- Introduction
- Materials and Methods
- Study design and setting.
- Sample collection and laboratory procedures.
- RNA extraction from clinical samples.
- One-step real-time reverse-transcription polymerase chain reaction for the detection of influenza viruses.
- Virus isolation and sequencing.
- Data management and analysis.
- Statistical analysis.
- Ethical considerations.
- Results
- Discussion
ProCite
RefWorks
Reference Manager
BibTeX
Zotero
EndNote
-
1.
Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, Garten RJ, Gubareva LV, Xu X, Bridges CB, Uyeki TM, 2009. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 360: 2605–2615.
-
2.
Enserink M, Cohen J, 2009. Virus of the year. The novel H1N1 influenza. Science 326: 1607.
-
3.
Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ, 2009. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197–201.
-
4.
World Health Organization, 2010. Pandemic (H1N1) 2009—Update 112. Available at: http://www.who.int/csr/don/2010_08_06/en/index.html.
-
5.
CDC, 2009. 2009 H1N1 Flu: International Situation Update. Atlanta, GA: Centers for Disease Control and Prevention.
-
6.
Dosseh A, Ndiaye K, Spiegel A, Sagna M, Mathiot C, 2000. Epidemiological and virological influenza survey in Dakar, Senegal: 1996–1998. Am J Trop Med Hyg 62: 639–643.
-
7.
World Health Organization, 2002. WHO Manual on Animal influenza Diagnosis and Surveillance. Geneva: World Health Organization.
-
8.
Hall TA, 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
-
9.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
-
10.
World Health Organization, 2009. Global Alert and Response (GAR). Situation Updates—Pandemic (H1N1) 2009. Geneva: World Health Organization.
-
11.
World Health Organization. Recommended Viruses for Influenza Vaccines for Use in the 2010–2011 Northern Hemisphere Influenza Season, 2010. Available at: http://www.who.int/influenza/vaccines/virus/recommendations/20100_Recommendation.pdf.
-
12.
Potdar VA, Chadha MS, Jadhav SM, Mullick J, Cherian SS, Mishra AC, 2010. Genetic characterization of the influenza A pandemic (H1N1) 2009 virus isolates from India. PLoS One 5: e9693.
-
13.
Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, Viboud C, Holmes E, Henrickson K, 2009. The early diversification of influenza A/H1N1pdm. PLoS Curr 1: RRN1126.
-
14.
Nzussouo NT, Michalove J, Diop OM, Njouom R, Monteiro M de L, Adje HK, Manoncourt S, Amankwa J, Koivogui L, Sow S, Elkory MB, Collard JM, Dalhatu I, Niang MN, Lafond K, Moniz F, Coulibaly D, Kronman KC, Oyofo BA, Ampofo W, Tamboura B, Bara AO, Jusot JF, Ekanem E, Sarr FD, Hwang I, Cornelius C, Coker B, Lindstrom S, Davis R, Dueger E, Moen A, Widdowson MA, 2012. Delayed 2009 pandemic influenza A virus subtype H1N1 circulation in West Africa, May 2009–April 2010. J Infect Dis 206 (Suppl 1): S101–S107.
-
15.
Lowen AC, Steel J, Mubareka S, Palese P, 2008. High temperature (30 degrees C) blocks aerosol but not contact transmission of influenza virus. J Virol 82: 5650–5652.
-
16.
Steel J, Palese P, Lowen AC, 2010. Transmission of a 2009 pandemic influenza virus shows similar sensitivity to temperature and humidity as an H3N2 seasonal strain. J Virol 85: 1400–1402.
-
17.
Jusot JF, Adamou L, Collard JM, 2012. Influenza transmission during a one-year period (2009–2010) in a Sahelian city: low temperature plays a major role. Influenza Other Respi Viruses 6: 87–89.
-
18.
Karageorgopoulos DE, Vouloumanou EK, Korbila IP, Kapaskelis A, Falagas ME, 2011. Age distribution of cases of 2009 (H1N1) pandemic influenza in comparison with seasonal influenza. PLoS One 6: e21690.
-
19.
