SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing

Araújo, Pedro M. M.; Martins, Joana S.; Osório, Nuno S.

doi:10.1093/ve/vez050

Title: SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing

Journal Article · 19 November 2019 · Virus Evolution

DOI: https://doi.org/10.1093/ve/vez050 · OSTI ID:1574552

Araújo, Pedro M. M. ^[1]; Martins, Joana S. ^[1];

^[1]

Life and Health Sciences Research institute (ICVS), School of Medicine, University of Minho, Braga, Portugal, ICVS/3B’s - PT Government Associate Laboratory, Braga, Guimarães, Portugal

Abstract Human immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and evolution studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web-servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for large-scale local HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analyzing full-length genomes or partial HIV-1 genomic regions (GAG, POL, and ENV) and recognizes more than ninety circulating recombinant forms. SNAPPy is freely available at: https://github.com/PMMAraujo/snappy/releases.

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Sponsoring Organization:: USDOE Office of Nuclear Energy (NE), Nuclear Fuel Cycle and Supply Chain

OSTI ID:: 1574552

Journal Information:: Virus Evolution, Journal Name: Virus Evolution Journal Issue: 2 Vol. 5; ISSN 2057-1577

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (35)

Implications of HIV diversity for the HIV-1 pandemic Hemelaar, Joris Journal of Infection, Vol. 66, Issue 5 https://doi.org/10.1016/j.jinf.2012.10.026	journal	May 2013
Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools Pineda-Peña, Andrea-Clemencia; Faria, Nuno Rodrigues; Imbrechts, Stijn Infection, Genetics and Evolution, Vol. 19 https://doi.org/10.1016/j.meegid.2013.04.032	journal	October 2013
Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences Pérez-Losada, Marcos; Arenas, Miguel; Galán, Juan Carlos Infection, Genetics and Evolution, Vol. 30 https://doi.org/10.1016/j.meegid.2014.12.022	journal	March 2015
Frequencies of Gag-restricted T-cell escape “footprints” differ across HIV-1 clades A1 and D chronically infected Ugandans irrespective of host HLA B alleles Serwanga, Jennifer; Nakiboneka, Ritah; Mugaba, Susan Vaccine, Vol. 33, Issue 14 https://doi.org/10.1016/j.vaccine.2015.02.037	journal	March 2015
Nextflow enables reproducible computational workflows Di Tommaso, Paolo; Chatzou, Maria; Floden, Evan W. Nature Biotechnology, Vol. 35, Issue 4 https://doi.org/10.1038/nbt.3820	journal	April 2017
Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries Araújo, Pedro M. M.; Carvalho, Alexandre; Pingarilho, Marta Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-43420-2	journal	May 2019
Subtype C Is Associated with Increased Vaginal Shedding of HIV‐1 John‐Stewart, Grace C.; Nduati, Ruth W.; Rousseau, Christine M. The Journal of Infectious Diseases, Vol. 192, Issue 3 https://doi.org/10.1086/431514	journal	August 2005
Web Resources for HIV Type 1 Genotypic-Resistance Test Interpretation Liu, T. F.; Shafer, R. W. Clinical Infectious Diseases, Vol. 42, Issue 11 https://doi.org/10.1086/503914	journal	June 2006
Rationale and Uses of a Public HIV Drug‐Resistance Database Shafer, Robert W. The Journal of Infectious Diseases, Vol. 194, Issue s1 https://doi.org/10.1086/505356	journal	September 2006
HIV‐1 Subtype D Infection Is Associated with Faster Disease Progression than Subtype A in Spite of Similar Plasma HIV‐1 Loads Baeten, Jared M.; Chohan, Bhavna; Lavreys, Ludo The Journal of Infectious Diseases, Vol. 195, Issue 8 https://doi.org/10.1086/512682	journal	April 2007
Effect of Human Immunodeficiency Virus Type 1 (HIV‐1) Subtype on Disease Progression in Persons from Rakai, Uganda, with Incident HIV‐1 Infection Kiwanuka, Noah; Laeyendecker, Oliver; Robb, Merlin The Journal of Infectious Diseases, Vol. 197, Issue 5 https://doi.org/10.1086/527416	journal	March 2008
A statistical model for HIV-1 sequence classification using the subtype analyser (STAR) Myers, R. E.; Gale, C. V.; Harrison, A. Bioinformatics, Vol. 21, Issue 17 https://doi.org/10.1093/bioinformatics/bti569	journal	July 2005
Biopython: freely available Python tools for computational molecular biology and bioinformatics Cock, P. J. A.; Antao, T.; Chang, J. T. Bioinformatics, Vol. 25, Issue 11 https://doi.org/10.1093/bioinformatics/btp163	journal	March 2009
