RHIVDB: A Freely Accessible Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients

Abstract

Human immunodeficiency virus (HIV) infection remains one of the most severe problems for humanity, particularly due to the development of HIV resistance. To evaluate an association between viral sequence data and drug combinations and to estimate an effect of a particular drug combination on the treatment results, collection of the most representative drug combinations used to cure HIV and the biological data on amino acid sequences of HIV proteins is essential. We have created a new, freely available web database containing 1,651 amino acid sequences of HIV structural proteins [reverse transcriptase (RT), protease (PR), integrase (IN), and envelope protein (ENV)], treatment history information, and CD4+ cell count and viral load data available by the user’s query. Additionally, the biological data on new HIV sequences and treatment data can be stored in the database by any user followed by an expert’s verification. The database is available on the web at http://www.way2drug.com/rhivdb.

Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations

“…Overall, 1763 protease sequences from 1497 patients reported in 30 studies who received either boosted or unboosted atazanavir as their first PI were available for the analysis ( Table 1 ). These sequences included 773 sequences from 740 patients in 27 studies from Stanford HIV Drug Resistance Database (HIVDB) [ 13 ], and previously unpublished sequences, including (i) 741 sequences from 562 patients from the EuResist Integrated Database (EIDB) [ 14 ]; (ii) 206 sequences from 152 patients from the Stanford University Hospital (SUH); and (iii) 43 sequences from 43 patients from the RHIVDB [ 15 ], a freely accessible database of HIV-1 sequences and clinical data of infected patients. Of the 184 patients with more than 1 sequence, 17 had sequences that differed from one another by one or more DRMs.…”

“…The analysis was last updated 31 December 2021. We supplemented the data in HIVDB with previously unpublished sequences performed at SUH and with previously unpublished sequences from two collaborating research groups: the EIDB [ 14 ] and the RHIVDB [ 15 ]. Additionally, we performed a PubMed search to identify studies describing HIV-1 group M protease sequences that were not present either in HIVDB or GenBank.…”

Computational analysis of viral drug resistance and treatment efficacy: case study for HIV-infection

“…The approach is based on the computational analysis of (i) HIV drug resistance, (ii) HIV drug exposure using treatment history, and (iii) the transcriptomic data of human blood samples obtained from HIV-positive patients. Data on drug resistance including HIV proteins sequences associated with drug resistance and HIV treatment history were obtained from the Stanford HIV drug resistance (StDB) [6] and RHIVDB databases [7,8]. The transcriptomic data were obtained from the key transcriptomic repositories (GEO, ArrayExpress).…”

RuSIDA: the online resource for the collection, storage and analysis of epidemiologicel, demographic and clinical laboratory data of patients

“…Анализируя информацию, хранящуюся в этих базах данных, можно создавать модели выбора терапии, сопоставляя данные о предсуществующей вариабельности генома ВИЧ с динамикой вирусной нагрузки пациентов, находящихся на различных схемах антиретровирусной терапии [20], прогнозировать ответ на антиретровирусную терапию [21], выявлять факторы, влияющие на развитие лекарственной устойчивости ВИЧ [22], изучать влияние мутаций полиморфизма ВИЧ на развитие лекарственной устойчивости [23], описывать модели передаваемой и приобретенной лекарственной устойчивости ВИЧ [24], определять детерминанты позднего выявления ВИЧ у пациентов [25] В России с 2009 г. формируется база данных устойчивости ВИЧ к антиретровирусным препаратам (RUHIV, https://hivresist.ru/), с помощью которой проводят координированный сбор информации о результатах секвенирования ВИЧ для последующего проведения молекулярно-эпидемиологического анализа вариантов ВИЧ-1, циркулирующих на территории РФ [26,27]. Кроме того, в 2019 г. в России была создана база данных RHIVDB, содержащая данные об аминокислотных последовательностях структурных белков ВИЧ (обратной транскриптазы (RT), протеазы (PR), интегразы (IN) и оболочечного белка (ENV)), информацию об истории лечения пациента и данные некоторых лабораторных показателей: количества CD4+ клеток и значения вирусной нагрузки [28].…”