Tracking a Shifting Threat: Genetic Analyses of HIV Variants Circulating in Korea
Update 13.12.2022
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
Authors
Title of original paper
Journal |
Sangmi
Ryou1, Myeongsu Yoo1, Kisoon Kim1, Sangsoo
Kim2, Sang Il Kim3, Youn Jeong Kim3, Dae Won
Park3, Jun Yong Choi4, Hyo Youl Kim5, Jung
Ho Kim4, Joon Young Song6, Shin‐Woo Kim7,
Hyun‐Ha Chang7, Bo Youl Choi8 and Mee‐Kyung Kee1 Characterization
of HIV‐1 recombinant and subtype B near full‐length genome among men who have
sex with men in South Korea Scientific
Reports |
|
|
DOI
Affiliations |
10.1038/s41598-021-82872-3
1Division of Viral Disease Research, Center for
Infectious Diseases Research, Korea National Institute of Health 2Department of Bioinformatics and Life Science,
Soongsil University 3Division of Infectious Disease, Department of Internal
Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic
University of Korea 4Department of Internal Medicine and AIDS Research
Institute, Yonsei University
College of Medicine 5Department of Internal Medicine, Yonsei
University Wonju College of Medicine 6Division of Infectious Disease, Department of
Internal Medicine, Korea University College of Medicine 7Department of Internal Medicine, School of
Medicine, Kyungpook National University 8Department of Preventive Medicine, College of Medicine,
Hanyang University |
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.