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

Large Evolutionary Rate Heterogeneity among and within HIV-1 Subtypes and CRFs

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of virus spread in a population and nature of the outbreak, among other factors. HIV-1 evolution is thus driven by a range of complex genetic, social, and epidemiological factors that complicates disease management and prevention. Here, we quantify the evolutionary (substitution) rate heterogeneity among major HIV-1 subtypes and recombinants by analyzing the largest collection of HIV-1 genetic data spanning the widest possible geographical (100 countries) and temporal (1981–2019) spread. We show that HIV-1 substitution rates vary substantially, sometimes by several folds, both across the virus genome and between major subtypes and recombinants, but also within a subtype. Across subtypes, rates ranged 3.5-fold from 1.34 × 10⁻³ to 4.72 × 10⁻³ in env and 2.3-fold from 0.95 × 10⁻³ to 2.18 × 10⁻³ substitutions site⁻¹ year⁻¹ in pol. Within the subtype, 3-fold rate variation was observed in env in different human populations. It is possible that HIV-1 lineages in different parts of the world are operating under different selection pressures leading to substantial rate heterogeneity within and between subtypes. We further highlight how such rate heterogeneity can complicate HIV-1 phylodynamic studies, specifically, inferences on epidemiological linkage of transmission clusters based on genetic distance or phylogenetic data, and can mislead estimates about the timing of HIV-1 lineages.

Epidemiological and phylogenetic analysis for non-B subtypes of human immunodeficiency virus type 1 in Busan, Korea

Recent data on non-B subtypes’ epidemiology among patients infected with human immunodeficiency virus-1 (HIV-1) in Korea are lacking. We aimed to assess the changing trends in the epidemiology of non-B subtypes of HIV-1 in Korea using phyloepidemiological analyses. We analyzed the demographic records and sequencing data obtained from genotypic drug resistance tests between 2005 and 2019 from 517 patients infected with HIV attending a tertiary care hospital in Busan, Korea. Subtyping and phylogenetic analyses with reference sequences were performed. Additionally, transmission clusters were identified via maximum-likelihood trees. Non-B subtypes accounted for 21.3% of the 517 sequences. CRF01_AE (52.7%) was the most common non-B subtype, followed by CRF02_AG (16.4%), A1 (11.8%), and C (5.5%). The prevalence of non-B subtypes decreased from 36.4 to 13.4% by 2009, while it increased to 27.4% between 2015 and 2019. Among patients with non-B subtypes, the proportion of overseas sailors decreased from 66.7 to 7.5%; contrarily, the proportion of men-who-have-sex-with-men (MSM) increased from 0 to 46.9% over the study period. We identified 8 transmission clusters involving non-B subtypes, with sizes ranging from 2 to 4 patients, including 3 clusters containing MSM. Our results highlight the changes in the epidemiological trends of non-B subtypes of HIV-1 in Korea.

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.

Estimation of the Number of HIV Infections and Time to Diagnosis in the Korea

BACKGROUND

Statistical data of undiagnosed people living with human immunodeficiency virus (PLHIV) are of great importance to human immunodeficiency virus (HIV) infection control. This study estimated the total number of PLHIV using nationwide claims data.

METHODS

This study used data of the incident HIV cases identified by the National Health Insurance System between 2009 and 2015. The number of patients with acquired immune deficiency syndrome (AIDS) was identified by diagnoses or prescription records. The estimated number of PLHIV and the time to diagnosis were calculated from the incident numbers of HIV and AIDS cases using the HIV Modeling Tool of the European Center for Disease Prevention and Control.

RESULTS

Between 2009 and 2015, a total of 7,033 PLHIV and 2,899 AIDS patients were diagnosed. In 2009, the number of incident HIV cases was 873 (460 AIDS patients), increasing to 995 (337 AIDS patients) in 2015. Besides, the estimated number of prevalent cases was 10,753 in 2009, compared to 14,880 in 2015. Patients visiting health facilities accounted for 42.9% (4,616/10,753) in 2009 and 64.1% (9,544/14,880) in 2015. In 2009, there were 8,363 (77.8%) undiagnosed HIV cases, experiencing a decline to 6,215 (41.8%) in 2015. It took a mean of 6.96 years to diagnose after HIV infection.

CONCLUSION

This study estimates the total burden of HIV infection in Korea for the first time using an internationally recognized HIV modeling tool. Claims data can be used to estimate the number of undiagnosed cases by identifying the total number of PLHIV and AIDS patients visiting health facilities.

