Abstract
We report here a novel HIV-1 circulating recombinant form (CRF) (CRF59_01B) comprised of CRF01_AE and subtype B, with two recombination breakpoints in the pol and vpu-env regions, respectively. CRF59_01B was identified from three epidemiologically unlinked men who have sex with men (MSM) in northeast China. This represents the second CRF identified in the MSM population in China.
GENOME ANNOUNCEMENT
Human immunodeficiency virus type 1 (HIV-1) is classified into four groups: M, O, N, and P (1, 2). The group M strains, responsible for the vast majority of HIV infections in the world, comprise eleven subtypes and sub-subtypes, as well as 58 circulating recombinant forms (CRFs) and various types of unique recombinant forms (URFs) (see http://www.hiv.lanl.gov).
In Asia, 12 CRFs have been reported to date: CRF01_AE (3), CRF15_01B (4), and CRF34_01B (5) in Thailand, CRF07_BC (6), CRF08_BC (7), and CRF55_01B in China (8), CRF33_01B (9), CRF48_01B (10), CRF53_01B (11), and CRF54_01B (12) in Malaysia, CRF51_01B in Singapore (13), and CRF52_01B in Thailand and Malaysia (14). CRF51_01B and CRF55_01B are the CRFs identified among men who have sex with men (MSM).
Wide cocirculation and dual infection of CRF01_AE and subtype B in various geographical regions in Asia led to the emergence of various novel CRFs. We describe the genome sequences of a novel CRF (CRF59_01B) isolated from three epidemiologically unlinked MSM in northeastern China.
Near-full-length genome (NFLG) sequences (9.0 kb) were determined from plasma RNA using a single genome amplification method with two sets of primers designed for the determination of the 5′ and 3′ halves of the HIV-1 genome (15, 16). Amplicons were directly sequenced using the internal walking primers with an ABI 3730XL Sanger-based genetic analyzer. The study was approved by the Institutional Review Board of the First Affiliated Hospital of China Medical University.
The three NFLG sequences of CRF59_01B (accession no. KC462190, KC462191, and JX960635) were 8,804, 8,795, and 8,380 bp in size for strains 11CN.LNSY300392, 10CN.LNSY300533, and 09LNA423, respectively, spanning the noncoding region, the gag, pol, env, tat, rev, vif, vpr, vpu, and nef genes, and part of 3′ long terminal repeat (LTR). These three strains formed a distinct monophyletic cluster and did not belong to any known HIV-1 subtype or CRF. Bootscanning and informative site analyses (17) identified four unique recombination breakpoints between CRF01_AE and subtype B at the nucleotide positions (relative to HXB2) 2570 and 2719 in the pol region and 6149 and 8244 in the vpu-env region. These recombination breakpoints were shared among all three strains. Subregion tree analyses further confirmed the parental origin of each region of the recombinant genome as follows: region I (positions relative to HXB2: 790 to 2569) is CRF01_AE, region II (positions relative to HXB2: 2570 to 2718) is B, region III (positions relative to HXB2: 2719 to 6419) is CRF01_AE, region IV (positions relative to HXB2: 6149 to 8243) is B, and region V (positions relative to HXB2: 8244 to 9600) is CRF01_AE. The recombinant structure of CRF59_01B is indeed distinct from any previously reported CRFs. Subregion tree analyses also indicated that subtype B regions were of U.S. or European origin, unlike the subtype B′ (Thailand variant of subtype B) (3, 18) lineage associated with bloodborne epidemics in Asia (19), while CRF01_AE regions were of Thailand CRF01_AE origin, not related to the CRF01_AE variants (clusters 1 and 2) that we recently identified among MSM in China (15).
CRF59_01B is the second CRF identified in the MSM population in China. CRF55_01B was identified recently among MSM in southern China, while the new CRF described here was identified among MSM in northeastern China. The emergence of CRF55_01B and CRF59_01B suggests the extensive ongoing generation of new recombinant forms involving the CRF01_AE and subtype B lineages among MSM in various regions in China.
Nucleotide sequence accession numbers.
The sequences are available in GenBank under accession no. KC462190, KC462191, and JX960635.
ACKNOWLEDGMENTS
This work was supported in part by mega projects of national science research for the 12th Five-Year Plan (2012ZX10001-006 and 2012ZX10001-002).
Footnotes
Citation Han X, An M, Zhang W, Zhao B, Chu Z, Takebe Y, Shang H. 2013. Genome sequences of a novel HIV-1 circulating recombinant form (CRF59_01B) identified among men who have sex with men in northeastern China. Genome Announc. 1(3):e00315-13. doi:10.1128/genomeA.00315-13.
