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Published on: October 16, 2018
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Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences
Soo-Yon Rhee1, Robert W Shafer1
1Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94301, USA.
Scientific Data
|August 1, 2018
Summary
Accurate HIV-1 subtyping is crucial for molecular epidemiology. Researchers developed a geographically stratified pol sequence set (GSPS) to better represent HIV-1 diversity for improved subtyping.
Area of Science:
- Virology
- Molecular Epidemiology
- Bioinformatics
Background:
- Accurate classification of Human Immunodeficiency Virus type 1 (HIV-1) group M lineages, or subtyping, is critical for global molecular epidemiology.
- Most HIV-1 sequencing focuses on the pol gene for genotypic resistance testing, necessitating representative pol sequences for diversity assessment.
- Complete genome sequences may not fully capture the diversity within the HIV-1 pol gene due to recombination points in circulating recombinant forms (CRFs).
Purpose of the Study:
- To develop a geographically stratified set of HIV-1 pol sequences that accurately represent the diversity of HIV-1 group M.
- To create a reference set that is optimized for HIV-1 pol subtyping and reflects real-world sequence data.
Main Methods:
- A software pipeline was used to compile 6,034 complete HIV-1 pol sequences from individual patients, annotated by country and year.
- Sequences represented 11 pure subtypes and 70 CRFs.
- A representative set of 716 sequences (Geographically-Stratified Pol Subtype/CRF - GSPS) was selected by minimizing the average distance to all other sequences within each subtype/CRF and country.
Main Results:
- A novel reference set of 716 geographically stratified pol sequences (GSPS) was generated, representing diverse HIV-1 group M subtypes and CRFs.
- The GSPS set is specifically curated to reflect HIV-1 pol sequence diversity, differing from complete genome sets.
- Extensive data on pol diversity within specific subtype/CRF and country combinations are provided.
Conclusions:
- The developed Geographically-Stratified Pol Subtype/CRF (GSPS) reference sequence set is a valuable resource for HIV-1 pol subtyping.
- This resource will enhance the accuracy of molecular epidemiology studies by providing a more representative dataset for the pol gene.
- The GSPS set addresses the limitations of using complete genomes for assessing pol gene diversity.
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