ABSTRACT
BACKGROUND: Despite the development of several methods for diagnosing COVID-19, long-term validation of such methods remains limited. In the early phase of the COVID-19 pandemic, we developed a rapid and sensitive diagnostic method based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) methodology, which is suitable for point-of-care application or for use in resource-limited settings to detect SARS-CoV-2. To assess the applicability of the RT-LAMP assay technique to resource-limited regions, such as rural areas in Africa, and to verify the usability of the method against various SARS-CoV-2 variants, the method was validated using clinical samples collected longitudinally during the pandemic. METHODOLOGY/PRINCIPAL FINDINGS: First, the sensitivity of the RT-LAMP assay for detecting 10 SARS-CoV-2 variants was evaluated using viral RNA samples extracted from cell culture with a portable battery-supported device, resulting in the successful detection of 20-50 copies of the viral genome within 15 min, regardless of the variant. COVID-19 positive samples collected in Gabon between March 2020 and October 2021 were used to evaluate the sensitivity of the assay and to calculate the copy number of the SARS-CoV-2 genome. More than 292 copies of the viral genome were detected with 100% probability within 15 min in almost all tests. CONCLUSIONS: This long-term validation study clearly demonstrated the applicability of the RT-LAMP assay for the clinical diagnosis of COVID-19 in resource-limited settings of Africa, such as rural areas in Gabon. The results show the potential of the assay as a promising COVID-19 diagnostic method, especially in rural and remote regions located far from the official diagnosis facilities in urban or semi-urban areas.
ABSTRACT
OBJECTIVE: Variants of concern (VOCs) associated with relatively high transmissibility appear to be rapidly spreading in Gabon. Therefore, it is imperative to understand the distribution of several VOCs in the population, which could have implications for transmissibility and vaccine efficacy. METHODS: Between February and May 2021, SARS-CoV-2 genomes were sequenced using the Oxford nanopore MinION method and the respective genome diversity was elucidated. Phylogenetic analysis was performed and genomes were classified using pangolin lineages. RESULTS: The results highlighted an increase (46%) in the alpha VOC (B.1.1.7) in the Gabonese population over the study period. In addition, an increase (31%) in the B.1.1.318 lineage, which is associated with high transmission and impaired vaccine efficacy (D614G+E484K+Y144del), was detected. CONCLUSION: With the second wave ongoing, these findings highlight the need for surveillance of the SARS-CoV-2 genome in the Republic of Gabon and should provide useful guidance to policymakers in selecting an appropriate vaccine for this population.
Subject(s)
COVID-19 , SARS-CoV-2 , Gabon/epidemiology , Humans , Incidence , Mutation , Phylogeny , Vaccine EfficacyABSTRACT
The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern with higher infectivity has already resulted in the enormous increase in infection cases worldwide. We report an unrecognized introduction of the variant B.1.1.7 in Gabon in December 2020, which was the initial phase of the variant introduction to Africa. The B.1.1.7 variant was also detected in a hospitalized patient in January 2021, indicating a rapid spread of the variant in Gabon since its first detection. Phylogenetic analysis revealed that the detected B.1.1.7 variants originated from the distinct regions, strongly suggesting that the B.1.1.7 variant had been repeatedly introduced to Gabon since December 2020. These results provide insights on the unrecognized risks of infections with variants of concern, and show the necessity to conduct continuous genomic monitoring for immediate alert and control of novel SARS-CoV-2 variant infections.