Phyloevolutionary analysis of SARS-CoV-2 in Nigeria

Awoyelu, Elukunbi Hilda; Oladipo, Elijah Kolawole; Adetuyi, Babatunde Oluwafemi; Senbadejo, Tosin Yetunde; Oyawoye, Olubukola Monisola; Oloke, Julius Kola

doi:10.1016/j.nmni.2020.100717

Cited by 45 publications

(11 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2,42 Several factors may contribute to the observed low CFRs in Africa, including younger population, cross-protection from existing immunity to other Coronaviruses, and early institution of safety protocols. In addition, local evolution of the virus as observed in this study, as well as others, 43 may be driven by existing immunity to other pathogens and environmental factors that are unique to Africa. It would be interesting to investigate in future studies how these locally generated variants impact on transmissibility and virulence of the virus.…”

Section: Discussionsupporting

confidence: 54%

Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Ngoi

Quashie

Morang’a

et al. 2020

Exp Biol Med (Maywood)

View full text Add to dashboard Cite

The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.

show abstract

Section: Discussionsupporting

confidence: 54%

Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Ngoi

Quashie

Morang’a

et al. 2020

Exp Biol Med (Maywood)

View full text Add to dashboard Cite

show abstract

“…Surprisingly, the later Europe-associated G-clades (G, GH, GR) emerged before the earlier clades L, S and V in West African sequenced samples. This could be due to founder effects introduced from France closely connected to Senegal and displaying a similar clade distribution and by migration and travel routes such as in the first registered Nigerian case infected in Italy 13 . Furthermore, the China-based L-, V- and S-clade samples were obtained in mid-March 2020, a time point within the Wuhan lockdown and when the epidemic in China was nearly over.…”

Section: Resultsmentioning

confidence: 98%

Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa

Wruck

Adjaye

2021

Sci Rep

View full text Add to dashboard Cite

SARS-CoV-2, the virus causing the COVID-19 pandemic emerged in December 2019 in China and raised fears it could overwhelm healthcare systems worldwide. Mutations of the virus are monitored by the GISAID database from which we downloaded sequences from four West African countries Ghana, Gambia, Senegal and Nigeria from February 2020 to April 2020. We subjected the sequences to phylogenetic analysis employing the nextstrain pipeline. We found country-specific patterns of viral variants and supplemented that with data on novel variants from June 2021. Until April 2020, variants carrying the crucial Europe-associated D614G amino acid change were predominantly found in Senegal and Gambia, and combinations of late variants with and early variants without D614G in Ghana and Nigeria. In June 2021 all variants carried the D614G amino acid substitution. Senegal and Gambia exhibited again variants transmitted from Europe (alpha or delta), Ghana a combination of several variants and in Nigeria the original Eta variant. Detailed analysis of distinct samples revealed that some might have circulated latently and some reflect migration routes. The distinct patterns of variants within the West African countries point at their global transmission via air traffic predominantly from Europe and only limited transmission between the West African countries.

show abstract

“…Nigeria: The comprehensive knowledge of phyloevolution and comparative discrimination of SARS-CoV-2 molecular characterization can be useful in the critical investigation of the virus pathogenesis, disease control, treatment and vaccine development. The study of SARS-CoV-2 evolution in Nigeria by [42] exhibited a concerted similarity with the Wuhan reference genome, which introduction into Nigeria was inferred to arrive from Wuhan through an Italian traveler. The study involved a 2-step analysis of multiple sequence alignment and phylogenetic analysis of 39 complete genome of SARS-Cov-2 with their various travel history.…”

Section: Sars-cov-2 Genome Analysis Of African Isolatesmentioning

confidence: 94%

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Ekpenyong¹,

Uzoka²,

Edoho³

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundThe increased number of accessible genomes has prompted large-scale comparative studies for decerning evolutionary knowledge of infectious diseases, but challenges such as non-availability of close reference sequence(s), incompletely assembled or large number of genomes, preclude real time multiple sequence alignment and sub-strain(s) discovery. This paper introduces a cooperatively inspired open-source framework, for intelligent mining of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes. We situate this study within the African context, to drive advancement on state-of-the-art, towards intelligent infectious disease characterization and prediction. The outcome is an enriched Knowledge Base, sufficient to provide deep understanding of the viral sub-strains’ identification problem. We also open investigation by gender, which to the best of our knowledge has been ignored in related research. Data for the study came from the Global Initiative on Sharing All Influenza Data database (https://gisaid.org) and processed for precise discovery of viral sub-strains transmission between and within African countries. To localize the transmission route(s) of each isolate excavated and provide appropriate links to similar isolate strain(s), a cognitive solution was imposed on the genome expression patterns discovered by unsupervised self-organizing map (SOM) component planes visualization. The Freidman-Nemenyi’s test was finally performed to validate our claim.ResultsEvidence of inter- and intra-genome diversity was noticed. While some isolates (or genomes) clustered differently, implying different evolutionary source (or high-diversity), others clustered closely together, indicating similar evolutionary source (or less-diversity). SOM component planes analysis revealed multiple sub-strains patterns, strongly suggesting local or intra-community and country to country transmissions. Cognitive maps of both male and female isolates revealed multiple transmission routes. Statistical results indicate significant difference between the various isolate groups at the 0.05 level of significance.ConclusionThe proposed framework offers explanations to SARS-CoV-2 diversity and provides real time identification to disease transmission routes, as well as rapid decision support for facilitating inter- and intra-country contact tracing of infected case(s). Intermediate data produced in this paper are helpful to enrich the genome datasets for intelligent characterization and prediction of COVID-19 and related pandemics, as well as the construction of intelligent device for accurate infectious disease monitoring.

show abstract

Phyloevolutionary analysis of SARS-CoV-2 in Nigeria

Cited by 45 publications

References 16 publications

Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

Detailed phylogenetic analysis tracks transmission of distinct SARS-COV-2 variants from China and Europe to West Africa

Real Time Viral Sub-Strains Discovery in Emerging Infectious Disease Situation – The African Perspective

Contact Info

Product

Resources

About