Genetic Diversity and Drug Resistance of Human Immunodeficiency Virus from Newly Diagnosed Human Immunodeficiency Virus-positive in Korean, 2022–2023

Abstract

Human immunodeficiency virus (HIV) infection can cause acquired immunodeficiency syndrome (AIDS). The high HIV mutation rate is a major hurdle in vaccine and drug development. In this study, we analyzed the distribution of HIV genotypes and drug resistance mutations in a Korean patient newly infected with HIV between 2022 and 2023. The Korean clade HIV genotype B type (KR-B) was the most predominant HIV genotype, accounting for 70.7% in 2018–2019. However, recent analysis results have confirmed that the distribution of genotypes other than KR-B will increase to 39.2% and 40.5% from 2022 and 2023, respectively. In particular the diversity of genotypes is expected to gradually increase as many recombinants which were not detected in 2018–2019 such as CRF_01B, CRF_0263, and CRF_01BC. In addition, the drug resistance rate in treatment-naive infected individuals is predicted to be 5.2% in 2022 and 6.7% in 2023. HIV drug resistance among the different classes of antiretroviral drugs was not significantly different. Therefore, the proportion of resistance mutations in the main drug classes will remain largely unchanged from 2022 to 2023. In conclusion, it is crucial to periodically analyze the current status of domestic and epidemiological correlations. Also we have to continuously improve process because of the increasing genetic diversity. A surveillance system must be established through periodic monitoring to analyze drug resistance rates that reflect the latest trends.

Key messages

① What is known previously?

It is known that genotype B accounts for about 70% in the Republic of Korea (ROK) and especially Korean clade B was the highest proportion. In addition, transmitted drug resistance (TDR) rate is estimated to be around 5%.

② What new information is presented?

Recombinants increased and additionally analyzed CRF_01B, CRF_0263, and CRF_01BC. The TDR in treatment-naive patients was was approximately 5% (average, 5.9%).

③ What are implications?

The proportion of Korean clade HIV genotype B type (KR-B) is gradually decreasing and that of other genotypes is increasing. The recombinants mixed with KR-B were analyzed continuously. This suggests that various genotypes have spread overseas and become indigenous to ROK. Because the current drug resistance rate is maintained at approximately 5%, continuous monitoring is necessary.

Introduction

According to the Joint United Nations Programme on HIV/AIDS (UNAIDS), the number of individuals infected with human immunodeficiency virus (HIV), the virus that causes acquired immunodeficiency syndrome (AIDS), is expected to reach 39.9 million by 2023 [1]. HIV belongs to the retrovirus and lentivirus families and can be further classified into two distinct subtypes: HIV-1 and HIV-2. Approximately 95% of all HIV infections worldwide are caused by HIV-1, which is further subdivided into four groups: major (M), new (N), outer (O), and pending the identification of further human case (P) [2]. The M group is comprised of nine single genotypes (A–D, F–H, J, and K), exhibiting 15–20% sequence variation within genotypes and 20–35% variation between genotypes, indicating a high level of genetic diversity within this virus [3]. In addition to the single genotype, there are 157 circulating recombinant forms (CRFs) and some unique recombinant forms (URFs), each of which exhibits a distinct distribution pattern across continents and countries. Currently, the Los Alamos National Laboratory database is regularly updated with the names of recombinant forms, with three or more recombinant forms being consistently reported [4]. The existence of numerous recombinant forms and a high degree of genetic diversity within HIV genotypes has resulted in the absence of a definitive HIV/AIDS vaccine and treatment. As a result, several countries are actively engaged in research on molecular diagnostic characteristics, including the distribution of genotypes and the phenomenon of drug resistance.

In the Republic of Korea (ROK), HIV genotyping and drug resistance studies using specimens have been conducted since the first confirmed case in the early 1980s, with type B reported as the main subtype in the distribution of genotypes. In particular, molecular epidemiological analysis indicated that the majority of genotypes formed a cluster; as such, the genotype B in this study was categorized into foreign-derived type B and Korean subtype B [5].