Falagas ME, Koletsi PK, Baskouta E, Rafailidis PI, Dimopoulos G, Karageorgopoulos DE, 2011. Pandemic A(H1N1) 2009 influenza: review of the Southern Hemisphere experience. Epidemiol Infect 139: 27–40.
-
20.
Hancock K, Veguilla V, Lu X, Zhong W, Butler EN, Sun H, Liu F, Dong L, DeVos JR, Gargiullo PM, Brammer TL, Cox NJ, Tumpey TM, Katz JM, 2009. Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus. N Engl J Med 361: 1945–1952.
-
21.
Niang MN, Dosseh A, Ndiaye K, Sagna M, Gregory V, Goudiaby D, Hay A, Diop OM, 2012. Sentinel surveillance for influenza in Senegal, 1996–2009. J Infect Dis 206 (Suppl 1): S129–S135.
-
22.
Ferreira JL, Borborema SE, Brígido LF, Oliveira MI, Paiva TM, Santos CL, 2011. Sequence analysis of the 2009 pandemic influenza A H1N1 virus haemagglutinin gene from 2009–2010 Brazilian clinical samples. Mem Inst Oswaldo Cruz 106: 613–616.
-
23.
Stevens J, Corper AL, Basler CF, Taubenberger JK, Palese P, Wilson IA, 2004. Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science 303: 1866–1870.
-
24.
World Health Organization, 2009. Pandemic (H1N1): Update 76. Geneva: World Health Organization.
-
25.
Reid AH, Fanning TG, Hultin JV, Taubenberger JK, 1999. Origin and evolution of the 1918 ‘Spanish’ influenza virus hemagglutinin gene. Proc Natl Acad Sci USA 96: 1651–1656.
-
26.
Glinsky GV, 2010. Genomic analysis of pandemic (H1N1) 2009 reveals association of increasing disease severity with emergencof novel hemagglutinin mutations. Cell Cycle 9: 958–970.
-
27.
Meijer A, Lackenby A, Hungnes O, Lina B, van-der-Werf S, Schweiger B, Opp M, Paget J, van-de-Kassteele J, Hay A, Zambon M, 2009. Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007–08 season. Emerg Infect Dis 15: 552–560.
| Past two years | Past Year | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 1183 | 1020 | 184 |
| Full Text Views | 413 | 10 | 0 |
| PDF Downloads | 88 | 12 | 0 |
A Subregional Analysis of Epidemiologic and Genetic Characteristics of Influenza A(H1N1)pdm09 in Africa: Senegal, Cape Verde, Mauritania, and Guinea, 2009–2010
Ndongo Dia
Ndongo Dia
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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Mbayame Niang Ndiaye
Mbayame Niang Ndiaye
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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Maria de Lourdes Monteiro
Maria de Lourdes Monteiro
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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Lamine Koivogui
Lamine Koivogui
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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Mohamed Ould Bara
Mohamed Ould Bara
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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Ousmane M. Diop
Ousmane M. Diop
Institut Pasteur de Dakar, Dakar, Senegal; Ministry of Health, Praia, Cape Verde; Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea; Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritania; Ministry of Health, Mauritania
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During the pandemic 2009 episode, we conducted laboratory-based surveillance in four countries from West Africa: Senegal, Mauritania, Cape Verde, and Guinea. Specimens were obtained from 3,155 patients: 2,264 patients from Senegal, 498 patients from Cape Verde, 227 patients from Mauritania, and 166 patients from Guinea; 911 (28.9%) patients were positive for influenza, 826 (90.7%) patients were positive for influenza A, and 85 (9.3%) patients were positive for influenza B. Among the influenza A positives, 503 (60.9%) positives were H1N1pdm09, 314 (38.0%) positives were H3N2, and 9 (1.1%) positives were seasonal H1N1. The highest detection rate for seasonal influenza viruses (17.1%) occurred in the 5–14 years age group. However, for A(H1N1)pdm09, the detection rate was highest in the 15–24 years age group (35.8%). Based on the present study data, the timeline of detection of A(H1N1)pdm09 viruses in these four countries should be Cape Verde, Guinea, Mauritania, and finally, Senegal. Genetic and antigenic analyses were performed in some isolates.
Author Notes
Financial support: This work was funded by Institut Pasteur de Dakar (Senegal), the WHO, the French Ministry of Health/Établissement de Préparation et de Réponse aux Urgences Sanitaires (EPRUS), and the US Department of Health and Human Services.
