Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.
Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana.
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DOI：
10.1093/infdis/jiab293
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发表时间：
2022-04-19
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影响因子：
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中科院分区：
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Human immunodeficiency virus (HIV)-1 genetic diversity increases during infection and can help infer the time elapsed since infection. However, the effect of antiretroviral treatment (ART) on the inference remains unknown. Participants with estimated duration of HIV-1 infection based on repeated testing were sourced from cohorts in Botswana (n = 1944). Full-length HIV genome sequencing was performed from proviral deoxyribonucleic acid. We optimized a machine learning model to classify infections as < or >1 year based on viral genetic diversity, demographic, and clinical data. The best predictive model included variables for genetic diversity of HIV-1 gag, pol, and env, viral load, age, sex, and ART status. Most participants were on ART. Balanced accuracy was 90.6% (95% confidence interval, 86.7%–94.1%). We tested the algorithm among newly diagnosed participants with or without documented negative HIV tests. Among those without records, those who self-reported a negative HIV test within <1 year were more frequently classified as recent than those who reported a test >1 year previously. There was no difference in classification between those self-reporting a negative HIV test <1 year, whether or not they had a record. These results indicate that recency of HIV-1 infection can be inferred from viral sequence diversity even among patients on suppressive ART. A single HIV virus is usually transmitted. HIV then replicates, making errors, and over time genetic diversity increases. We found that time since HIV infection can be estimated from within-patient HIV genetic diversity, even when patients are on treatment.
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DOI：
10.1093/cid/ciq164
发表时间：
2011-02-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Kouyos RD;von Wyl V;Yerly S;Böni J;Rieder P;Joos B;Taffé P;Shah C;Bürgisser P;Klimkait T;Weber R;Hirschel B;Cavassini M;Rauch A;Battegay M;Vernazza PL;Bernasconi E;Ledergerber B;Bonhoeffer S;Günthard HF;Swiss HIV Cohort Study
通讯作者：
Swiss HIV Cohort Study
DOI：
10.1073/pnas.1802028115
发表时间：
2018-09-18
影响因子：
11.1
作者：
Jones BR;Kinloch NN;Horacsek J;Ganase B;Harris M;Harrigan PR;Jones RB;Brockman MA;Joy JB;Poon AFY;Brumme ZL
通讯作者：
Brumme ZL
影响因子：
6.7
作者：
Kearney MF;Spindler J;Shao W;Yu S;Anderson EM;O'Shea A;Rehm C;Poethke C;Kovacs N;Mellors JW;Coffin JM;Maldarelli F
通讯作者：
Maldarelli F
影响因子：
3.7
作者：
Novitsky V;Bussmann H;Logan A;Moyo S;van Widenfelt E;Okui L;Mmalane M;Baca J;Buck L;Phillips E;Tim D;McLane MF;Lei Q;Wang R;Makhema J;Lockman S;DeGruttola V;Essex M
通讯作者：
Essex M
影响因子：
7.7
作者：
Brodin, Johanna;Zanini, Fabio;Albert, Jan
通讯作者：
Albert, Jan