Molecular phylogenetic analysis of human immunodeficiency virus type 1 strains obtained from Korean patients: env gene sequences

Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

In Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.

Molecular Epidemiology of Human Immunodeficiency Virus

During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea.

Molecular linkage tracing of HIV-1 transmission events in seroconcordant couples in Guangxi Province, Southeastern China

Background

Guangxi Province in Southeastern China has one of the highest HIV-1 infection and transmission rates in stable couples. However, the mode of transmission at the molecular level has seldom been reported amongst this group. It is important to investigate this issue to support the treatment-as-prevention approach and for efficient interventions.

Methods

HIV-1 subgenomic regions (1.2 kb of pol and a 660-bp env C2V5 fragment) were sequenced in 42 couples. A couple linkage assessment was performed by phylogenetic analysis of sequences and Bayesian analysis of genetic distances. A subset of pairs was selected for single-genome amplification.

Results

Thirty-five pairs (83.3 %, 35/42) were identified as linked, 3 pairs (7.1 %, 3/42) were identified as indeterminate, and 4 pairs (9.5 %) were identified as unlinked. The predominant intra-couple-transmitted HIV-1 subtype was CRF01_AE (80 %, 28/35). The median genetic distance of linked couples was 0.5 %.

Conclusion

The majority of HIV-1 transmission events in this study occurred within the partnership, and the predominant HIV-1 subtype was CRF01_AE. Further research on the mode of HIV transmission in other locations is needed.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-3578-2) contains supplementary material, which is available to authorized users.

HIV-1 subtype B: Traces of a pandemic

Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.

Phylogenetic analysis of full-length pol gene from Korean hemophiliacs and plasma donors infected with Korean subclade B of HIV type 1

There was an outbreak of HIV-1 transmission among 20 out of 122 Korean hemophiliacs from 1990. We assessed the genetic relationships among HIV-1 viruses found in three cash-paid plasma donors whose preseroconversion plasma was used to produce Korean-made clotting factor, 20 hemophiliacs infected with HIV-1 in Korea, three hemophiliacs infected with HIV-1 from clotting factor manufactured outside Korea, and 71 local control patients infected with the Korean subclade of HIV-1 subtype B (KSB). Full-length pol gene sequences (2841 bp) of viruses from frozen stored serum, samples obtained 1-3 years after diagnosis, were amplified by RT-PCR and sequenced by direct DNA sequencing. Phylogenetic and signature pattern analyses were used to investigate the relationships among the sequences. Donors O and P were associated with two clusters, of 8 and 12 hemophiliacs, respectively, which were demarcated from the 71 KSB-infected local control patients and donor R. These data confirm that HIV-1 transmission to 20 hemophiliacs occurred through infusion of Korean-made clotting factor.

Broad neutralizing antibody response and genetic variation in HIV-1 env genes in Koreans with primary HIV-1 infections

To determine the neutralization profiles induced by HIV-1 Korean clade B, which has a monophyletic lineage and relative limited genetic diversity, we investigated the ability of HIV variants to elicit neutralizing antibodies in the immune response to primary infection. We selected seven Korean drug-naïve subjects with an HIV-1 primary infection and did pseudovirion-based neutralization assays using env genes of Korean HIV origin. The neutralizing antibody responses to the Korean clade B showed broad reactivity to subtype B but a highly subtype-specific pattern. The lengths of the amino acid sequences and the PNGS numbers in the V1-V5 region were positively correlated with neutralization. These results imply that the genetic characteristics of HIV-1 env may affect neutralizing antibody responses in HIV-1-infected individuals. This is the first report describing the relationship between neutralizing antibody responses and HIV-1 genetic characteristics in Korean subjects. It can be useful for developing AIDS vaccines against HIV-1 subtype B strains.

Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on nef and vif sequences

Molecular phylogenetic studies of the HIV-1 isolated from Koreans have suggested the presence of the so-called "Korean clade", which can be defined as a cluster free of foreign isolates. The Korean clade accounts for more than 60% of Korean isolates and exerts characteristic amino acid sequences. Thus, it is merited to estimate when this Korean clade first emerged in order to understand the evolutionary pattern of the Korean clade. We analyzed and reconstructed the most recent common ancestor (MRCA) sequences from nef (n=229) and vif (n=179) Korean clade sequences. Linear regression analyses of sequence divergence estimates were plotted against sampling years to infer the year in which there was zero divergence from the MRCA sequences. MRCA sequences suggested the Korean clade was first emerged around 1984, before the first detection of HIV-1 in Korea in 1985. Further studies on synonymous and nonsynonymous substitution rates suggested positive selection event for the Korean clade, while other subtype B had undergone negative to neutral evolution.