Authors' addresses: Ndongo Dia, Mbayame Niang Ndiaye, and Ousmane M. Diop, Institut Pasteur de Dakar, Dakar, Senegal, E-mails: ndia@pasteur.sn, niang@pasteur.sn, and diopo@who.int. Maria de Lourdes Monteiro, Ministry of Health, Praia, Cape Verde, E-mail: marial.Monteiro@ms.gov.cv. Lamine Koivogui, Laboratoire de Virologie, Hôpital Donka, Conackry, Guinea, E-mail: koivogui@biasy.net. Mohamed Ould Bara, Institut National de Recherches en Santé Publique (INRSP), Laboratoire de Virologie, Nouakchott, Mauritanie, E-mail: elbaraahmed@yahoo.fr.
Reprint requests: Mbayame Niang Ndiaye, Institut Pasteur de Dakar, 36 Avenue Pasteur, Dakar, Senegal, BP 220, E-mail: niang@pasteur.sn.
- Introduction
- Materials and Methods
- Study design and setting.
- Sample collection and laboratory procedures.
- RNA extraction from clinical samples.
- One-step real-time reverse-transcription polymerase chain reaction for the detection of influenza viruses.
- Virus isolation and sequencing.
- Data management and analysis.
- Statistical analysis.
- Ethical considerations.
- Results
- Discussion
ProCite
RefWorks
Reference Manager
BibTeX
Zotero
EndNote
-
1.
Dawood FS, Jain S, Finelli L, Shaw MW, Lindstrom S, Garten RJ, Gubareva LV, Xu X, Bridges CB, Uyeki TM, 2009. Emergence of a novel swine-origin influenza A (H1N1) virus in humans. N Engl J Med 360: 2605–2615.
-
2.
Enserink M, Cohen J, 2009. Virus of the year. The novel H1N1 influenza. Science 326: 1607.
-
3.
Garten RJ, Davis CT, Russell CA, Shu B, Lindstrom S, Balish A, Sessions WM, Xu X, Skepner E, Deyde V, Okomo-Adhiambo M, Gubareva L, Barnes J, Smith CB, Emery SL, Hillman MJ, Rivailler P, Smagala J, de Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD Jr, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ, 2009. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 325: 197–201.
-
4.
World Health Organization, 2010. Pandemic (H1N1) 2009—Update 112. Available at: http://www.who.int/csr/don/2010_08_06/en/index.html.
-
5.
CDC, 2009. 2009 H1N1 Flu: International Situation Update. Atlanta, GA: Centers for Disease Control and Prevention.
-
6.
Dosseh A, Ndiaye K, Spiegel A, Sagna M, Mathiot C, 2000. Epidemiological and virological influenza survey in Dakar, Senegal: 1996–1998. Am J Trop Med Hyg 62: 639–643.
-
7.
World Health Organization, 2002. WHO Manual on Animal influenza Diagnosis and Surveillance. Geneva: World Health Organization.
-
8.
Hall TA, 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
-
9.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
-
10.
World Health Organization, 2009. Global Alert and Response (GAR). Situation Updates—Pandemic (H1N1) 2009. Geneva: World Health Organization.
-
11.
World Health Organization. Recommended Viruses for Influenza Vaccines for Use in the 2010–2011 Northern Hemisphere Influenza Season, 2010. Available at: http://www.who.int/influenza/vaccines/virus/recommendations/20100_Recommendation.pdf.
-
12.
Potdar VA, Chadha MS, Jadhav SM, Mullick J, Cherian SS, Mishra AC, 2010. Genetic characterization of the influenza A pandemic (H1N1) 2009 virus isolates from India. PLoS One 5: e9693.
-
13.
Nelson M, Spiro D, Wentworth D, Beck E, Fan J, Ghedin E, Halpin R, Bera J, Hine E, Proudfoot K, Stockwell T, Lin X, Griesemer S, Kumar S, Bose M, Viboud C, Holmes E, Henrickson K, 2009. The early diversification of influenza A/H1N1pdm. PLoS Curr 1: RRN1126.
-
14.
