS, Engel EJ, Roberts Yerkes N, Kanneh L, Koninga J, Gbakie MA, Alhasan F, Kanneh FB, Kanneh IM, Kamara FK, Momoh M, Yillah MS, Foday M, Okoli A, Zeoli A, Weldon C, Bishop CM, Zheng C, Hartnett J, Chao K, Shore K, Melnik LI, Mucci M, Bond NG, Doyle P, Yenni R, Podgorski R, Ficenec SC, Moses L, Shaffer JG, Garry RF, Schieffelin JS. Seroprevalence of anti-Lassa Virus IgG antibodies in three districts of Sierra Leone: A cross-sectional, population-based study. PLoS Negl Trop Dis 2023; 17:e0010938. [PMID: 36758101 PMCID: PMC9946222 DOI: 10.1371/journal.pntd.0010938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 02/22/2023] [Accepted: 11/09/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Lassa virus (LASV), the cause of the acute viral hemorrhagic illness Lassa fever (LF), is endemic in West Africa. Infections in humans occur mainly after exposure to infected excrement or urine of the rodent-host, Mastomys natalensis. The prevalence of exposure to LASV in Sierra Leone is crudely estimated and largely unknown. This cross-sectional study aimed to establish a baseline point seroprevalence of IgG antibodies to LASV in three administrative districts of Sierra Leone and identify potential risk factors for seropositivity and LASV exposure. METHODOLOGY AND PRINCIPAL FINDINGS Between 2015 and 2018, over 10,642 participants from Kenema, Tonkolili, and Port Loko Districts were enrolled in this cross-sectional study. Previous LASV and LF epidemiological studies support classification of these districts as "endemic," "emerging," and "non-endemic", respectively. Dried blood spot samples were tested for LASV antibodies by ELISA to determine the seropositivity of participants, indicating previous exposure to LASV. Surveys were administered to each participant to assess demographic and environmental factors associated with a higher risk of exposure to LASV. Overall seroprevalence for antibodies to LASV was 16.0%. In Kenema, Port Loko, and Tonkolili Districts, seroprevalences were 20.1%, 14.1%, and 10.6%, respectively. In a multivariate analysis, individuals were more likely to be LASV seropositive if they were living in Kenema District, regardless of sex, age, or occupation. Environmental factors contributed to an increased risk of LASV exposure, including poor housing construction and proximity to bushland, forested areas, and refuse. CONCLUSIONS AND SIGNIFICANCE In this study we determine a baseline LASV seroprevalence in three districts which will inform future epidemiological, ecological, and clinical studies on LF and the LASV in Sierra Leone. The heterogeneity of the distribution of LASV and LF over both space, and time, can make the design of efficacy trials and intervention programs difficult. Having more studies on the prevalence of LASV and identifying potential hyper-endemic areas will greatly increase the awareness of LF and improve targeted control programs related to LASV.
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Affiliation(s)
- Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Emily J. Engel
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Nicole Roberts Yerkes
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - James Koninga
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael A. Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Fatima K. Kamara
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Adaora Okoli
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Ashley Zeoli
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Caroline Weldon
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher M. Bishop
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Crystal Zheng
- Department of Internal Medicine, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jessica Hartnett
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Karissa Chao
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Kayla Shore
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Lilia I. Melnik
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Mallory Mucci
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Nell G. Bond
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Philip Doyle
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachael Yenni
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Rachel Podgorski
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Samuel C. Ficenec
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Lina Moses
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - John S. Schieffelin
- Department of Pediatrics, Sections of Pediatric Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
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Doumbia S, Toure M, Sogoba N, Alifrangis M, Diakite M, Diarra A, Keita M, Konaté D, Diawara SI, Thiam SM, Keita S, Tounkara M, Cissé I, Sanogo V, Magassa MH, Barry AE, Winch PJ, Marker HC, Shaffer JG, Traoré SF, Müller GC, Cui L, Beier JC, Mihigo J. The West Africa ICEMR Partnerships for Guiding Policy to Improve the Malaria Prevention and Control. Am J Trop Med Hyg 2022; 107:84-89. [PMID: 36228908 PMCID: PMC9662222 DOI: 10.4269/ajtmh.21-1330] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/06/2022] [Indexed: 12/01/2022] Open
Abstract
The Mali National Malaria Control Program (NMCP) recently established a phased set of goals for eliminating malaria in Mali by 2030. Over the past decade, the scale-up of NMCP-led malaria control interventions has led to considerable progress, as evidenced by multiple malariometric indicators. The West Africa International Center of Excellence in Malaria Research (WA-ICEMR) is a multidisciplinary research program that works closely with the NMCP and its partners to address critical research needs for malaria control. This coordinated effort includes assessing the effectiveness of control interventions based on key malaria research topics, including immune status, parasite genetic diversity, insecticide and drug resistance, diagnostic accuracy, malaria vector populations and biting behaviors, and vectorial capacity. Several signature accomplishments of the WA-ICEMR include identifying changing malaria age demographic profiles, testing innovative approaches to improve control strategies, and providing regular reporting on drug and insecticide resistance status. The NMCP and WA-ICEMR partnership between the WA-ICEMR and the NMCP offers a comprehensive research platform that informs the design and implementation of malaria prevention and control research programs. These efforts build local expertise and capacity for the next generation of malaria researchers and guide local policy, which is crucial in sustaining efforts toward eliminating malaria in West Africa.
