SARS-CoV-2 genome analysis could boost disease surveillance

Continued monitoring of the evolution of the virus that causes COVID-19 as the pandemic progresses could strengthen disease surveillance systems and aid preparedness for new variants, a study suggests.

Last year, the World Health Organization (WHO) indicated that identifying the genetic makeup of the virus that causes COVID-19 called SARS-CoV-2 could play a critical role in managing the COVID-19 pandemic.

According to the study published in nature communication this month (May 6) researchers assessed the genetic diversity of the variants of SARS-CoV-2 linked to infections in Ghana from March 2020 to September 2021.

We observed the entry of several variants, including variants of concern (Alpha, Beta, Eta and Kappa) in January and March 2021, and subsequent detection of Delta in June 2021.”


Collins Morang’a, study co-author and bioinformatician from the Ghana-based West African Center for Cell Biology of Infectious Pathogens at the University of Ghana

“Travellers from neighboring countries such as Burkina Faso, Ivory Coast and Nigeria had some of these variants, although they had not yet been reported in these countries at the time.”

According to the study, a total of 1,123 genomes, consisting of samples from 121 travelers and 1,002 community members, were analyzed, resulting in the observation that several variants were responsible for the COVID-19 disease waves in the country.

“Genetic diversity of SARS-CoV-2 infections represents the intrinsic differences between the SARS-CoV-2 variants … which could enhance the ability of the virus to readily bind to the human cells, the ability of the human immune system to the virus, reduce the ability to detect the virus during testing and/or increase the ability of the virus to multiply in the body,” the study said.

Morang’a, explained that the study provides valuable insight into the variants that are circulating or in circulation and how they may limit the effectiveness of vaccines.

Morang’a said all genomic data storage and bioinformatics analyzes were performed on the high-performance computing cluster of the University of Ghana and then deposited in a database of GISAID, a global flu data sharing initiative, which openly is accessible.

“Unexpectedly, a variant monitored in countries like Mauritius was discovered in travelers from Gabon and Nigeria and suddenly dominated infections from April to June 2021,” he said, adding that after the Delta variant was detected in travelers who were most dominant variant (32 percent), it quickly spread across the country and became the most dominant lineage in July 2021 and remained so in Ghana until September 2021.

The study aimed to provide a framework for ongoing monitoring of SARS-CoV-2 evolution in Ghana and Africa in general, Morang’a explained, adding that it represents an important milestone in local genome sequencing capacity building. and analysis in Sub-Saharan Africa.

Segun Fatumo, group leader of African Computational Genomics and associate professor of epidemiology of non-communicable diseases at the London School of Hygiene & Tropical Medicine in England, said the study represented the most comprehensive genomic analysis of COVID-19 viruses in Ghana.

“Using the SARS-CoV-2 genomic sequence of over a thousand individuals, the authors were able to track molecular evolution and their variants in Ghana, showing the transfer of SARS-CoV-2 variants from other countries to Ghana. Fatumo said.

He added that the study offered African policymakers the opportunity to strengthen disease surveillance systems and create policies that would help prepare for the next pandemic.

Morang’a said the COVID-19 pandemic is unlikely to end and Africa must remain vigilant to fight it as new variants may emerge around the world, adding that vaccinations and therapeutic options should be prioritized.

Source:

Reference magazine:

Morang’a, CM, et al. (2022) Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021. Nature Communication. doi.org/10.1007/s12274-022-4457-5

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