Table 1.
Comparison of AUTO-TUNE and published thresholds from prior studies using partial HIV-1 polymerase gene sequences.
| Reference | N | L | E[D] | Scope | Location/Country | Timespan | Common Subtypes | Distance threshold, sub/site | |
|---|---|---|---|---|---|---|---|---|---|
| Published | AUTO-TUNE | ||||||||
| Zai et al. (2020) | 209 | 1056 | 1.5% | Country | China | 2007–2015 | CRF55/01B | ¶ 0.002 | 0.00255 |
| Liu et al. (2020) | 2087/1907 ● | 1053 | 5.3% | City | Shenyang, China | 2008–2016 | CRF01, CRF07, B | ¶ 0.005/0.007 † | 0.00621 |
| Dalai et al. (2018) | 317 | 1044 | 5.5% | City | San Mateo, CA, USA | 1997–2008 | 96% B | 0.02 | 0.01944 |
| Chato et al. (2020) | 808 | 1017 | 5.6% | Province | Northern Alberta, Canada | 2007–2013 | B | ¶0.0104 | 0.01201 |
| Little et al. (2014) | 648/646 ● | 1212 | 5.9% | City | San Diego, CA, USA | 1996–2011 | 98.5% B | 0.015 | 0.02495 |
| Pérez-Losada et al. (2017) | 1879/3411 ● | 1027 | 6.0% | City | Washington DC, USA | 1987–2015 | B | 0.010 | 0.01733 |
| Rhee et al. (2019) | 4553 | 897 | 6.1% | State | CA, USA | 1998–2016 | 95.5% B | 0.015 | 0.01139★ |
| Chato et al. (2020) | 2779/2750 ● | 1398 | 6.3% | State | Tennessee, USA | 2001–2015 | B | ¶0.016 | 0.01872 |
| Temereanca et al. (2017) | 37 | 1302 | 6.7% | City | Bucharest, Romania | 2010–2013 | F1, G, B | 0.015 | 0.00194 |
| Brenner et al. (2021) | 10945/448 ● | 738 | 6.7% | Province | Quebec, Canada | 2002–2020 | B | 0.015/0.025 | 0.02741 |
| Sivay et al. (2018) | 201 | 1302 | 6.9% | Province | Mpumalanga, South Africa | 2011–2015 | C | 0.025 | 0.02506 |
| Li et al. (2022) | 295 | 1206 | 7.8% | Prefecture | Pu’er, China | 2021 | CRF08, CRF01, CRF07 | ¶ 0.013 | 0.01483 ★ |
| Yu et al. (2022) | 316 | 1074 | 7.9% | Province | Guangxi, China | 2012–2018 | CRF01, CRF08, CRF07 | ¶0.013 | 0.01178 |
| Yan et al. (2021) | 1695/1569 ● | 1569 | 8.4% | City | Guangzhou, China | 2008–2012 | CRF01, CRF07, CRF55,G | 0.015 | 0.00839 |
| Billings et al. (2019) | 150 | 1597 | 8.5% | City | Lagos, Nigeria | 2013–2016 | CRF02, URF | 0.015 | 0.0233 |
| Chen et al. (2023) | 1975/209 ● | 1050 | 8.7% | Province | Guangxi, China | 2016–2018 | CRF01, CRF07, CRF08 | ¶0.0075 | 0.01295 |
| Fabeni et al. (2020) | 726/3499 ● | 1029 | 9.2% | Country | Italy | 1998–2018 | B | 0.010 | 0.0037 |
| Leal et al. (2020) | 630/633 ● | 990 | 9.2% | State | Maranhão, Brazil | 2008–2017 | B | 0.020 | 0.04033 |
| Bbosa et al. (2020) | 2018 | 1257 | 9.3% | Country | Uganda | 2009–2016 | N.R | 0.015 | 0.02035 ★ |
| Stecher et al. (2018) | 2774 | 1028 | 12.1% | Multi-City | Germany | 1999–2016 | B | 0.015 | 0.03056 |
| Chato et al. (2020) | 1653/1840 ● | 1020 | 5.5% | City | Seattle, ISA | 2000–2013 | B | ¶0.016 | 0.01538 |
N : the number of sequences; L: length of the multiple sequence alignment, bp; E[D] mean pairwise TN93 distance; (the studies are sorted on this column, in ascending order)
¶:
the original study performed threshold tuning (varied methods)
†:
distance thresholds were specific to subtypes
★:
the corresponding AUTO-TUNE score is ≥ 1.9
●:
only a subset of the complete dataset was made available (privacy, data use restrictions, incomplete GenBank submissions), the number of sequences analyzed here is shown after the / symbol; N.R: not reported