Table 1. Summary of sequence data characteristics.
Length is the median length of nucleotide (nt) sequences. HXB2 coords = reference nucleotide coordinates in the HXB2 genome (Genbank accession K03455). Year type: sequences are annotated with year of sample collection, and in some cases date of HIV diagnosis. N = Total sample size, including both old and new sequences. Incid = number of sequences in ‘incident’ subset (most recent year). Subtype classifications were derived from the original data sources, when available, or generated de novo with SCUEAL [60].
| Location | Length (nt) | HXB2 coords | Year type | N | Incid | Date range | Subtypes |
|---|---|---|---|---|---|---|---|
| Washington, USA | 985 | 2,256–3,240 | diagnosis | 6,583 | 253 | 1982–2019 | B (89%), C (4%), A1 (1%), other (10%) |
| collection | 6,583 | 253 | 1999–2019 | ||||
| Alberta, Canada | 1,017 | 2,253–3,269 | collection | 1,051 | 155 | 2007–2013 | B (77%), C (20%), A1 (3%) |
| Tennessee, USA | 1,296 | 2,253–3,548 | collection | 2,741 | 162 | 2001–2015 | B (93%), C (2%), other (5%) |
| diagnosis | 2,338 | 129 | 1977–2011 | ||||
| Beijing, China | 1,004 | 2,273–3,276 | collection | 3,916 | 1,196 | 2005–2015 | 01AE (50%), 07BC (25%), B (19%), other (6%) |