National Institute of Health

Scientists extract near-complete genomes of HIV from blood samples to analyze genetic diversity and dynamics among different strains in Korea

The HIV-1 virus, which causes AIDS, mutates rapidly and can exchange genetic material between different variants, giving rise to “recombinant” strains. Most studies could not track these strains in circulation because they used incomplete or “partial” genomes. Now, scientists in Korea have successfully extracted near full-length genomes of HIV-1 from a cohort of Korean men, shedding light on the genetic dynamics and diversity of the HIV-1 epidemic and revitalizing domestic HIV research.

It’s essential to obtain full-length genomic sequences from HIV-1 variants in local circulation to see the full picture of domestic HIV epidemics  

Photo courtesy: Shutterstock

The human immunodeficiency virus-1 (HIV-1), which causes AIDS, is hard not only for our bodies to combat, but also for scientists to genetically analyze. This is mainly due to HIV-1’s high mutation rate; in short, if two or more HIV-1 variants coexist in a person, they can exchange genetic material among themselves during replication to give rise to new strains. The fact that new HIV-1 recombinant variants can emerge and spread rapidly is a testament to their adaptability. If we are to develop effective treatments for HIV-1 infections (and understand how the epidemic grows), we need to keep track of the different HIV-1 variants that go around and how they change over time and space. 

In Korea, the number of new HIV-1 cases has been substantially increasing since the first was reported in 1985. Virtually all transmissions occur through sexual contact, and males make up for over 90% of HIV-1 cases. According to multiple studies over the past three decades, “HIV-1 Subtype B” is predominant in Korea, with a unique strain of this subtype called “Korean clade B” accounting for over 88% of infections. However, most genetic analyses were conducted using only partial or incomplete genomes, which makes it impossible to completely characterize the complex landscape of recombinant and/or mutated variants.

In a recent study, a team of scientists including Dr. Sangmi Ryou and Dr. Mee-Kyung Kee of the National Institute of Health, Korea, addressed this important gap in HIV epidemiologic literature. They analyzed fifty blood samples from a long-term cohort of HIV-positive men who have sex with men that had been established in 2006. From these samples, the researchers managed to reconstruct 12 near full-length genomes (NFLGs), which were then used for further genomic characterization and to establish the epidemiological history of HIV-1 in Korea. The study was published online earlier this year in Nature’s Scientific Reports, and was supported by an intramural grant of the Korea National Institute of Health (2017-NI51003-00).

Reconstructing full-length genomes is no straightforward task, as reliable results require complex genetic sequencing techniques and algorithms. Furthermore, various forms of statistical analysis are needed to establish the genetic relatedness between the obtained genomes to locate them in a potential “family tree.” The extraction of 12 HIV-1 NFLGs out of 50 samples (24%) is a significant improvement over previous studies, where only 10% of the samples yielded NFLGs. Out of these 12, ten NFLGs corresponded to the widely spread Subtype B, and the remaining two were recombinant variants. While one of these two was a common variant, the other one was new, estimated to have emerged in 2003.

Dr. Kee highlights the importance of acquiring full-length HIV-1 genomes and identifying their molecular dynamics and variations for developing effective treatments and vaccines suitable for the Korean population. “There is a need for studies focusing on obtaining full genome sequences to better understand the impact of the viral diversity and dynamics of recombinants because these events affect most aspects of the HIV pandemic,” he remarks.

The team also hopes that their efforts will help revitalize and promote domestic HIV epidemiologic research. By analyzing the evolution of domestic HIV isolates currently in circulation, it may be possible to predict the future rates of transmission and the potential impact of infections, as well as plan accordingly. “The results of our study could be important for understanding the transmission patterns and epidemiologic characteristics of domestic HIV epidemics in Korea and elsewhere,” concludes Dr. Ryou.

Let us hope further research efforts give us an edge against HIV-1 in its many forms.

Reference

About National Institute of Health in Korea 

The Korea National Institute of Health (KNIH), one of the major operating components of the Ministry of Health and Welfare, leads the nation’s medical research. Over the past seven decades, the KNIH has made unwavering efforts to enhance the public’s health and innovate biomedical research. The KNIH seeks to eradicate diseases and make people healthier. The KNIH establishes a scientific basis and evidence underlying health policy as well as provides national research infrastructures. We also promote public health research. To this end, we make efforts to enrich a health research environment by granting funds to research projects and keeping our resources, data, and facilities more open and accessible to researchers.

Website: http://www.nih.go.kr/eng/

About Dr. Mee‑Kyung Kee

Dr. Mee‑Kyung Kee expanded the infrastructure for HIV, hepatitis B, and HPV research by establishing a national chronic infectious disease cohort and research in the epidemiology and diagnosis field of infectious diseases. He also contributed to the establishment of the basis for prompt and accurate diagnosis and preventive policy. Currently, he is actively conducting research as the head of research planning at the International Tuberculosis Research Center in Korea.