Background Deadly emerging infectious pathogens pose an unprecedented challenge to health systems worldwide, especially in the Republic of Congo, where health care infrastructure is limited. Thus the COVID-19 pandemic has been an opportunity to improve the national genomic platform that could be expand to all circulating pathogens serving surveillance, prevention and response actions. This work aimed to establish the genomic platform for the effective control of infectious pathogens in the Republic of Congo.

Methods By 2021, we established the Oxford Nanopore Technology platform for the first time in the Republic of Congo to respond firstly to the COVID-19 pandemic and secondly to other pathogens like Plasmodium falciparum, Mycobacterium tuberculosis, HIV and others. Between April 2020 and August 2022, a total of 1200 oropharyngeal samples were tested positive for SARS-CoV-2 by RT-PCR. Of these samples, 589 with Ct< 28 were selected for sequencing by ONT next generation sequencing (NGS). All the complete sequenced genomes were submitted on GISAID for publication, and variants were identified using Pangolin and Nextclade nomenclature.

Results A total of 381 SARS-CoV-2 whole genomes were successfully sequenced and submitted on GISAID. Our results revealed the circulation of 21 SARS-CoV-2 variants in the Republic of Congo during the study period, with the presence of variants of concern such as alpha (B.1.1.7), delta (B.1.617.2) and Omicron (B.1.1.519). Four waves of the virus epidemics were observed during this study period. The B.1.640.1 variant was reported for the first time in the Republic of Congo through this study, and was observed to be spreading locally and regionally.

Conclusion This work contributed to monitor in a daily basis the spread of SARS-CoV-2 in the country to support the national containment strategies of the pandemic. This established platform is serving for the identification of other pathogens that could represent a threat of public health.