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Affiliation(s)
- Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamoudou Toure
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Mahamadou Diakite
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ayouba Diarra
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moussa Keita
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Drissa Konaté
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sory I. Diawara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sidibé M’Baye Thiam
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Soumba Keita
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moctar Tounkara
- Department of Public Health, Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Idrissa Cissé
- National Malaria Control Program, Ministry of Health, Bamako, Mali
| | - Vincent Sanogo
- National Malaria Control Program, Ministry of Health, Bamako, Mali
| | | | | | - Peter J. Winch
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Hannah C. Marker
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Jeffrey G. Shaffer
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - Sékou F. Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Günter C. Müller
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Liwang Cui
- Division of Infectious Diseases and Internal Medicine, Department of Internal Medicine, University of South Florida, Tampa, Florida
| | - John C. Beier
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, Florida
| | - Jules Mihigo
- U.S. President’s Malaria Initiative, United States Agency for International Development Office, Bamako, Mali
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6
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Koch MR, Kanneh L, Wise PH, Kurina LM, Alhasan F, Garry RF, Schieffelin JS, Shaffer JG, Grant DS. Health seeking behavior after the 2013-16 Ebola epidemic: Lassa fever as a metric of persistent changes in Kenema District, Sierra Leone. PLoS Negl Trop Dis 2021; 15:e0009576. [PMID: 34260615 PMCID: PMC8312964 DOI: 10.1371/journal.pntd.0009576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/26/2021] [Accepted: 06/19/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The West African Ebola epidemic of 2013-2016 killed nearly 4,000 Sierra Leoneans and devastated health infrastructure across West Africa. Changes in health seeking behavior (HSB) during the outbreak resulted in dramatic underreporting and substantial declines in hospital presentations to public health facilities, resulting in an estimated tens of thousands of additional maternal, infant, and adult deaths per year. Sierra Leone's Kenema District, a major Ebola hotspot, is also endemic for Lassa fever (LF), another often-fatal hemorrhagic disease. Here we assess the impact of the West African Ebola epidemic on health seeking behaviors with respect to presentations to the Kenema Government Hospital (KGH) Lassa Ward, which serves as the primary health care referral center for suspected Lassa fever cases in the Eastern Province of Sierra Leone. METHODOLOGY/PRINCIPAL FINDINGS Presentation frequencies for suspected Lassa fever presenting to KGH or one of its referral centers from 2011-2019 were analyzed to consider the potential impact of the West African Ebola epidemic on presentation patterns. There was a significant decline in suspected LF cases presenting to KGH following the epidemic, and a lower percentage of subjects were admitted to the KGH Lassa Ward following the epidemic. To assess general HSB, a questionnaire was developed and administered to 200 residents from 8 villages in Kenema District. Among 194 completed interviews, 151 (78%) of respondents stated they felt hospitals were safer post-epidemic with no significant differences noted among subjects according to religious background, age, gender, or education. However, 37 (19%) subjects reported decreased attendance at hospitals since the epidemic, which suggests that trust in the healthcare system has not fully rebounded. Cost was identified as a major deterrent to seeking healthcare. CONCLUSIONS/SIGNIFICANCE Analysis of patient demographic data suggests that fewer individuals sought care for Lassa fever and other febrile illnesses in Kenema District after the West African Ebola epidemic. Re-establishing trust in health care services will require efforts beyond rebuilding infrastructure and require concerted efforts to rebuild the trust of local residents who may be wary of seeking healthcare post epidemic.
