Protocols for sequencing the HIV whole genome or specific gene fragment using capillary electrophoresis:

Here we provide detailed full protocols. The protocols are linked to the primary papers in which they were 1st published. You can also access a summary of publications that have used the same protocol and referenced the primary paper. For each protocol there is also a comment section which should be used by users to discuss issues related to implementation of the protocol.

Protocol name, publication title, journal and authors (ordered by publication date) Ranked by Impact Factor (I.F) - Top 10


DNA and RNA Long-range HIV genotyping Harvard-Botswana

Manuscript: Long-range HIV genotyping using viral RNA and proviral DNA for analysis of HIV drug-resistance and HIV clustering.
Novitsky V, Zahralban-Steele M, McLane MF, Moyo S, Widenfelt E, Gaseitsiwe S, Makhema J, Essex M, Journal of Clinical Microbiology (2015), in press:in press


SATuRN/Life Techonologies protocol

Manuscript: An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings.
Manasa J, Danaviah S, Pillay S, Padayachee P, Mthiyane H, Seebregts C, Rinke De Wit TF, Viljoen J, Katzenstein D, De Oliveira T , Journal of Visualized Experiments (JoVE) (2014), (85):e51242, doi:10.3791/51242


Paser Ultra-light

Manuscript: A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only.
Aitken SC, Bronze M, Wallis CL, Stuyver L, Steegen K, Balinda S, Kityo C, Stevens W, Rinke De Wit TF & Schuurman R., J Clin Microbiol (2013), 51:1757-1761


Universal whole HIV-1 genome WT Sanger

Manuscript: Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes.
Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P, Journal of Clinical Microbiology (2012), 50(12):doi:10.1128/JCM.01516-12


Chen and colleagues protocol

Manuscript: In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong.
Chen JH, Wong KH, Li PC, Chan KK, Lee MP, To SW, Yam WC , Hong Kong Med J (2012), 18:20-24


CDC protocol

Manuscript: Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings..
Zhou Z, Wagar N, Devos JR, Rottinghaus E, Diallo K, Nguyen DB, Bassey O, Ugbena R, Wadonda-Kabondo N, Mcconnell MS, Zulu I, Chilima B, Nkengasong J, Yang C , PLoS One (2011), 6:e28184


Wallis and colleagues protocol

Manuscript: Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1.
Wallis CL, Papathanasopoulos MA, Lakhi S, Karita E, Kamali A, Kaleebu P, Sanders E, Anzala O, Bekker LG, Stevens G, De Wit TF, Stevens W , J Virol Methods (2010), 163:505-508


NICD protocol

Manuscript: Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004.
Pillay V, Ledwaba J, Hunt G, Rakgotho M, Singh B, Makubalo L, Bennett D E, Puren A, Morris L , Antivir Ther (2008), 13 Suppl 2:101-107

Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.. PLoS One (2011), I.F.:4.411

A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only. J Clin Microbiol (2013), I.F.:4.068

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes. Journal of Clinical Microbiology (2012), I.F.:3.993

Long-range HIV genotyping using viral RNA and proviral DNA for analysis of HIV drug-resistance and HIV clustering. Journal of Clinical Microbiology (2015), I.F.:3.993

Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004. Antivir Ther (2008), I.F.:3.07

Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. J Virol Methods (2010), I.F.:2.065

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings. Journal of Visualized Experiments (JoVE) (2014), I.F.:1.2

In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong. Hong Kong Med J (2012), I.F.:0.26

Ranked by Citations - Top 10

Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004. Antivir Ther (2008), Citations:72

Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. J Virol Methods (2010), Citations:31

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes. Journal of Clinical Microbiology (2012), Citations:20

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings. Journal of Visualized Experiments (JoVE) (2014), Citations:11

Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.. PLoS One (2011), Citations:11

A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only. J Clin Microbiol (2013), Citations:3

In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong. Hong Kong Med J (2012), Citations:1

Long-range HIV genotyping using viral RNA and proviral DNA for analysis of HIV drug-resistance and HIV clustering. Journal of Clinical Microbiology (2015), Citations:1


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