Author(s)

Ibrahim Keita¹, Garan Dabo^1,2, Lassina Doumbia¹, Youssouf Diarra¹, Ibrahim Traoré¹, Mariam Traoré¹, Lansana Sangaré¹, Yacouba Toloba³, Mahamadou Alpha Diallo¹, Djeneba Sy¹, Andres H. Gutierrez⁴, Aliou Sissako¹, Ibrahim Guindo⁵, Mohamed Diallo⁵, Akory Ag Iknane⁵, Anne S. De Groot^4,6, Ousmane Aliou Koita¹

¹Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences, Techniques et des Technologies de Bamako, Bamako, Mali.
²Hôpital du Mali, Ministère de la Santé Publique et du Développement Social, Bamako, Mali.
³Centre Hospitalo-Universitaire du Point G, Ministère de la Santé Publique et du Développement Social, Bamako, Mali.
⁴EpiVax, Inc. Providence, USA.
⁵Institut National de Santé Publique, Ministère de la Santé Publique et du Développement Social, Bamako, Mali.
⁶Center for Vaccines and Immunology, College of Veterinary Medicine University of Georgia, Athens, USA.

Background: Quantitative PCR (qPCR) can be used to detect and quantify a load of a pathogen. It is a good indicator of the degree of transmissibility. While performing routine qPCR, we observed an unusually short cycle threshold (Ct) value of SARS-CoV-2 for a clinical specimen obtained in Bamako, Mali. This prompted us to sequence the short-cycle SARS-CoV-2 sample to identify potential mutations in the Spike gene (S gene) gene. Methods: Post-infection, Quantitative Reverse Transcription (qRT-PCR) was performed over a defined time course to estimate the Ct of the SARS-CoV-2 specimen collected from the patient. Sanger sequencing was done on the entire fragment of the S gene to identify mutations. Findings: Sanger sequencing revealed mutations in the lineage of interest, designated B.1.525 by Pango, and also known as “Eta” using the nomenclature defined by WHO. This variant was originally found in Nigeria and Italy. The four novel mutations identified in Eta (D228N, Y451N, I1172M, and C1250F) were otherwise observed with a low frequency worldwide. Although the initial Ct was 10 in the case study patient, he did not exhibit severe symptoms of SARS-CoV-2, for example, pneumonia. However, we observed a longer viral clearance period than usual, of 3 weeks. We note that as compared to SARS-CoV-2 samples obtained during the first peaks of SARS-CoV-2 infection in Mali, when the infection was at its peak in March 2020 (Ct = 30.4), circulating strains evaluated at the time the Eta sample was obtained demonstrated a lower mean Ct (Ct = 24). Conclusions: The short cycle threshold associated with this variant, and the temporal association with a decrease in the mean Ct in the region of Bamako, may indicate higher levels of transmissibility due to a circulating variant. This variant is a lineage of interest designated B.1.525 by Pango or Eta by WHO.

SARS-CoV-2, Variant Eta, Ct Value, Mali

Keita, I. , Dabo, G. , Doumbia, L. , Diarra, Y. , Traoré, I. , Traoré, M. , Sangaré, L. , Toloba, Y. , Diallo, M. , Sy, D. , Gutierrez, A. , Sissako, A. , Guindo, I. , Diallo, M. , Iknane, A. , De Groot, A. and Koita, O. (2022) Mutations in Spike Gene of SARS-CoV-2 that Are Associated with a Higher Viral Load: A Clinical Case Study. Case Reports in Clinical Medicine, 11, 474-486. doi: 10.4236/crcm.2022.1111065.