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Affiliation(s)
- Mikaela R. Koch
- Program in Human Biology, Stanford University, Stanford, California, United States of America
- * E-mail: (MRK); (JGS); (DSG)
| | - Lansana Kanneh
- Pediatrics–Neonatal and Developmental Medicine, Stanford University, Stanford, California, United States of America
| | - Paul H. Wise
- Pediatrics–Neonatal and Developmental Medicine, Stanford University, Stanford, California, United States of America
| | - Lianne M. Kurina
- Program in Human Biology, Stanford University, Stanford, California, United States of America
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, Louisiana, United States of America
- Zalgen Labs, LCC, Germantown, MD, United States of America
| | - John S. Schieffelin
- Sections of Infectious Disease, Department of Pediatrics, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Bioinformatics, Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- * E-mail: (MRK); (JGS); (DSG)
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- * E-mail: (MRK); (JGS); (DSG)
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7
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Shaffer JG, Schieffelin JS, Momoh M, Goba A, Kanneh L, Alhasan F, Gbakie M, Engel EJ, Bond NG, Hartnett JN, Nelson DKS, Bush DJ, Boisen ML, Heinrich ML, Rowland MM, Branco LM, Samuels RJ, Garry RF, Grant DS. Space-Time Trends in Lassa Fever in Sierra Leone by ELISA Serostatus, 2012-2019. Microorganisms 2021; 9:microorganisms9030586. [PMID: 33809204 PMCID: PMC8000031 DOI: 10.3390/microorganisms9030586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lassa fever (LF) is a viral hemorrhagic disease found in Sub-Saharan Africa and is responsible for up to 300,000 cases and 5000 deaths annually. LF is highly endemic in Sierra Leone, particularly in its Eastern Province. Kenema Government Hospital (KGH) maintains one of only a few LF isolation facilities in the world with year-round diagnostic testing. Here we focus on space-time trends for LF occurring in Sierra Leone between 2012 and 2019 to provide a current account of LF in the wake of the 2014–2016 Ebola epidemic. Data were analyzed for 3277 suspected LF cases and classified as acute, recent, and non-LF or prior LF exposure using enzyme-linked immunosorbent assays (ELISAs). Presentation rates for acute, recent, and non-LF or prior LF exposure were 6.0% (195/3277), 25.6% (838/3277), and 68.4% (2244/3277), respectively. Among 2051 non-LF or prior LF exposures, 33.2% (682/2051) tested positive for convalescent LF exposure. The overall LF case-fatality rate (CFR) was 78.5% (106/135). Both clinical presentations and confirmed LF cases declined following the Ebola epidemic. These declines coincided with an increased duration between illness onset and clinical presentation, perhaps suggesting more severe disease or presentation at later stages of illness. Acute LF cases and their corresponding CFRs peaked during the dry season (November to April). Subjects with recent (but not acute) LF exposure were more likely to present during the rainy season (May to October) than the dry season (p < 0.001). The findings here suggest that LF remains endemic in Sierra Leone and that caseloads are likely to resume at levels observed prior to the Ebola epidemic. The results provide insight on the current epidemiological profile of LF in Sierra Leone to facilitate LF vaccine studies and accentuate the need for LF cohort studies and continued advancements in LF diagnostics.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - John S. Schieffelin
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Lansana Kanneh
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
| | - Emily J. Engel
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Nell G. Bond
- Sections of Infectious Disease, Departments of Pediatrics and Internal Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (E.J.E.); (N.G.B.)
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Jessica N. Hartnett
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
| | - Diana K. S. Nelson
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Duane J. Bush
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Matthew L. Boisen
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan L. Heinrich
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Megan M. Rowland
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Luis M. Branco
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Robert J. Samuels
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TE 37203, USA
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA 70112, USA; (J.N.H.); (R.F.G.)