Nzussouo NT, Michalove J, Diop OM, Njouom R, Monteiro M de L, Adje HK, Manoncourt S, Amankwa J, Koivogui L, Sow S, Elkory MB, Collard JM, Dalhatu I, Niang MN, Lafond K, Moniz F, Coulibaly D, Kronman KC, Oyofo BA, Ampofo W, Tamboura B, Bara AO, Jusot JF, Ekanem E, Sarr FD, Hwang I, Cornelius C, Coker B, Lindstrom S, Davis R, Dueger E, Moen A, Widdowson MA, 2012. Delayed 2009 pandemic influenza A virus subtype H1N1 circulation in West Africa, May 2009–April 2010. J Infect Dis 206 (Suppl 1): S101–S107.
-
15.
Lowen AC, Steel J, Mubareka S, Palese P, 2008. High temperature (30 degrees C) blocks aerosol but not contact transmission of influenza virus. J Virol 82: 5650–5652.
-
16.
Steel J, Palese P, Lowen AC, 2010. Transmission of a 2009 pandemic influenza virus shows similar sensitivity to temperature and humidity as an H3N2 seasonal strain. J Virol 85: 1400–1402.
-
17.
Jusot JF, Adamou L, Collard JM, 2012. Influenza transmission during a one-year period (2009–2010) in a Sahelian city: low temperature plays a major role. Influenza Other Respi Viruses 6: 87–89.
-
18.
Karageorgopoulos DE, Vouloumanou EK, Korbila IP, Kapaskelis A, Falagas ME, 2011. Age distribution of cases of 2009 (H1N1) pandemic influenza in comparison with seasonal influenza. PLoS One 6: e21690.
-
19.
Falagas ME, Koletsi PK, Baskouta E, Rafailidis PI, Dimopoulos G, Karageorgopoulos DE, 2011. Pandemic A(H1N1) 2009 influenza: review of the Southern Hemisphere experience. Epidemiol Infect 139: 27–40.
-
20.
Hancock K, Veguilla V, Lu X, Zhong W, Butler EN, Sun H, Liu F, Dong L, DeVos JR, Gargiullo PM, Brammer TL, Cox NJ, Tumpey TM, Katz JM, 2009. Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus. N Engl J Med 361: 1945–1952.
-
21.
Niang MN, Dosseh A, Ndiaye K, Sagna M, Gregory V, Goudiaby D, Hay A, Diop OM, 2012. Sentinel surveillance for influenza in Senegal, 1996–2009. J Infect Dis 206 (Suppl 1): S129–S135.
-
22.
Ferreira JL, Borborema SE, Brígido LF, Oliveira MI, Paiva TM, Santos CL, 2011. Sequence analysis of the 2009 pandemic influenza A H1N1 virus haemagglutinin gene from 2009–2010 Brazilian clinical samples. Mem Inst Oswaldo Cruz 106: 613–616.
-
23.
Stevens J, Corper AL, Basler CF, Taubenberger JK, Palese P, Wilson IA, 2004. Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus. Science 303: 1866–1870.
-
24.
World Health Organization, 2009. Pandemic (H1N1): Update 76. Geneva: World Health Organization.
-
25.
Reid AH, Fanning TG, Hultin JV, Taubenberger JK, 1999. Origin and evolution of the 1918 ‘Spanish’ influenza virus hemagglutinin gene. Proc Natl Acad Sci USA 96: 1651–1656.
-
26.
Glinsky GV, 2010. Genomic analysis of pandemic (H1N1) 2009 reveals association of increasing disease severity with emergencof novel hemagglutinin mutations. Cell Cycle 9: 958–970.
-
27.
Meijer A, Lackenby A, Hungnes O, Lina B, van-der-Werf S, Schweiger B, Opp M, Paget J, van-de-Kassteele J, Hay A, Zambon M, 2009. Oseltamivir-resistant influenza virus A (H1N1), Europe, 2007–08 season. Emerg Infect Dis 15: 552–560.
| Past two years | Past Year | Past 30 Days | |
|---|---|---|---|
| Abstract Views | 1183 | 1020 | 184 |
| Full Text Views | 413 | 10 | 0 |
| PDF Downloads | 88 | 12 | 0 |