National survey of prevalent HIV strains: limited genetic variation of Korean HIV-1 clade B within the population of Korean men who have sex with men

The evolution of HIV is the result of an explosive combination of factors-a high rate of mutation, replication dynamics, frequent recombination, and natural selection. To understand the evolution of the distinctive Korean HIV-1 B clade, we investigated the characteristics of the genetic variation of the HIV-1 subtype B env gene within the group of Korean men who have sex with men (MSM). From 1985 to 2005, 700 HIV-1-infected Koreans were sequenced at the V1 to V5 region of the HIV-1 env gene. In the phylogenetic analysis, 560 isolates were identified as HIV-1 subtype B, and 489 of the 560 isolates were HIV-1 Korean clade B. Based on epidemiologic investigation, 249 of 700 HIV-1-infected patients were HIV-1 subtype B-infected MSM. Interestingly, the proportion of the GPGS motif in MSM infected by Koreans was 1.6 times higher than in MSM infected by foreigners, and the genetic expansions of diversity and divergence for HIV-1 subtype B in Korean MSM were 2.1% and 2.5%, respectively. This was much lower than those observed in other countries. Therefore, our findings imply that the HIV strains in this group were closely related. This result may be helpful for understanding the evolution of the distinct HIV-1 Korean B clade.

Characterization and signature pattern analysis of Korean clade HIV-1 using nef gene sequences

Phylogenetic studies of the HIV-1 gene sequences isolated from Korean patients have suggested that most of Korean isolates belong to the subtype B strain. This study aims to characterize the Korean clade by molecular phylogenetic analysis using all of the Korean nef gene sequences registered in the NCBI GenBank (N=422), in addition to 41 reference strains and 94 foreign isolates. Through phylogenetic analyses, we verified that most of the Korean isolates belonged to the subtype B, where 78.8% are clustered exclusively of foreign isolates. This cluster has been named the Korean clade subtype B (KCB) in order to distinguish it from other subtype B clusters. Genetic distance analysis suggested that the KCB cluster was more homogeneous and clearly distinctive from the non-Korean clade subtype B (NKCB). Comparison of consensus amino acid sequences from KCB and NKCB revealed that characteristic KCB signature amino acid patterns composed of 11 amino acid residues, whose frequencies in the KCB were significantly higher than in the NKCB. The KCB signature amino acid residues were critical in identifying KCB from NKCB, since substitution of the NKCB sequences with KCB signature amino acids relocated them to the Koran clade, and vice versa.

Molecular epidemiologic study of a human immunodeficiency virus 1 outbreak in haemophiliacs B infected through clotting factor 9 after 1990

BACKGROUND AND OBJECTIVES

Twenty haemophiliacs were diagnosed as infected with human immunodeficiency virus 1 (HIV-1), 1 to 2 years after exposure to clotting factor 9 manufactured in Korea, beginning in early 1990. This study assessed the genetic relationships between viruses found in plasma donors and haemophiliacs.

MATERIALS AND METHODS

Sequencing of the nef and pol genes of viruses from infected haemophiliacs, plasma donors whose plasma was used in domestic clotting factor manufacture, haemophiliacs infected outside Korea, and local controls were determined by nested polymerase chain reactions and direct DNA sequencing. Phylogenetic analysis was used to investigate the relationships among the sequences.

RESULTS

Both plasma donors and the haemophiliacs were infected with a subclade of subtype B that is a founder effect lineage in Korea.

CONCLUSION

Our data indicate that HIV-1 transmission to 20 haemophiliacs occurred through intravenous injection of Korean-made clotting factor.

SUMMARY

A clotting factor made in Korea from blood from cash-paid donors infected at least 20 haemophiliacs with HIV-1 subtype B.

Monophyletic clade of HIV-1 subtype B in Korea: evolutionary pressure or single introduction?

We have previously shown that many of the nef sequences from Korean HIV-1 subtype B carriers were grouped together in phylogenetic tree analyses. To determine whether this pattern was originated from either a single HIV-1-infected person or some biological pressure which directs the HIV-1 genomic mutation by the Korean specific immunological characters, we analyzed nef sequences from HIV-1-infected individuals with different time intervals. Thirty-two out of 46 analyzed patients formed a Korean monophyletic (KM) clade with 93% bootstrapping value. Eighteen patients' nef sequences were analyzed 1-9 years after first analysis. None of the patients shifted their clade from the first clustered clade (KM or non-KM), and all of the re-analyzed isolates were clustered close to the first analyzed clade. Isolates of the KM dade and non-KM clade in nef analysis showed the same pattern as in env analysis. Phylogenetic clustering evidences from both nef and C2/V3 trees strongly support the idea that introduction of the KM clade in subtype B strains originated from a common source. Thus, treatment and development of an AIDS vaccine may be somewhat easier than in other countries with multiple strains of HIV-1.