HIV drugs are categorized into nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and integrase inhibitors (INSTIs). In accordance with the recommendations of the International AIDS Society (IAS), pre-treatment resistance testing is advised when the drug resistance rate among treatment-naive patients in the community exceeds 5%. A recent study reported a domestic drug resistance rate of 3.8%, with the average resistance level estimated to be approximately 5% [6]. The aim of the present study was to analyze the genotyping and drug resistance rates of newly diagnosed HIV-positive individuals in 2022–2023 to provide insights into the status of the HIV epidemic in ROK.

Methods

1. Selection of Specimens for Analysis

The specimens utilized in this study were derived from new HIV infections occurring during the 2022–2023 period. Specimens exceeding the limit of detection (20 copies/ml) in the nucleic acid quantitative test (NAT) assay were selected for analysis based on the diagnostic test results. In addition, for samples without NAT test results, analytes were added based on the results of antibody detection tests (western blotting).

2. Analysis Methods

The HIV nucleic acid were extracted and amplified using nested reverse transcription polymerase chain reaction (RT-PCR), with the specific targets being the env, gag, and pol locations, respectively. The amplified PCR product was sequenced by Sanger sequencing. Of the domestic specimens, the genotyping of 254 specimens (121 in 2022 and 133 in 2023) was performed and analyzed using HIV DB BLAST (https://hiv.lanl.gov/content/sequence/BASIC_BLAST/basic_blast.html), an online analysis-based program at Los Alamos National Laboratory, USA. The genotype results were analyzed based on similarity percentage, and the genotype results of env, gag, and pol were combined for subsequent analysis. An analysis of HIV drug resistance was conducted using the Stanford drug resistance database, following the criteria outlined in the analysis guide provided by the World Health Organization (WHO) [7]. The analysis encompassed PIs, NNRTIs, NRTIs, and INSTIs with a particular focus on major drug resistance variant locations. Furthermore, the analysis was conducted using the Stanford University HIV Drug Resistance Program (http://hivdb.stanford.edu/hivdb). All variants exhibiting drug resistance were included, with the exception of those exhibiting potential drug resistance.

Results

1. HIV-1 Genotype Distribution

The genotyping of 254 Korean specimens among new HIV infections demonstrated that Korean subtype B exhibited the highest average prevalence (42.5%, 43.0% in 2022 and 42.1% in 2023) and was identified as the predominant genotype of HIV-1 infection in ROK. Recombinant forms accounted for an average of 50.7%, with CRF01_AE accounting for the most at 19.5%. Other genotypes included CRF_01B (11.2%), CRF_0263 (6.9%), and CRF_01BC (6.4%). Additionally, CRF02_AG (4.8%), CRF_BC (1.1%), and CRF_cpx (0.8%) were all within 5% (Figure 1) [8].

Figure 1. Prevalence of HIV genotypes among new diagnoses from 2022–2023.

A total of 254 samples were analyzed genotypes using an online analysis program based in Los Alamos database. HIV=human immunodeficiency virus; CRF=circulating recombinant form; cpx=complex; KR-B=Korean clade HIV genotype B type. *Data from the article of Park et al. (Public Health Wkly Rep 2020;13:2948-55) [8].

2. Resistance Analysis Results by Types of Antiretroviral Drugs

When examining resistance based on the type of antiretroviral drugs, treatment-naive patients had a higher likelihood of developing resistance to INSTIs (6.8%), followed by NNRTIs (6.4%), PIs (6.2%), and NRTIs (4.2%), with an average resistance rate of approximately 5.9% (Figure 2). Based on the analysis of each genetic variant, drug resistance variants that reduce drug susceptibility in PIs were analyzed in L23I, M46L, and N83D in 2022, with only V32I evaluated in 2023. Regarding NRTIs, the T215Y (or A, S) variant exhibited the highest drug resistance rate, with three reported cases. By 2023, however, the site had decreased to one case, whereas K70N was the most frequently analyzed with two cases, followed by L210W and T215S with one case each. Among NNRTIs, the P225H variant, which was not identified in 2022, was the most frequently analyzed variant, with two cases, one each at K103N and V179E (or F). In contrast, only V179F was analyzed among the variants identified in 2022. INSTIs demonstrated the most notable diversity of variation among the four agents, with three cases each of E92Q (or V) and Y143R (or S), and a single case of G118PRSW analyzed in 2022. In contrast, only one case of each of the E92Q, G118LRV, E138K, Q148HP, S230QR, and R263K sites was observed in 2023. Furthermore, the incidence of resistance events associated with dolutegravir (DTG) agents increased from one occurrence in 2022 to five occurrences in 2023.

