Upasana Ramphal

1. Wilkinson et al., 2021. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. https://www.medrxiv.org/content/10.1101/2021.05.12.21257080v1.full.pdf+html
2. Karim et al., 2021. Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection" to the New England Journal of Medicine. NEJM 21-09406_Proof_hi.pdf
3. Tegally et al., 2021. Rapid replacement of the Beta variant by the Delta variant in South Africa. Nature. https://doi.org/10.1101/2021.09.23.21264018
4. Bandawe et al., 2021. Management and containment of a SARS-CoV-2 Beta variant outbreak at the Malawi University of Science and Technology. Manuscript
5. Arumugam T, Ramphal U, et al., 2021. Deciphering DNA Methylation in HIV Infection. Frontiers Microbial Immunology.
6. Scheepers et al., 2021. Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern. Nature communications. https://doi.org/10.1101/2021.08.20.21262342
7. Tshiabuila et al, 2022. Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq. BMC genomics. https://doi.org/10.1186/s12864-022-08541-5
8. Mwangi et al., 2022. SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to September 2021. Frontiers Virology. http://dx.doi.org/10.3389/fviro.2022.935131
9. Viana et al., 2022. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. https://doi.org/10.1038/d41586-021-03832-5
10. Bbosa et al., 2022. Rapid replacement of SARS-CoV-2 variants by Delta and subsequent arrival of Omicron in Uganda, 2021. Emerging infectious diseases. DOI: 10.3201/eid2805.220121
11. Subramoney K et al., 2022. Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021. Journal of Medical Virology.
12. Tegally, H et al. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. 10.1101/2022.04.17.22273906
13. Tegally, H., Moir, M., Everatt, J. et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med (2022). https://doi.org/10.1038/s41591-022-01911-2
14. Ismael, N et al. Genomic epidemiology of SARS CoV-2 during the first four waves in Mozambique. Submitted to PLOS Global Public Health (2022).
15. Brito, AF et al., 2022. Global disparities in SARS-CoV-2 genomic surveillance. Nature Communications 13 (1):7003. http://dx.doi.org/10.1038/s41467-022-33713-y
16. Subramoney, K et al. Impact of intra-host immune adaptations on the evolution of SARS-CoV-2 S protein among individuals with SARS-CoV-2 infections in South Africa, 2020 to 2022. Preprint available at http://dx.doi.org/10.22541/au.166305249.90395426/v1
17. Ramphal, U et al. Comparing SARS-CoV-2 sequencing methodologies during early phase detection of the Delta variant in South Africa. Draft Submitted to BMC Genomic Data. https://dx.doi.org/10.21203/rs.3.rs-2310293/v1
18. Sisay, A et al., 2023. Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022. Genes. https://doi.org/10.3390/genes14030705