Evaluation of two bioinformatic algorithms for the interpretation of HIV-1 drug resistance and subtyping in Cameroon: Translational application for ART optimization in low-and middle-income countries.
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Fokam Joseph, Etame Naomi-Karell, Ngoufack Jagni Semengue Ezechiel, Chenwi Collins Ambe, Inzaule Seth C, Takou Désiré, Molimbou Evariste, Nka Alex Durand, Tambe Ayuk Ngwese Derrick, Gouissi Anguechia Davy-Hyacinthe, Ka'e Aude Christelle, Beloumou Angong Grâce, Djupsa Ndjeyep Sandrine Claire, Kengni Ngueko Aurelie Minelle, Nayang Mundo Rachel Audrey, Moko Fotso Larissa Gaelle, Tueguem Pamela Patricia, Mekel Vincent Kamaël, Tommo Tchouaket Michel Carlos, Sosso Samuel Martin, Ajeh Awoh Rogers, Santoro Maria-Mercedes, Ceccherini-Silberstein Francesca, Bissek Zoung-Kanyi Anne-Cecile, Cappelli Giulia, Colizzi Vittorio, Perno Carlo-Federico, Ndembi Nicaise, Mbopi-Keou Francois-Xavier, Ndjolo Alexis
Аннотация
METHODS: A laboratory-based comparative study was conducted among treatment-experienced people living with HIV attending the Chantal BIYA International Reference Centre in Yaoundé-Cameroon from October-2022 through July-2023. For each individual, raw data of HIV-1 sequences were analyzed simultaneously using RECall (semi-automated) vs. Exatype (automated) algorithms. Outputs were compared for DRMs, polymorphisms and subtyping between the two algorithms, with significance at p<0.05.
RESULTS: Overall, 221 participants were included (mean-age 32±15 years, 52.5% female). Validation of sequence quality was 70.1% (155/221) by RECall vs. 60.2% (133/221) by Exatype, Ka=0.78 (p<0.0001), indicating a good agreement between both algorithms. Importantly, a perfect concordance (100%) was found in HIV-1 clade inference (CRF02_AG [82/82], A1 [29/29], G [5/5], F2 [5/5] and others [12/12]). Similarly, high concordances were found for the identification of DRMs to protease-inhibitors (99.0%), nucleoside reverse-transcriptase inhibitors (98.0%), non-nucleoside reverse-transcriptase inhibitors (98.6%) and integrase-inhibitors (100.0%). The average turn-around-time was two-folds longer with RECall (5.5±1.7 min) vs. Exatype (2.5±1.1 min); giving a lower efficiency (i.e. validation rate/time) with RECall (12.7) vs. Exatype (24.1).
CONCLUSIONS: Semi-automated (RECall) and automated (Exatype) tools showed excellent agreement in detecting HIV-1 clades and DRMs, supporting their interoperability in clinical practice. Following efficiency, Exatype can be considered preferential, while RECall remains a quite suitable alternative for LMICs.