- Zalgen Labs, LLC, Germantown, MD 20876, USA; (D.K.S.N.); (D.J.B.); (M.L.B.); (M.L.H.); (M.M.R.); (L.M.B.)
| | - Donald S. Grant
- Lassa Fever Program, Kenema Government Hospital, Kenema, Sierra Leone; (M.M.); (A.G.); (L.K.); (F.A.); (M.G.); (R.J.S.)
- Correspondence: (J.G.S.); (J.S.S.); (D.S.G.); Tel.: +1-504-988-1142 (J.G.S.); +1-504-988-5117 (D.S.G.)
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Samuels RJ, Moon TD, Starnes JR, Alhasan F, Gbakie M, Goba A, Koroma V, Momoh M, Sandi JD, Garry RF, Engel EJ, Shaffer JG, Schieffelin JS, Grant DS. Lassa Fever among Children in Eastern Province, Sierra Leone: A 7-year Retrospective Analysis (2012-2018). Am J Trop Med Hyg 2020; 104:585-592. [PMID: 33241780 PMCID: PMC7866338 DOI: 10.4269/ajtmh.20-0773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 01/09/2023] Open
Abstract
Pediatric Lassa fever (LF) usually presents as a nonspecific febrile illness, similar to other endemic diseases in countries like Sierra Leone, where LF is considered to be hyperendemic. The nonspecificity of presentation and lack of research have made it difficult to fully understand best practices for pediatric management. We aim to describe clinical characteristics of hospitalized pediatric patients suspected or diagnosed with LF and assess factors associated with hospital outcomes among those with LF antigen-positive results. We conducted a 7-year retrospective cohort study using routine data for all children younger than 18 years admitted at the Kenema Government Hospital's LF ward. A total of 292 children with suspected or confirmed LF were analyzed. Overall, mortality was high (21%). Children with antigen-positive results had a high case fatality rate of 63% (P < 0.01). In univariate analyses, children who presented with unexplained bleeding (odds ratio [OR]: 3.58; 95% CI: 1.08-11.86; P = 0.040) and confusion (altered sensorium) (OR: 5.37; 95% CI: 1.34-21.48; P = 0.020) had increased odds of death. Abnormal serum levels of alanine aminotransferase (P = 0.001), creatinine (P = 0.004), and potassium (P = 0.003) were associated with increased likelihood of death in these children. Treatment with ribavirin was not significantly associated with survival (P = 0.916). Our findings provide insights into current pediatric LF clinical presentation and management. More evidence-based, high-quality research in creating predictive algorithms of antigen-positivity and hospital outcomes is needed in the management of pediatric LF.
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Affiliation(s)
- Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone.,Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Troy D Moon
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph R Starnes
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Foday Alhasan
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Michael Gbakie
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Veronica Koroma
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mambu Momoh
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Robert F Garry
- Department of Immunology and Microbiology, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Emily J Engel
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana
| | - Jeffrey G Shaffer
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana
| | - John S Schieffelin
- Department of Pediatrics and Internal Medicine, Sections of Pediatric and Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, Louisiana.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S Grant
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone.,Lassa Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
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Kenmoe S, Tchatchouang S, Ebogo-Belobo JT, Ka'e AC, Mahamat G, Guiamdjo Simo RE, Bowo-Ngandji A, Demeni Emoh CP, Che E, Tchami Ngongang D, Amougou-Atsama M, Nzukui ND, Mbongue Mikangue CA, Mbaga DS, Kenfack S, Kingue Bebey SR, Amvongo Adjia N, Efietngab AN, Tazokong HR, Modiyinji AF, Kengne-Nde C, Sadeuh-Mba SA, Njouom R. Systematic review and meta-analysis of the epidemiology of Lassa virus in humans, rodents and other mammals in sub-Saharan Africa. PLoS Negl Trop Dis 2020; 14:e0008589. [PMID: 32845889 PMCID: PMC7478710 DOI: 10.1371/journal.pntd.0008589] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/08/2020] [Accepted: 07/13/2020] [Indexed: 12/27/2022] Open
Abstract
