Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. by Pineda-Peña, A, Faria, N, Imbrechts, S, Libin, P, Abecasis, AB, Deforche, K, Gómez-López, A, Camacho, R, de Oliveira, T, Vandamme, A

“…METHODOLOGY: HIV-1 pol sequences (PR+RT) for 4674 patients retrieved from the Portuguese HIV Drug Resistance Database, and 1872 pol sequences trimmed from full-length genomes retrieved from the Los Alamos database were classified with statistical-based tools such as COMET, jpHMM and STAR; similarity-based tools such as NCBI and Stanford; and phylogenetic-based tools such as REGA version 2 (REGAv2), REGAv3, and SCUEAL. …”

HIV-1 virologic failure and acquired drug resistance among first-line antiretroviral experienced adults at a rural HIV clinic in coastal Kenya: a cross-sectional study by Hassan, A, Nabwera, H, Berkley, J, al., E

“…To prevent unnecessary/premature switches, targeted HIV drug resistance testing for patients with confirmed VF should be considered.…”

HIV-1 virologic failure and acquired drug resistance among first-line antiretroviral experienced adults at a rural HIV clinic in coastal Kenya: a cross-sectional study. by Hassan, A, Nabwera, H, Mwaringa, S, Obonyo, C, Sanders, E, Rinke de Wit, T, Cane, P, Berkley, J

“…To prevent unnecessary/premature switches, targeted HIV drug resistance testing for patients with confirmed VF should be considered.…”

Trends in CD4 counts in HIV-infected patients with HIV viral load monitoring while on combination antiretroviral treatment: results from the TREAT Asia HIV observational database by Zhou, J.L., Sirisanthana, T., Kiertiburanakul, S., Chen, Y.M.A., Han, N., Lim, P.L., Kumarasamy, N., Choi, J.Y., Merati, T.P., Yunihastuti, E., Oka, S., Kamarulzaman, Adeeba, Phanuphak, P., Lee, C.K.C., Li, P.C.K., Pujari, S., Saphonn, V., Law, M.G.

“…The effect on long-term outcomes through the possible development of HIV drug resistance remains uncertain.…”

Analysis of ART effects and drug resistance in adult HIV/AIDS patients in Meigu County, Liangshan Prefecture, China by Li Yuan, Kaiyou Chen, Yuanfang Cai, Zhonghui Zhou, Ju Yang, Wuti Jiqu, Qirong Zhu, Hong Zhang, Shaowei Niu, Hui Sun

“…Plasma specimens with HIV-1 RNA ≥ 1000 copies/mL were sent to the laboratory for nucleic acid extraction, PCR, electrophoresis and sequencing, and the sequencing results were submitted to the HIV drug resistance database of Stanford University for subtyping to determine the drug resistance mutation sites and drug sensitivity levels. …”
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DOLAMA 200: Effectiveness and Safety of a Dual Therapy with Dolutegravir Plus Lamivudine in Treatment-Experienced HIV-1 Infected Real World Participants in Spain by Sergio Sequera-Arquelladas, Carmen Hidalgo-Tenorio, Luis López-Cortés, Alicia Gutiérrez, Jesús Santos, Francisco Téllez, Mohamed Omar, Sergio Ferra-Murcia, Elisa Fernández, Rosario Javier, Coral García-Vallecillos, Juan Pasquau

“…The continuous pharmacological advances in antiretroviral treatment (ART) and the increasing understanding of HIV drug resistance has led to a change in the paradigm of ART optimization in the setting of the viral suppression of treatment-experienced patients with the emerging evidence of the effectiveness and safety of dual therapies. …”
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The mother-to-child transmission of HIV-1 and profile of viral reservoirs in pediatric population: A systematic review with meta-analysis of the Cameroonian studies. by Aude Christelle Ka'e, Alex Durand Nka, Bouba Yagai, Irénée Domkam Kammogne, Ezechiel Ngoufack Jagni Semengue, Aubin Joseph Nanfack, Celine Nkenfou, Michel Carlos Tommo Tchouaket, Desire Takou, Samuel Martin Sosso, Nadine Fainguem, Aissatou Abba, Willy Pabo, Nelly Kamgaing, Edith Temgoua, Boris Tchounga, Patrice Tchendjou, Suzie Tetang, Anne Esther Njom Nlend, Francesca Ceccherini-Silberstein, Maria Mercedes Santoro, Joseph Fokam