Phylogenetic transmission clusters among newly diagnosed antiretroviral drug-naïve patients with human immunodeficiency virus-1 in Korea: A study from 1999 to 2012

Population-level phylogenetic patterns reflect both transmission dynamics and genetic changes, which accumulate because of selection or drift. In this study, we determined whether a longitudinally sampled dataset derived from human immunodeficiency virus (HIV)-1-infected individuals over a 14-year period (1999–2012) could shed light on the transmission processes involved in the initiation of the HIV-1 epidemic in Korea. In total, 927 sequences were acquired from 1999 to 2012; each sequence was acquired from an individual patient who had not received treatment. Sequences were used for drug resistance and phylogenetic analyses. Phylogenetic and other analyses were conducted using MEGA version 6.06 based on the GTR G+I parameter model and SAS. Of the 927 samples, 863 (93.1%) were classified as subtype B and 64 were classified as other subtypes. Phylogenetic analysis demonstrated that 104 of 927 patient samples (11.2%) were grouped into 37 clusters. Being part of a transmission cluster was significantly associated with subtype-B viruses, infection via sexual contact, and the infection of young males. Of all clusters, three (~8.1%) that comprised 10 individual samples (22.2% of 45 individuals) included at least one member with total transmitted drug resistance (TDR). In summary, HIV transmission cluster analyses can integrate laboratory data with behavioral data to enable the identification of key transmission patterns to develop tailored interventions aimed at interrupting transmission chains.

Signature pattern analysis for the full-length env gene of the earliest Korean subclade B of HIV-1: outbreak among Korean hemophiliacs

The epidemiological link in the hypervariable env gene between viruses infecting HIV-positive hemophiliacs (HPs) and plasma donors was not studied. We determined full-length env gene sequences in 20 HPs, 3 plasma donors whose plasma was used for domestic clotting factor (DCF) production, and 54 local controls (LCs). Env genes from viruses in frozen stored sera obtained 1-3 years after diagnosis and from samples collected several years after infection were amplified via RT-PCR and subjected to direct sequencing. Phylogenetic analysis indicated that all sequences were subtype B, including 133 sequences from 77 cases (20 HPs, 3 plasma donors, and 54 LCs) belonging to the Korean subclade B (KSB) and 6 sequences from 5 cases that did not belong to the KSB. Env gene sequences from donors O and P and those of the 20 HPs comprised 2 subclusters within the KSB, although phylogenetic analysis did not support significant bootstrap values. In contrast, signature pattern analysis indicated signature nucleotides at 43 positions between the HPs and LCs (P < 0.05). In particular, specific signature nucleotides at 4 positions were fully conserved in the HPs, but not in the LCs (P < 0.0001). Furthermore, there were 26 signature residues within the KSB and were distinct from the worldwide consensus for subtype B. In conclusion, signature pattern analysis for the hypervariable env gene revealed an epidemiological link that the 20 HPs in this study had been infected with viruses from the DCF used for treatment, consistent with our previous finding.

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.

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.

Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals

To evaluate if HIV transmission networks could be elucidated from data collected in a short time frame, 131 HIV-1 pol sequences were analyzed which were generated from treatment-naïve Korean individuals who were sequentially identified over 1 year. A transmission linkage was inferred when there was a genetic distance <1.5% and a total of 16 clusters, involving 39/131 (29.8%), were identified. Younger age and heterosexual exposure were independently related with clustering in the inferred network, which demonstrated that molecular epidemiology with currently generated data (i.e., drug resistance genotypes) can be used to identify local transmission networks, even over a short timeframe. J. Med. Virol. 88:1832-1835, 2016. © 2016 Wiley Periodicals, Inc.

Functional characteristics of the natural polymorphisms of HIV-1 gp41 in HIV-1 isolates from enfuvirtide-naïve Korean patients

HIV-1 gp41 plays a key role in viral entry. The insertion of Thr at position 4 and Met/Val/Phe substitutions at position 7 are frequently observed in the fusion peptide (FP) motif of gp41 without major enfuvirtide resistance associated with mutation in heptad repeats 1/2 (HR1/2) of HIV-1 isolates from Korean patients. Here, the influence of these mutations on their biological function was evaluated by employing HIV-1 variants with mutant FPs as shown previously and with recombinant HIV-1 using the env genes of 20 HIV-1 isolates from Korean patients. In an infectivity assay, all FP mutants showed lower infectivity than the wild-type NL4-3. In particular, the substitutions at position 7 led to much greater reductions in infectivity than the insertions at position 4. Nevertheless, the replication kinetics of most mutants were similar to those of the wild type, except that the FP mutants with an Ile insertion at position 4 and a Phe substitution at position 7 showed reduced replication. Moreover, most point mutants showed lower IC50 values for enfuvirtide than the wild type, whereas the L7M substitution resulted in a slightly increased IC50 value. The infectivity using the HIV-1 env recombinant viruses decreased in 14 cases but increased slightly in six cases compared with the wild type. Most recombinants were more susceptible to enfuvirtide than the wild type, except for three recombinants that showed slight resistance. Our findings may help to explain the potential mechanisms corresponding to the natural polymorphism of gp41 and to predict the efficiency of enfuvirtide in treatment of HIV-1-infected patients in Korea.

