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
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.
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.
- 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.
- To conduct SARS-CoV-2 genomic sequencing in immunocompromised individuals, particularly those living with HIV.
- To conduct molecular characterization of genomes and drug resistance strains of HIV in Ghana.
- To conduct pathogen genomics data analysis and strengthen bioinformatics capacity in Ghana and the sub-region.
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
- 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
- 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
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