Snakemake--a scalable bioinformatics workflow engine Koster, J.; Rahmann, S. Bioinformatics, Vol. 28, Issue 19 https://doi.org/10.1093/bioinformatics/bts480	journal	August 2012
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Nguyen, Lam-Tung; Schmidt, Heiko A.; von Haeseler, Arndt Molecular Biology and Evolution, Vol. 32, Issue 1 https://doi.org/10.1093/molbev/msu300	journal	November 2014
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data Huerta-Cepas, Jaime; Serra, François; Bork, Peer Molecular Biology and Evolution, Vol. 33, Issue 6 https://doi.org/10.1093/molbev/msw046	journal	February 2016
A web-based genotyping resource for viral sequences Rozanov, M.; Plikat, U.; Chappey, C. Nucleic Acids Research, Vol. 32, Issue Web Server https://doi.org/10.1093/nar/gkh419	journal	July 2004
jpHMM: Improving the reliability of recombination prediction in HIV-1 Schultz, A. -K.; Zhang, M.; Bulla, I. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp371	journal	May 2009
COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification Struck, Daniel; Lawyer, Glenn; Ternes, Anne-Marie Nucleic Acids Research, Vol. 42, Issue 18 https://doi.org/10.1093/nar/gku739	journal	August 2014
A V106M mutation in HIV-1 clade C viruses exposed to efavirenz confers cross-resistance to non-nucleoside reverse transcriptase inhibitors Brenner, Bluma; Turner, Dan; Oliveira, Maureen AIDS, Vol. 17, Issue 1 https://doi.org/10.1097/00002030-200301030-00001	journal	January 2003
Preferential in-utero transmission of HIV-1 subtype C as compared to HIV-1 subtype A or D Renjifo, Boris; Gilbert, Peter; Chaplin, Beth AIDS, Vol. 18, Issue 12 https://doi.org/10.1097/01.aids.0000131392.68597.34	journal	January 2004
Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G Abecasis, Ana Barroso; Deforche, Koen; Snoeck, Joke AIDS, Vol. 19, Issue 16 https://doi.org/10.1097/01.aids.0000188422.95162.b7	journal	January 2005
Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity Gifford, Robert; de Oliveira, Tulio; Rambaut, Andrew AIDS, Vol. 20, Issue 11 https://doi.org/10.1097/01.aids.0000237368.64488.ae	journal	January 2006
Antiretroviral resistance in different HIV-1 subtypes: impact on therapy outcomes and resistance testing interpretation Camacho, Ricardo Jorge; Vandamme, Anne-Mieke Current Opinion in HIV and AIDS, Vol. 2, Issue 2 https://doi.org/10.1097/COH.0b013e328029824a	journal	January 2007
Analysis of the history and spread of HIV-1 in Uganda using phylodynamics Ragonnet-Cronin, Manon; Ssemwanga, Deogratius; Logue, Christopher H. Journal of General Virology, Vol. 96, Issue 7 https://doi.org/10.1099/vir.0.000107	journal	July 2015
HIV-1 Nomenclature Proposal Robertson, D. L. Science, Vol. 288, Issue 5463 https://doi.org/10.1126/science.288.5463.55d	journal	April 2000
Comparative Evaluation of Subtyping Tools for Surveillance of Newly Emerging HIV-1 Strains Fabeni, Lavinia; Berno, Giulia; Fokam, Joseph Journal of Clinical Microbiology, Vol. 55, Issue 9 https://doi.org/10.1128/JCM.00656-17	journal	July 2017
Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form Abecasis, A. B.; Lemey, P.; Vidal, N. Journal of Virology, Vol. 81, Issue 16 https://doi.org/10.1128/JVI.00463-07	journal	June 2007
The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. Gao, F.; Robertson, D. L.; Morrison, S. G. Journal of virology, Vol. 70, Issue 10 https://doi.org/10.1128/JVI.70.10.7013-7029.1996	journal	January 1996
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics Abecasis, Ana B.; Wensing, Annemarie MJ; Paraskevis, Dimitris Retrovirology, Vol. 10, Issue 1 https://doi.org/10.1186/1742-4690-10-7	journal	January 2013
Impact of HIV‐1 viral subtype on disease progression and response to antiretroviral therapy Easterbrook, Philippa J.; Smith, Mel; Mullen, Jane Journal of the International AIDS Society, Vol. 13, Issue 1 https://doi.org/10.1186/1758-2652-13-4	journal	January 2010
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1 Kosakovsky Pond, Sergei L.; Posada, David; Stawiski, Eric PLoS Computational Biology, Vol. 5, Issue 11 https://doi.org/10.1371/journal.pcbi.1000581	journal	November 2009
Origin and Epidemiological History of HIV-1 CRF14_BG Bártolo, Inês; Abecasis, Ana B.; Borrego, Pedro PLoS ONE, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pone.0024130	journal	September 2011

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