Figure 2. Proportion of drug resistance rate in transmitted drug resistance over time, 2022–2023.

We performed analysis of drug resistance by antiretroviral drug classes (PI, NRTI, NNRTI: 145; INSTI 190) and used the online Stanford university HIV drug resistance database. PI=proteinase inhibitor; NRTI=nucleoside reverse transcriptase inhibitor; NNRTI=non-nucleoside reverse transcriptase inhibitor; INSTI=integrase inhibitor; HIV=human immunodeficiency virus.

Discussion

The study examined the genotype distribution and antiretroviral drug resistance among individuals diagnosed with HIV in ROK during 2022–2023. As a chronic virus, HIV exhibits a high degree of genetic diversity, and the number of reported recombinant forms between genotypes is increasing at a rapid rate due to enhanced population mobility. According to the Los Alamos National Laboratory database, 157 recombinant forms have been reported to date (as of July 21, 2023), with the number of cases continuing to increase [4]. Analysis of the distribution of genotypes in ROK among 254 people with HIV revealed that the most prevalent genotype was Korean subtype B, followed by CRF01_AE and CRF_01B, consistent with findings of previous studies. However, compared to 70.7% of Korean subtype B analyzed during 2018–2019 [8], the prevalence of Korean subtype B decreased sharply to 43.0% and 42.1% in 2022 and 2023, respectively. In contrast, recombinant forms increased from 23.9% to 47.9% in 2022 and 53.4% in 2023, with further growth anticipated in the future. This is consistent with the worldwide trend of increasing diversity in HIV genotypes. Furthermore, a recent analysis of recombinant forms occurring in ROK identified new genotypes (e.g., CRF_01B, CRF_cpx, CRF_BC, and CRF_01BC), in which Korean subtype B was recombined with the previously prevalent CRF01_AE and CRF02_AG. These findings indicate that the emergence of domestic recombinant forms is influenced by recombination between prevalent domestic genotypes and overseas introductions, suggesting the circulation of diverse recombinant forms. Although not part of the findings of this study owing to the limited number of individuals analyzed, genotyping of some foreign nationals revealed genotypes that are predominantly prevalent within their respective continents of origin. In particular, CRF01_AE, which is known to be the predominant genotype in Southeast Asia, is the focus of most analyses of foreign nationals from the region [9], underscoring the need for continued surveillance of globally prevalent genotypes.

Among treatment-naive individuals, the antiretroviral resistance rate was found to be 5.9% on average, which did not differ significantly from the known national resistance rate (approximately 5%). Although slight increases were observed annually (5.2% in 2022 and 6.7% in 2023), these changes were not significant. Although there is a degree of variability in the level of resistance exhibited by the various agents, the analysis revealed no statistically significant difference (p>0.05) in the resistance rates across the four types of drugs. As there have been sporadic analyses of variants at specific locations that reduce susceptibility to an agent, it has been challenging to identify prescription drugs with notably high rates of resistance in ROK. Nevertheless, among the genetic variants analyzed on three or more occasions in 2022, the INSTI E92Q variant demonstrated high resistance to elvitegravir, whereas the Y143R variant exhibited notable drug resistance to raltegravir, emphasizing the need for caution. This study also analyzed the number of drug resistance cases for the INSTI DTG [10], currently recommended for monitoring by the WHO. As a result, the number of cases was found to increase from one in 2022 to five in 2023. This highlights the need for the continuous monitoring of DTG drug resistance, with drug resistance analysis reflecting the latest analytical trends.

The substantial increase in the genotypic diversity of HIV observed within the country highlights the crucial importance of comprehending the characteristics of the epidemic and its transmission, through epidemiological association analysis. Moreover, given the increasing diversity of genotypes, it will be essential to stay updated on international analytical developments and continuous method enhancements for detecting different genotypes.

In the future, additional research will be necessary to identify epidemiologic associations and analyze the evolving rates of drug resistance with treatment, incorporating molecular phylogenetic analysis of genotypes. Despite slight increases in drug resistance rates observed in recent years, they have remained relatively stable, emphasizing the necessity for ongoing research to determine yearly trends.