Accurate data on the Lassa virus (LASV) human case fatality rate (CFR) and the prevalence of LASV in humans, rodents and other mammals are needed for better planning of actions that will ultimately reduce the burden of LASV infection in sub-Saharan Africa. In this systematic review with meta-analysis, we searched PubMed, Scopus, Africa Journal Online, and African Index Medicus from 1969 to 2020 to obtain studies that reported enough data to calculate LASV infection CFR or prevalence. Study selection, data extraction, and risk of bias assessment were conducted independently. We extracted all measures of current, recent, and past infections with LASV. Prevalence and CFR estimates were pooled using a random-effect meta-analysis. Factors associated with CFR, prevalence, and sources of between-study heterogeneity were determined using subgroup and metaregression analyses. This review was registered with PROSPERO, CRD42020166465. We initially identified 1,399 records and finally retained 109 reports that contributed to 291 prevalence records from 25 countries. The overall CFR was 29.7% (22.3-37.5) in humans. Pooled prevalence of LASV infection was 8.7% (95% confidence interval: 6.8-10.8) in humans, 3.2% (1.9-4.6) in rodents, and 0.7% (0.0-2.3) in other mammals. Subgroup and metaregression analyses revealed a substantial statistical heterogeneity explained by higher prevalence in tissue organs, in case-control, in hospital outbreak, and surveys, in retrospective studies, in urban and hospital setting, in hospitalized patients, and in West African countries. This study suggests that LASV infections is an important cause of death in humans and that LASV are common in humans, rodents and other mammals in sub-Saharan Africa. These estimates highlight disparities between sub-regions, and population risk profiles. Western Africa, and specific key populations were identified as having higher LASV CFR and prevalence, hence, deserving more attention for cost-effective preventive interventions.
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Affiliation(s)
- Sebastien Kenmoe
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | | | - Jean Thierry Ebogo-Belobo
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Aude Christelle Ka'e
- Virology Department, Chantal Biya International Reference Centre, Yaoundé, Cameroon
| | - Gadji Mahamat
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Arnol Bowo-Ngandji
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Emmanuel Che
- Vaccinology and Biobank, Chantal Biya International Reference Centre, Yaounde, Cameroon
| | - Dimitri Tchami Ngongang
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Marie Amougou-Atsama
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Nathalie Diane Nzukui
- School of Health Sciences-Catholic University of Central Africa, Department of Medical Microbiology, Yaoundé, Cameroon
| | | | - Donatien Serge Mbaga
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Sorel Kenfack
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Nathalie Amvongo Adjia
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Atembeh Noura Efietngab
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Hervé Raoul Tazokong
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Abdou Fatawou Modiyinji
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Department of Animals Biology and Physiology, Faculty of Science, The University of Yaoundé I, Yaoundé, Cameroon
| | - Cyprien Kengne-Nde
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Yaoundé, Cameroon
| | | | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
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Abstract
In a pattern repeated across a range of ecological niches, arenaviruses have evolved a compact four-gene genome to orchestrate a complex life cycle in a narrow range of susceptible hosts. A number of mammalian arenaviruses cross-infect humans, often causing a life-threatening viral hemorrhagic fever. Among this group of geographically bound zoonoses, Lassa virus has evolved a unique niche that leads to significant and sustained human morbidity and mortality. As a biosafety level 4 pathogen, direct study of the pathogenesis of Lassa virus is limited by the sparse availability, high operating costs, and technical restrictions of the high-level biocontainment laboratories required for safe experimentation. In this chapter, we introduce the relationship between genome structure and the life cycle of Lassa virus and outline reverse genetic approaches used to probe and describe functional elements of the Lassa virus genome. We then review the tools used to obtain viral genomic sequences used for phylogeny and molecular diagnostics, before shifting to a population perspective to assess the contributions of phylogenetic analysis in understanding the evolution and ecology of Lassa virus in West Africa. We finally consider the future outlook and clinical applications for genetic study of Lassa virus.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA
| | - Samar B Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Judith U Oguzie
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Paul E Oluniyi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Matthias G Pauthner
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA
| | | | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute , La Jolla, CA, USA.
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemers University, Ede, Osun State, Nigeria
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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