Presentation of available CTL epitopes that induction of cell-mediated immune response against HIV-1 Koran clade B strain using computational technology

OBJECTIVE

Theoretical predicting cytotoxic T lymphocyte (CTL) epitopes are an important tool in vaccine design and CTL therapy for enhancing our understanding of the cellular immune system. We would like to identify available CTL epitopes against HIV-1 Korean clade B. CTL activity was assessed in freshly isolated peripheral blood mononuclear cells from Korean HIV patients in order to assess whether these CTL epitopes induce a cell-mediated immune response (CMI).

METHODS

NetCTLpan1.1 software, which is the most popular prediction computer software package, and full atom-based simulation (FABS), which is a 3D modelling system for binding activity between epitopes and human leucocyte antigen (HLA) molecules, were used to predict the peptide-spanning Env region binding to HLA-A*24:02, HLA-A*02:01 and HLA-B*15:01, which are frequently found in the Korean population. Granzyme B and interferon-γ ELISPOT assays were used to determine whether identified CTL epitopes induce CMI.

RESULTS

Three HIV-1 Korean clade B-specific Env CTL epitopes were identified: Gp41-RYL and Gp41-RQG are localized within gp41, and Gp120-LLQ within gp120. In in vitro assays using granzyme B ELISPOT, Gp120-LLQ and Gp41-RQG induced epitope-specific CTL responses in HLA-restricted cells. In ex vivo assay using IFN-γ ELISPOT, cell-mediated immune responses to Gp41-RYL were present in 50% of HLA-matched patients, and responses to Gp120-LLQ and Gp41-RQG were found in 33% of HLA-matched patients.

CONCLUSION

In this study, we found that a prediction pipeline for CTL epitopes might be based on the most popular computer prediction software and FABS methods. Our results suggest that these CTL epitopes may provide useful tools and information for the development of a therapeutic vaccine against HIV-1 Korean clade B.

Prevalence of HIV-1 subtypes among men who have sex with men in China: a systematic review

The distribution of prevalent HIV-1 strains are still complex in China. Men who have sex with men (MSM) play an important bridging role in spreading HIV. The aim of our study was to quantitatively evaluate the prevalence of HIV-1 subtypes among the MSM population in China from published studies. Relevant studies were searched by selection criteria from CNKI, CBM, Pubmed, etc. We computed the estimates of the pooled proportion of HIV-1 subtypes. Heterogeneity between studies was investigated and measured using Cochran's Q statistic and the I (2) statistic. All analyses were conducted by the R statistical package version 2.13.1. A meta-analysis was performed, which included 19 articles. For comprehensive analysis of env, gag and pol genes, the pooled estimates for the prevalence of subtype B was 28.25% (95% CI: 18.10-39.66%), CRF01_AE was 53.46% (95% CI: 46.11-60.74%), CRF07_BC was 18.66% (95% CI: 13.06-25.01%) and CRF08_BC was 5.85% (95% CI: 2.73-10.07%), respectively. In subgroup analysis, the proportion of subtype B decreased, while the proportion of CRF01_AE and CRF07_BC showed an increasing tendency. Beijing, Guangdong and Henan provinces had high proportions of subtype CRF01_AE while Guangdong and Hebei provinces had the highest proportions of subtype B and CRF07_BC, respectively. A high genetic variability of HIV-1 presents a serious challenge for HIV prevention and treatment strategies among MSM in China.

Neutralizing Antibody Responses and Evolution of the Viral Envelope in the Course of HIV-1 Korean Clade B Infection

Objectives

HIV is able to continuously adapt to and evade the evolving neutralizing antibody responses of the host. We investigated the ability of HIV variants to evade neutralizing antibodies in order to understand the distinct characteristics of HIV-1 Korean clade B.

Methods

Three drug-naive subjects were enrolled in this study who were infected with HIV-1 Korean clade B. Neutralizations were performed using autologous plasma and pseudovirion-based assays in order to analyze and compare changes in the env gene.

