Dataset Information

Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021.

ABSTRACT: The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

SUBMITTER: Morang'a CM

PROVIDER: S-EPMC9076825 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021.

Morang'a Collins M CM Ngoi Joyce M JM Gyamfi Jones J Amuzu Dominic S Y DSY Nuertey Benjamin D BD Soglo Philip M PM Appiah Vincent V Asante Ivy A IA Owusu-Oduro Paul P Armoo Samuel S Adu-Gyasi Dennis D Amoako Nicholas N Oliver-Commey Joseph J Owusu Michael M Sylverken Augustina A Fenteng Edward D ED M'cormack Violette V VV Tei-Maya Frederick F Quansah Evelyn B EB Ayivor-Djanie Reuben R Amoako Enock K EK Ogbe Isaac T IT Yemi Bright K BK Osei-Wusu Israel I Mettle Deborah N A DNA Saiid Samirah S Tapela Kesego K Dzabeng Francis F Magnussen Vanessa V Quaye Jerry J Opurum Precious C PC Carr Rosina A RA Ababio Patrick T PT Abass Abdul-Karim AK Akoriyea Samuel K SK Amoako Emmanuella E Kumi-Ansah Frederick F Boakye Oliver D OD Mibut Dam K DK Odoom Theophilus T Ofori-Boadu Lawrence L Allegye-Cudjoe Emmanuel E Dassah Sylvester S Asoala Victor V Asante Kwaku P KP Phillips Richard O RO Osei-Atweneboana Mike Y MY Gyapong John O JO Kuma-Aboagye Patrick P Ampofo William K WK Duedu Kwabena O KO Ndam Nicaise T NT Bediako Yaw Y Quashie Peter K PK Amenga-Etego Lucas N LN Awandare Gordon A GA

Nature communications 20220506 1

The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driv ...[more]

PMID: 35523782

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Project description:BackgroundVaccines for coronavirus disease 2019 (COVID-19) are proving to be very effective in preventing severe illness; however, although rare, post-vaccine infections have been reported. The present study focuses on virological and serological features of 94 infections that occurred in Lazio Region (Central Italy) between 27 December 2020, and 30 March 2021, after one or two doses of mRNA BNT162b2 vaccine.MethodsWe evaluated clinical features, virological (viral load; viral infectiousness; genomic characterisation), and serological (anti-nucleoprotein Ig; anti-Spike RBD IgG; neutralising antibodies, nAb) characteristics of 94 post-vaccine infections at the time of diagnosis. Nasopharyngeal swabs (NPSs) and serum samples were collected in the framework of the surveillance activities on SARS-CoV-2 variants established in Lazio Region (Central Italy) and analysed at the National Institute for Infectious Diseases "L. Spallanzani" in Rome.ResultsThe majority (92.6%) of the post-vaccine infections showed pauci/asymptomatic or mild clinical course, with symptoms and hospitalisation rate significantly less frequent in patients infected after full vaccination course as compared to patients who received a single dose vaccine. Although differences were not statistically significant, viral loads and isolation rates were lower in NPSs from patients infected after receiving two vaccine doses as compared to patients with one dose. Most cases (84%) had nAb in serum at the time of infection diagnosis, which is a sub-group of vaccinees, were found similarly able to neutralise Alpha and Gamma variants. Asymptomatic individuals showed higher nAb titres as compared to symptomatic cases (median titre: 1:120 vs. 1:40, respectively). Finally, the proportion of post-vaccine infections attributed either to Alpha and Gamma variants was similar to the proportion observed in the contemporary unvaccinated population in the Lazio region, and mutational analysis did not reveal enrichment of a defined set of Spike protein substitutions depending on the vaccination status.ConclusionOur study conducted using real-life data, emphasised the importance of monitoring vaccine breakthrough infections, through the characterisation of virological, immunological, and clinical features associated with these events, in order to tune prevention measures in the next phase of the COVID-19 pandemic.

Dataset Information

Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021.

Publications

Genetic diversity of SARS-CoV-2 infections in Ghana from 2020-2021.

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