A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings
Bonsall D., Golubchik T., de Cesare M., Limbada M., Kosloff B., MacIntyre-Cockett G., Hall M., Wymant C., Ansari MA., Abeler-Dörner L., Schaap A., Brown A., Barnes E., Piwowar-Manning E., Eshleman S., Wilson E., Emel L., Hayes R., Fidler S., Ayles H., Bowden R., Fraser C.
Viral genetic sequencing can be used to monitor the spread of HIV drug resistance, identify appropriate antiretroviral regimes, and characterize transmission dynamics. Despite decreasing costs, next-generation sequencing (NGS) is still prohibitively costly for routine use in generalized HIV epidemics in low- and middle-income countries. Here, we present veSEQ-HIV, a high-throughput, cost-effective NGS sequencing method and computational pipeline tailored specifically to HIV, which can be performed using leftover blood drawn for routine CD4 cell count testing.