HIV-1 molecular epidemiology and drug resistance-associated mutations among treatment-naïve blood donors in China

Abstract

Surveillance of human immunodeficiency virus (HIV) molecular diversity and drug resistance-associated mutations (DRMs) among treatment-naïve blood donors is critical for monitoring viral evolution and blood safety. From 2016-2017, 199 plasma samples were collected from 24 blood centers and confirmed as HIV viral load positive or serologically reactive in National Centers for Clinical Laboratories (NCCL), of which 179 were sequenced and subtyped in the gag, protease (PR)-reverse transcriptase (RT), integrase (IN) and/or envelope (env) regions. DRMs in PR-RT and IN regions were analyzed in Stanford HIVdb Program. The majority of subtypes were circulating recombinant form (CRF) 07_BC (34.6%) and CRF01_AE (32.4%); many unique recombinant forms (URFs) (39, 21.8%) and other rare CRFs were observed in the study. Notably, CRF02_AG and CRF06_cpx strains typically found in Africa were firstly identified amongst Chinese blood donors. DRMs were common, with 28 of 179 (15.6%) specimens carrying DRMs, including the PR N88S and RT K103N mutations, which have been implicated in elevated resistance to antiretroviral drugs. Furthermore, 4 HIV-1 isolates (2.4%, 4/168) had surveillance drug-resistance mutation (SDRM), including 3 nonnucleosidereverse transcriptase inhibitors (NNRTI) SDRMs (1 K101E, 2 K103N) and 1 protease inhibitor (PI) SDRM (M46I). The HIV viral diversity among blood donors observed in this study suggest that ongoing HIV-1 recombination is becoming progressively complex in China, and lots of DRMs found in the study exacerbate the primary drug resistance landscape, which highlight the necessity of timely genotypic drug resistance monitoring and molecular surveillance of HIV-1 among blood donors.

Figure 1

Neighbor-joining phylogenetic tree analysis of HIV-1 isolates in blood donors. Sequences from HIV-1 infected blood donors and references are respectively in red and black in the trees and boxes indicate relevant nodes with >70 bootstrap. (a) Phylogenetic tree analysis of gag sequences. (b) Phylogenetic tree analysis of PR-RT sequences. (c) Phylogenetic tree analysis of IN sequences. (d) Phylogenetic tree analysis of env sequences.

Figure 2

The geographic distribution of HIV- I subtype among blood donors. (a) The Northwestern District of China was excluded on account of the small sample sizes. Others represent the rare CRFs including CRF02_AG, CRF55_01B, CRF59_01B, CRF65_cpx, CRF67_01B, CRF79_0107 and CRF85_BC.

Figure 3

Bootscan plots of the three rare recombinant partial-genome sequences from the HIV-1 infected blood donors. Each bootscan plot was performed with Kimura-2 model of nucleotide substitution with a window size of 200 and a step size of 20. The color-coded key represents the different subtypes, sub-subtypes and CRFs of HIV-1. (a) Shaanxi-001 env sequence. (b) Shaanxi-001 IN sequence. (c) Shaanxi-015 env sequence. (d) Shaanxi-015 IN sequence. (e) Shaanxi-017 env sequence.

Figure 4

Similarity plots of the three rare recombinant partial-genome sequences from the HIV-1 infected blood donors. Each similarity plot was performed with Kimura-2 model of nucleotide substitution with a window size of 200 and a step size of 20. The color-coded key represents the different subtypes, sub-subtypes and CRFs of HIV-1. (a) Shaanxi-001 env sequence. (b) Shaanxi-001 IN sequence. (c) Shaanxi-015 env sequence. (d) Shaanxi-015 IN sequence. (e) Shaanxi-017 env sequence.

Figure 5

Three rare recombinant partial-genome maps. (a) Shaanxi-001. (b) Shaanxi-015. (c) Shaanxi-017.