Results

In the early phase of infection, neutralizing activities against autologous virus variants gradually increased, which was followed by a decline in the humoral immune response against the subsequent viral escape variants. The amino acids lengths and number of potential N-linked glycosylation sites (PNGS) in HIV-1 env gene was positively correlated with neutralized antibody responses during the early stages of infection.

Conclusion

This study suggests that change within the env domains over the course of infection influences reactivities to neutralized antibodies and may also have an impact on host immune responses. This is the first longitudinal study of HIV-1 humoral immunity that took place over the entire course of HIV-1 Korean clade B infection.

Estimating the origin and evolution characteristics for Korean HIV type 1 subtype B using Bayesian phylogenetic analysis

The majority of Korean human immunodeficiency virus type 1 (HIV-1) isolates are composed of the Korean clade B strain that is distinct from the subtype B prevalent in North America and Europe. However, it is still not clear how HIV-1 was introduced, transmitted, and evolved within the Korean population. To identify the evolutionary characteristics of Korean HIV-1, we estimate the molecular epidemic history of HIV-1 subtype B gp120 env in Korea in comparison with sequences isolated from other geographic locations. A Bayesian Markov chain Monte Carlo (MCMC) statistical inference was used to estimate the time of divergence of subtype B. The estimated time of divergence of subtype B and the distinct monophyletic Korean B cluster was estimated to be in the early and mid-1960s, respectively. Substitution rates were estimated at 7.3×10(-3) and 8.0×10(-3) substitutions per site per year for HIV-1 subtype B and Korean clade B, respectively. The demographic dynamics of two Korean data sets showed that the effective number of infections in Korea increased rapidly until the early 1980s, and then the rate only slowly increased until the mid-1990s when the population growth approached a steady-state. These results suggest that the growth rate of prevalent HIV-1 strains in Korea was lower than in other countries, suggesting that the evolution of HIV-1 Korean clade B was relatively slow. Furthermore, the limited transmission of HIV-1 within the Korean population likely led to the independent evolution of this virus to form the HIV-1 Korean clade B.

Molecular evidence of HIV-1 transmission in 20 Korean individuals with haemophilia: phylogenetic analysis of the vif gene

To assess whether a genetic relationship exists between the viruses infecting HIV-positive patients with haemophilia and those infecting plasma donors, we determined the vif sequences in 169 individuals, including 20 haemophilia patients, 3 plasma donors, and 146 local controls. Twenty haemophilia patients were diagnosed with HIV-1 at 1-2 years after exposure to factor IX (FIX) manufactured in Korea, beginning in 1989-1990. Plasma samples from donors O and P were used to manufacture clotting factors including FIX used to treat the 20 haemophiliacs. The vif gene from frozen stored serum samples obtained 1-3 years after diagnosis was amplified by RT-PCR, and subjected to direct sequencing. Phylogenetic analysis revealed that vif sequences from 128 of the samples (including haemophilia patients and donors) belonged to the Korean subclade of HIV-1 subtype B (KSB). Sequences from 41 other participants were identified as subtype B, but outside the Korean subclade. Sequences of the vif gene from donors O and P plus the 20 individuals with haemophilia comprised two subclusters within KSB. In addition, signature pattern analysis disclosed the presence of conserved nucleotides at two positions in donors and haemophiliacs only. Together with information on KSB, dates of plasma donations and seroconversion of haemophilia patients, our results suggest that the haemophiliacs examined here became infected by viruses in the domestic clotting factor used for treatment.

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.

National survey for drug-resistant variants in newly diagnosed antiretroviral drug-naive patients with HIV/AIDS in South Korea: 1999-2005

We investigated the prevalence of drug-resistant variants and assessed their severity against antiretroviral drugs among patients in South Korea. Three hundred antiretroviral drug-naive patients were collected and drug-resistant variants were analyzed using the Stanford database with sequences and mutation data of the HIV-1 genes for protease (codons 1-99) and reverse transcriptase (codons 1-250). Of this group, 199 isolates (66.3%) showed at least 1 or more sites related to drug resistance. However, the average prevalence of drug resistance for patients newly diagnosed with HIV-1 but still treatment-naive between 1999 and 2005 was very low (4.3%, by "SIR" interpretation) compared with other countries. Most of the newly infected patients carried HIV subtype B (96%, n = 288) based on phylogenetic analysis of the conserved pol region. In summary, there has been no significant increase in the prevalence of drug resistance among antiretroviral drug-naive patients infected with HIV-1 for the last 7 years in South Korea. This study is quite significant regarding its larger scale of prevalence study for drug-resistant variants comparing to other drug-resistant studies using small scale of populations in South Korea. It is also important to provide suitable guidelines of genotyping assays for Korean drug-naive patients.