“…Regarding viral reservoirs, a pro-viral DNA mean of 3.34±1.05 log10/mL was observed among 5/57 children and archived HIV drug resistance mutations were identified in pro-viral DNA marker among 21/79 infected-children.…”
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Low level of HIV-1C integrase strand transfer inhibitor resistance mutations among recently diagnosed ART-naive Ethiopians by Mulugeta Kiros, Dessalegn Abeje Tefera, Henok Andualem, Alene Geteneh, Abebech Tesfaye, Tamirayehu Seyoum Woldemichael, Eleni Kidane, Dawit Hailu Alemayehu, Melanie Maier, Adane Mihret, Woldaregay Erku Abegaz, Andargachew Mulu

“…INSTIs RMs were examined using calibrated population resistance tool version 8.0 from Stanford HIV drug resistance database while both REGA version 3 online HIV-1 subtyping tool and the jumping profile Hidden Markov Model from GOBICS were used to examine HIV-1 genetic diversity. …”
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Low-level viraemia: An emerging concern among people living with HIV in Uganda and across sub-Saharan Africa by Nicholus Nanyeenya, Noah Kiwanuka, Damalie Nakanjako, Gertrude Nakigozi, Simon P.S. Kibira, Susan Nabadda, Charles Kiyaga, Isaac Sewanyana, Esther Nasuuna, Fredrick Makumbi

“…However, recent studies have associated LLV with increased risks of HIV drug resistance, virologic failure and transmission. …”
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Prevalence of HIV Transmitted Drug Resistance in Nanjing from 2018 to 2021 by Su Y, Qi M, Zhong M, Yu N, Chen C, Ye Z, Cheng C, Hu Z, Zhang H, Wei H

“…The sequencing result was compared with the HIV drug resistance database from Stanford University to elucidate the rates of antiviral drug resistance and distribution of drug-resistant mutation sites. …”
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High Level of Pre-Treatment HIV-1 Drug Resistance and Its Association with HLA Class I-Mediated Restriction in the Pumwani Sex Worker Cohort by Rachel Willim, Elnaz Shadabi, Raghavan Sampathkumar, Lin Li, Robert Balshaw, Joshua Kimani, Francis A. Plummer, Ma Luo, Binhua Liang

“…Eighteen potentially relevant (<i>p</i> < 0.05) positive correlations were found between HLA class 1 alleles and HIV drug-resistant variants. Conclusions: High levels of HIV drug resistance were found in all classes of antiretroviral drugs included in the current first-line ART regimens in Africa. …”
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Drug Resistance to Integrase Strand-Transfer Inhibitors among HIV-1-Infected Adults in Guangdong, China by Yun Lan, Linghua Li, Ruolei Xin, Xuemei Ling, Xizi Deng, Junbin Li, Liya Li, Weiping Cai, Feng Li, Fengyu Hu

“…INSTI mutations and susceptibility were interpreted using the Stanford HIV Drug Resistance Database HIVdb program. Results: Of the 1208 enrolled individuals, 2.65% (32/1208) carried at least one INSTI major or accessory drug resistance mutation (DRM), with 1.49% (6/404) being from ART-naive individuals and 3.23% (26/804) from ART-experienced individuals. …”
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Drug Resistance Profile Among HIV-1 Infections Experiencing ART with Low-Level Viral Load in Guangdong China During 2011&ndash;2022: A Retrospective Study by Lan Y, Ling X, Deng X, Lin Y, Li J, Li L, He R, Cai W, Li F, Li L, Hu F

“…The risk factors associated with HIV drug resistance should be seriously considered for better control.Keywords: HIV, low-level viral load, drug resistance mutation, drug resistance…”
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Potential role of doravirine for the treatment of HIV-1-infected persons with transmitted drug resistance by Soo-Yon Rhee, Jonathan M. Schapiro, Francesco Saladini, Maurizio Zazzi, Saye Khoo, Robert W. Shafer