Natural polymorphisms of protease in protease inhibitor-naive HIV-1 infected patients in Korea: a novel L63M in subtype B

To establish a baseline for monitoring resistance mutation to protease inhibitors (PI), we determined protease(PR) sequences in peripheral blood mononuclear cells obtained from 43 PI-naive Korean HIV-1 infected patients. Interestingly, phylogenetic analysis revealed that 41 of the sequences belonged to subtype B, one belonged to subtype A, and one was unique, not clustering with any subtype. Thirty-one (76%) of the 41 sub-type B sequences formed a subclade within subtype B, a so-called "Korean B cluster." Polymorphisms were observed at 34 (34.3%) of the PR codons. One patient (2.3%) harbored a primary resistance-conferring mutation, L90M along with L63P and A71V, and all 43 strains showed some secondary associated with drug resistance. The percentage of patients with 7, 5, 4, 3, 2, and 1, resistance mutations were 2%, 2%, 14%, 23%,37%, and 9%, respectively. A novel polymorphism in subtype B, L63M was detected in two patients. Another patient showed a gross deletion (257 bp) after codon 91. The average genetic distance of the 41 subtype B sequences to the HXB2 sequence was 3.0% (range, 1.0-5.1%). Six hemophiliacs were infected with a domestic strain of HIV-1 subtype B, while the other two hemophiliacs were infected with nondomestic subtype B and had lived outside Korea. Although this is the first report on the molecular nature of PR in Korea, there is also a need to establish baselines for nonsubtype B HIV-1.

Determination of genetic subtypes of HIV type 1 isolated from Korean AIDS patients

To determine HIV-1 subtypes in Korean patients, we analyzed the nucleotide sequences of the HIV-1 env gene isolated from 19 Korean patients. DNA was extracted from cultured lymphocytes and the proviral V3 env gene was amplified by nested polymerase chain reaction. DNA sequences were determined using a cycle sequencer with fluorescence-labeled dye terminators, and aligned using a set of reference sequences. The phylogenetic tree was constructed by the neighbor-joining method. Most of the enrolled patients were in the advanced stage of AIDS with CD4+ lymphocyte counts ranging from 10 to 560 (median 50) per mm3. Eighteen of the nineteen patients' sequences fall into subtype B (95%) and one was subtype A (5%). The tetrameric motifs at the tip of the V3 loop were comprised of GPGR (10 cases, 53%), GPGS (5 cases, 26%), and GPGQ, GPGG, GQGR, and APGS (one case each, 5%). Subtype B was found to be the most predominant clade of HIV-1 in our AIDS patients.

Reanalysis of the HIV-1 circulating recombinant form A/E (CRF01_AE): evidence of A/E/G recombination

Circulating recombinant form (CRF) 01_AE caused an extensive HIV-1 epidemic in Thailand and Southeast Asia. Reanalysis of the recombination pattern of CRF01_AE suggested a more complicated pattern of mosaicism consisting of subtypes A, G, and E. These findings provide evidence that CRF01_AE originated from recombination between at least three different subtypes.

Phylogenetic analysis of reverse transcriptase in antiretroviral drug-naive Korean HIV type 1 patients

To study whether genotypic antiretroviral resistance testing (GART) is needed to guide initial antiretroviral therapy in Korea, we determined partial pol sequences in peripheral blood mononuclear cells (PBMCs) obtained from 29 antiretroviral drug-naive HIV-1 patients. Phylogenetic analysis revealed four subtypes: B (23 patients), D (1 patient), recombinant strain (2 patients), and "untyped" (3 patients). Eighteen (78.3%) of the 23 subtype B isolates formed a distinct monophyletic cluster. The average genetic distances of 23 subtype B compared with reference strain HXB2 were 2.7% (range, 1.5-4.6%). Only one patient harbored variant virus containing a V179D mutation causing resistance to efavirenz. These data derived from therapy-naive patients suggest that potential use of primary resistance testing to guide initial antiretroviral therapy should be considered in Korea. This is the first report on the molecular nature of HIV-1 RT in Korea.

Introduction of HIV type 1 subtype E virus into South Korea

Subtype E HIV-1 is the most prevalent strain in Southeast Asia. Although subtype B is prevalent in Korea, geographical distance and increases in travel may lead to the spread of subtype E in Korea. Therefore, we tried to identify and monitor the patterns of HIV subtype E virus introduction into Korea. The divergence of nucleotide sequences within the envelope region (V3 to V5) of Korean subtype E isolates ranged from 4.3 to 14.6% (n = 8; mean, 9.5 +/- 2.8%). In pairwise comparisons of subtype E isolates between Korea and other regions, the divergence of nucleotide sequences between 8 Korean and 16 Asian subtype E variants ranged from 1.3 to 15.2% (mean, 7.8 +/- 2.6%), whereas the divergence of nucleotide sequences between 8 Korean and 2 African variants ranged from 11.7 to 20.7% (mean, 15.4 +/- 2.2%). A phylogenetic tree showed that Korean subtype E isolates cluster with the Asian isolates but far from the African isolates. These epidemiological and molecular epidemiological data suggest that HIV-1 subtype E strains have been transmitted into Korea from endemic areas of Southeast Asia rather from Africa.