No detectable differences in Nef-mediated downregulation of HLA-I and CD4 molecules amongst HIV-1 group M lineages circulating in Cameroon, where the pandemic originated Provisionally Accepted

Nelson Sonela^{1, 2, 3} Jaclyn Mann⁴ Godwe Celestin^{1, 5} Hamadama Oumarou Goni^{1, 6} Mérime Tchakoute⁷ Nathalie Nkoue⁸ Eitel Mpoudi Ngole⁹ Tulio de Oliveira^{10, 11} Mark Brockman^{12, 13, 14} Zabrina L. Brumme^{13, 14} Thumbi Ndung'u^{4, 15, 16, 17, 18} Tongo marcel^1*

• ¹Institute of Medical Research and Study of Medicinal Plants (IMPM), Center for Research on Emerging and Re-Emerging Diseases (CREMER), Cameroon
• ²Chantal BIYA International Reference Center (CBIRC), Cameroon
• ³Department of Medicine, Weill Cornell Medicine, Cornell University, United States
• ⁴HIV Pathogenesis Programme, University of KwaZulu-Natal, South Africa
• ⁵Department of Biochemistry, Faculty of Science, University of Douala, Cameroon
• ⁶Department of Microbiology, Faculty of Sciences, University of Yaounde I, Cameroon
• ⁷Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, P.O. Box : 495 Yaoundé, Cameroon, Cameroon
• ⁸5Programmes de Santé et développement au sein du Groupement de la Filière Bois du Cameroun, P.O. Box : 495 Yaoundé, Cameroon., Cameroon
• ⁹Institute of Medical Research and Study of Medicinal Plants (IMPM), Center for Research on Emerging and Re-Emerging Diseases (CREMER), Cameroon
• ¹⁰Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, South Africa
• ¹¹KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), South Africa
• ¹²Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Canada
• ¹³Faculty of Health Sciences, Simon Fraser University, Canada
• ¹⁴British Columbia Centre for Excellence in HIV/AIDS, Canada
• ¹⁵Max Planck Institute for Infection Biology, Germany
• ¹⁶Africa Health Research Institute (AHRI), South Africa
• ¹⁷Ragon Institute, United States
• ¹⁸Division of Infection and Immunity, Faculty of Medical Sciences, University College London, United Kingdom

HIV-1 group M (HIV-1M) lineages downregulate HLA-I and CD4 expression via their Nef proteins.We hypothesized that these Nef functions may be partially responsible for the differences in prevalence of viruses from different lineages that co-circulate within an epidemic. Here, we characterized these two Nef activities in HIV-1M isolates from Cameroon, where multiple variants have been circulating since the pandemic's origin. Single HIV-1 Nef clones from 234 HIV-1-ART naïve individuals living in remote villages and two cosmopolitan cities of Cameroon, sampled between 2000 and 2013, were isolated from plasma HIV RNA and analyzed for their capacity to downregulate HLA-I and CD4 molecules. We found that, despite a large degree of within-and interlineage variation, the ability of Nef to downregulate HLA-I was similar across these different viruses.Moreover, Nef-mediated CD4 downregulation activity was also well conserved across the different lineages found in Cameroon. In addition, we observed a trend towards higher HLA-I downregulation activity of viruses circulating in the cosmopolitan cities versus the remote villages, whereas the CD4 downregulation activities were similar across the two settings. Furthermore, we noted a significant decline of HLA-I downregulation activity from 2000 to 2013, providing additional evidence supporting the attenuation of the global HIV-1M population over time. Finally, we identified 18 amino acids associated with differential HLA-I downregulation and 13 amino acids associated with differential CD4 downregulation within the dominant CRF02_AG lineage. Our lack of observation of HIV lineage-related differences in Nef-mediated HLA-I and CD4 downregulation function suggests that these activities do not substantively influence the prevalence of different HIV-1M lineages in Cameroon.