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Updated: Mar 14, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
Published on: October 16, 2018
A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data
Jose Ángel Fernández-Caballero Rico1, Natalia Chueca Porcuna1, Marta Álvarez Estévez1
1Servicio de Microbiología Clínica, Hospital Universitario San Cecilio, Complejo Hospitalario Universitario Granada e Instituto de Investigación IBS, Granada, España.
Objective:
To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies.
Material And Methods:
Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies.
Results:
At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100).
Conclusion:
A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies.
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