“…NNRTI drug resistance mutations (DRMs) were defined as those with a Stanford HIV Drug Resistance Database doravirine penalty score either alone or in combination with other mutations. …”
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HIV-1 drug resistance and genetic transmission network among newly diagnosed people living with HIV/AIDS in Ningbo, China between 2018 and 2021 by Hang Hong, Chunlan Tang, Yuhui Liu, Haibo Jiang, Ting Fang, Guozhang Xu

“…TDR was determined using the Stanford University HIV Drug Resistance Database. Genetic transmission network was visualized using Cytoscape with the genetic distance threshold of 0.013. …”
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Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations by Soo-Yon Rhee, Michael Boehm, Olga Tarasova, Giulia Di Teodoro, Ana B. Abecasis, Anders Sönnerborg, Alexander J. Bailey, Dmitry Kireev, Maurizio Zazzi, the EuResist Network Study Group, Robert W. Shafer

“…A total of 264 (18%) sequences had a PI drug-resistance mutation (DRM) defined as having a Stanford HIV Drug Resistance Database mutation penalty score. Among sequences with a DRM, nine major DRMs had a prevalence >5%: I50L (34%), M46I (33%), V82A (22%), L90M (19%), I54V (16%), N88S (10%), M46L (8%), V32I (6%), and I84V (6%). …”
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HIV-1 Subtype C Drug Resistance Mutations in Heavily Treated Patients Failing Integrase Strand Transfer Inhibitor-Based Regimens in Botswana by Kaelo K. Seatla, Dorcas Maruapula, Wonderful T. Choga, Tshenolo Ntsipe, Nametso Mathiba, Mompati Mogwele, Max Kapanda, Bornapate Nkomo, Dinah Ramaabya, Joseph Makhema, Mompati Mmalane, Madisa Mine, Ishmael Kasvosve, Shahin Lockman, Sikhulile Moyo, Simani Gaseitsiwe

“…Sanger sequencing of the HIV-1 Pol gene was performed from residual plasma samples and drug resistance mutational (DRM) analysis performed using the Stanford University HIV drug resistance database. 40 HIV-1C integrase sequences were generated from 34 individuals, 24 of whom were on DTG cART, three on RAL cART and seven on an unknown (DTG or RAL)-anchored cART at time of GRT. 11/34 (32%) individuals had DRMs to DTG and other integrase inhibitors. 7/11 (64%) patients had exposure to a RAL-based cART at the time of sampling. …”
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Presence of V72I, G123S and R127K Integrase Inhibitor polymorphisms could reduce ART effectiveness: a retrospective longitudinal study by Anna Celotti, Franco Gargiulo, Eugenia Quiros-Roldan, Martina Properzi, Maria Antonia De Francesco, Davide Coletto, Francesca Caccuri, Ilaria Izzo, Arnaldo Caruso, Francesco Castelli, Emanuele Focà

“…We analyzed integrase resistance mutations using the Stanford University HIV Drug Resistance Database (HIVdb Program, version 6.3.0). …”
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Affordable drug resistance genotyping of HIV-1 reverse transcriptase, protease and integrase genes, for resource limited settings by Sontaga Manyana, Melendhran Pillay, Lilishia Gounder, Aabida Khan, Pravi Moodley, Kogieleum Naidoo, Benjamin Chimukangara

“…We genotyped samples by Sanger sequencing and assessed HIVDR mutations using the Stanford HIV drug resistance database. We compared drug resistance mutations with previous genotypes and calculated method cost-estimates. …”
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Effect of Switching Antiretroviral Treatment Regimen in Patients With Drug-Resistant HIV-1 Infection: Retrospective Observational Cohort Study by Yiping Li, Qinjian Wang, Shu Liang, Chuanteng Feng, Hong Yang, Hang Yu, Dan Yuan, Shujuan Yang

“… BackgroundEvidence on the efficacy of antiretroviral therapy (ART) regimen switches on the mortality of patients with HIV drug resistance (HIVDR) is limited. ObjectiveWe aim to provide policy guidance for ART regimen selection and evaluate the effectiveness of ART regime switches for people living with HIV and HIV-1 drug resistance. …”
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