Sequencer 4

Sequencer 4.10.1 (GeneCodes, Ann Arbor, MI) was used for sequence splicing, and the secondary peak threshold was set to 30% to identify ambiguities. The sequence was aligned with the reference sequences using BioEdit (version 7.0.9, Informer Technologies Inc.). Reference sequences were downloaded from the Los Alamos HIV database and included the major international epidemic strains A-D, F-H, and J-K, as well as the major epidemic recombinant strains in China. A phylogenetic tree with the maximum likelihood (ML) method was constructed for confirmation using the FastTree 2.1. The nucleotide substitution model was GTR + G + I, and support values were calculated by Shimodaira Hasegawa-like test. Clusters with a bootstrap value higher than 0.90 (90%) were defined as the same subtype. The ML phylogenetic tree was imported to FigTree v 1.4.4 for visualization.

Sequencer 4.10.1 (GeneCodes Corporation, Ann Arbor, MI, United States) was used for sequence splicing, the secondary peak threshold was set to 20% to identify ambiguities. The sequence was aligned using BioEdit (version 7.0.9, Informer Technologies Inc.). A phylogenetic tree with the neighbor-joining method was constructed using MEGA (version 6.06), reference sequences from HIV Databases¹ and the bootstrap was set to 1,000, the check value was 70% to identify the subtype, control for potential laboratory contamination and sample contamination. Other sequence quality controls were monitored using the WHO HIVDR QC tool.² We defined PDR using the Stanford HIV Drug Resistance Database.³ Drug susceptibility was classified into four categories depending on mutation score and degree: susceptible (< 15), low—(15–29), intermediate (30–59), and high-level (≥ 60) resistance. Drug resistance was defined by a drug resistance score ≥ 15 or drug resistance grade ≥ 3 for one or more of the 20 HIV antiretroviral drugs in the three categories of non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) currently listed in the HIV database of Stanford University (18 ).