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African Pathogen Genomics Initiative (Noguchi Africa CDC/WHO Regional Sequencing Hub): HIV drug resistance profile, SARS-CoV-2 and Bacterial Infections in Persons Living with HIV

African Pathogen Genomics Initiative (Noguchi Africa CDC/WHO Regional Sequencing Hub): HIV drug resistance profile, SARS-CoV-2 and Bacterial Infections in Persons Living with HIV

Project Lead(s)
DR. BRIGHT ADU (SENIOR RESEARCH FELLOW)
Dr. Bright Adu
Senior Research Fellow
Project Background 

The emergence of new and more transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe is of major public health concern. These variants are termed variants of concern (VOC) and have been associated with immune escape. It has been reported that immunosuppressed HIV individuals who are on ineffective antiretroviral therapy (ART) have persisted SARS-CoV-2 infections leading to the emergence of mutations that are distinct from the common circulating ones in the population.  

In this project we aim at strengthening pathogen genomics in Ghana and the West African sub-region which includes Togo, Benin, Liberia and Sierra Leone to detect the emergence of potential VOC of SARS-CoV-2 either in the general population or in immunosuppressed individuals. This will be achieved through Next Generation Sequencing and bioinformatics training at the Noguchi Memorial Institute for Medical Research (NMIMR) of the University of Ghana which is a Regional Genomic Sequencing Laboratory under the Africa Pathogen Genomics Initiative (Africa-PGI) as well as the National HIV genotyping reference laboratory for Ghana. Another major impact of the project will be its direct contribution to the success of ART outcomes in HIV patients since resistance can be detected promptly to inform quick and effective changes in drugs being administered. Also, it will contribute significantly to the availability of HIV genomes from Ghana in the international genome repositories for the wider scientific community. Finally, this project will ensure the availability of critically needed expertise in post-analysis of genomic sequencing data which is currently lacking in Africa. 

Objectives/Research Areas 

With SARS-CoV-2 gradually becoming an endemic pathogen, it is imperative to devise innovative strategies of rapidly detecting the emergence of VOC for effective public health intervention to mitigate their spread. Since 2021, the NMIMR has built substantial capacity in Next Generation Sequencing (NGS) and supported the regional countries, namely Ghana, Benin, Togo, Liberia and Sierra Leone assigned to it under the Africa-PGI through sequencing of nearly 4,000 SARS-CoV-2 samples. Therefore, the aim of this project is to conduct SARS-CoV-2 genomic surveillance in Ghana and support Togo, Benin, Liberia and Sierra Leone do same in addition to providing HIV drug resistance genomic data to support effective ART in Ghana. 

  

 Specific aims 

  1. To conduct genomic surveillance to detect circulating and emergence of new variants of SARS-CoV-2 that may become VOC in Ghana and the West African sub-region.  
  2.  To conduct SARS-CoV-2 genomic sequencing in immunocompromised individuals, particularly those living with HIV. 
  3. To conduct molecular characterization of genomes and drug resistance strains of HIV in Ghana.   
  4. To conduct pathogen genomics data analysis and strengthen bioinformatics capacity in Ghana and the sub-region.  
Key Findings 

The study has revealed the pattern of spread of new SARS-CoV-2 variants in the Ghanaian population. 

In collaboration with other members of the Africa-PGI, our aggregated data in phase 1 of the project has shown the pattern of importation and exportation of SARS-CoV-2 variants within and outside of Africa 

Ongoing Activities  
  • Continuous genomic surveillance of SARS-CoV-2 variants in the Ghanaian population and within the sub-region. 
  • Training of laboratory personnel from Togo in SARS-CoV-2 genomic sequencing and bioinformatics. 
  • Preparation for the initiation of HIV and bacterial drug resistance surveillance in HIV patients 
Key Publications  
  1. Bright Adu, Joseph H.K. Bonney, Beverly Egyir, Isaac Darko Otchere, Prince Asare, Francis E. Dennis, Evelyn Yayra Bonney, Richard Akuffo, Ivy A. Asante, Evangeline Obodai, Selassie Kumordjie, Joyce Appiah-Kubi, Quaneeta Mohktar, Hilda Opoku Frempong, Franklin Asiedu-Bekoe, Mildred A. Adusei-Poku, James O. Aboagye, Bright Agbodzi, Clara Yeboah, Seyram B. Agbenyo, Peace O. Uche, Keren O. Attiku, Bernice Twenewaa Sekyere, Dennis Laryea, Kwame Buabeng, Helena Lamptey, Anita Ghansah, Dorothy Yeboah-Manu, Abraham K. Anang, William K. Ampofo, George B. Kyei, John K. Odoom. SARS-CoV-2 molecular evolutionary dynamics in the Greater-Accra region of Ghana. Under review 
  2. Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri AN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang'a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O'Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science. 2022 Sep 15;:eabq5358. doi: 10.1126/science.abq5358. [Epub ahead of print] PubMed PMID: 36108049. 
  3.  
Team 
External Collaborator(s) 
Dr. Afiwa Wemboo Halatoko, Institut National d'Hygiène Lomé; Togo
Dr. Fahn M. Taweh, National Public Health Reference Laboratory-National Public Health Institute of Liberia, Charlesville, Margibi County-Liberia
Ms. Doris Harding, National Program Manager, Public Health Laboratories, Sierra Leone
Dr. Anges Yadouleton, Laboratoire des Fièvres Virales Hémorragiques (LFVH)/ Ministère de la Santé du Bénin
Funder(s) 
African Union Commission and African Society for Laboratory Medicine