REFERENCES
- 1. Plantier JC, Leoz M, Dickerson JE, De Oliveira F, Cordonnier F, Lemée V, Damond F, Robertson DL, Simon F. 2009. A new human immunodeficiency virus derived from gorillas. Nat. Med. 15:871–872 [DOI] [PubMed] [Google Scholar]
- 2. Van Heuverswyn F, Li Y, Neel C, Bailes E, Keele BF, Liu W, Loul S, Butel C, Liegeois F, Bienvenue Y, Ngolle EM, Sharp PM, Shaw GM, Delaporte E, Hahn BH, Peeters M. 2006. Human immunodeficiency viruses: SIV infection in wild gorillas. Nature 444:164. [DOI] [PubMed] [Google Scholar]
- 3. Ou CY, Takebe Y, Weniger BG, Luo CC, Kalish ML, Auwanit W, Yamazaki S, Gayle HD, Young NL, Schochetman G. 1993. Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand. Lancet 341:1171–1174 [DOI] [PubMed] [Google Scholar]
- 4. Tovanabutra S, Watanaveeradej V, Viputtikul K, De Souza M, Razak MH, Suriyanon V, Jittiwutikarn J, Sriplienchan S, Nitayaphan S, Benenson MW, Sirisopana N, Renzullo PO, Brown AE, Robb ML, Beyrer C, Celentano DD, McNeil JG, Birx DL, Carr JK, McCutchan FE. 2003. A new circulating recombinant form, CRF15_01B, reinforces the linkage between IDU and heterosexual epidemics in Thailand. AIDS Res. Hum. Retroviruses 19:561–567 [DOI] [PubMed] [Google Scholar]
- 5. Tovanabutra S, Kijak GH, Beyrer C, Gammon-Richardson C, Sakkhachornphop S, Vongchak T, Jittiwutikarn J, Razak MH, Sanders-Buell E, Robb ML, Suriyanon V, Birx DL, Michael NL, Celentano DD, McCutchan FE. 2007. Identification of CRF34_01B, a second circulating recombinant form unrelated to and more complex than CRF15_01B, among injecting drug users in northern Thailand. AIDS Res. Hum. Retroviruses 23:829–833 [DOI] [PubMed] [Google Scholar]
- 6. Su L, Graf M, Zhang Y, von Briesen H, Xing H, Köstler J, Melzl H, Wolf H, Shao Y, Wagner R. 2000. Characterization of a virtually full-length human immunodeficiency virus type 1 genome of a prevalent intersubtype (C/B′) recombinant strain in China. J. Virol. 74:11367–11376 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Piyasirisilp S, McCutchan FE, Carr JK, Sanders-Buell E, Liu W, Chen J, Wagner R, Wolf H, Shao Y, Lai S, Beyrer C, Yu XF. 2000. A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant. J. Virol. 74:11286–11295 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Han X, An M, Zhang W, Cai W, Chen X, Takebe Y, Shang H. 2013. Genome sequences of a novel HIV-1 circulating recombinant form, CRF55_01B, identified in China. Genome Announc. 1():e00050-12. doi:10.1128/genomeA.00050-12 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Tee KK, Li XJ, Nohtomi K, Ng KP, Kamarulzaman A, Takebe Y. 2006. Identification of a novel circulating recombinant form (CRF33_01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia. J. Acquir. Immune Defic. Syndr. 43:523–529 [DOI] [PubMed] [Google Scholar]
- 10. Li Y, Tee KK, Liao H, Hase S, Uenishi R, Li XJ, Tsuchiura T, Yang R, Govindasamy S, Yong YK, Tan HY, Pybus OG, Kamarulzaman A, Takebe Y. 2010. Identification of a novel second-generation circulating recombinant form (CRF48_01B) in Malaysia: a descendant of the previously identified CRF33_01B. J. Acquir. Immune Defic. Syndr. 54:129–136 [DOI] [PubMed] [Google Scholar]
- 11. Chow WZ, Al-Darraji H, Lee YM, Takebe Y, Kamarulzaman A, Tee KK. 2012. Genome sequences of a novel HIV-1 CRF53_01B identified in Malaysia. J. Virol. 86:11398–11399 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Ng KT, Ong LY, Takebe Y, Kamarulzaman A, Tee KK. 2012. Genome sequence of a novel HIV-1 circulating recombinant form 54_01B from Malaysia. J. Virol. 86:11405–11406 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Ng OT, Eyzaguirre LM, Carr JK, Chew KK, Lin L, Chua A, Leo YS, Redd AD, Quinn TC, Laeyendecker O. 2012. Identification of new CRF51_01B in Singapore using full genome analysis of three HIV type 1 isolates. AIDS Res. Hum. Retroviruses 28:527–530 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Liu Y, Li L, Bao Z, Li H, Zhuang D, Liu S, Wang X, Li T, Jia L, Yang S, Li J. 2012. Identification of a novel HIV type 1 circulating recombinant form (CRF52_01B) in Southeast Asia. AIDS Res. Hum. Retroviruses 28:1357–1361 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. An M, Han X, Xu J, Chu Z, Jia M, Wu H, Lu L, Takebe Y, Shang H. 2012. Reconstituting the epidemic history of CRF01_AE among MSM in Liaoning, northeastern China: implication in expanding MSM epidemic in China. J. Virol. 22:12402–12406 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 16. Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM. 2009. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206:1273–1289 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 73:152–160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18. Kalish ML, Baldwin A, Raktham S, Wasi C, Luo CC, Schochetman G, Mastro TD, Young N, Vanichseni S, Rübsamen-Waigmann H, et al. 1995. The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand: implications for HIV vaccine trials. AIDS 9:851–857 [DOI] [PubMed] [Google Scholar]
- 19. Li Y, Uenishi R, Hase S, Liao H, Li XJ, Tsuchiura T, Tee KK, Pybus OG, Takebe Y. 2010. Explosive HIV-1 subtype B′ epidemics in Asia driven by geographic and risk group founder events. Virology 402:223–227 [DOI] [PubMed] [Google Scholar]