Many viruses and bacteria that cause disease have different strains or genetic varieties. Right now, we are in flu season. We get flu vaccinations each year because the main strain responsible for the flu changes every year and we must develop a new vaccine. The Human papilloma virus which causes genital warts, cervical and anal cancers, and head and neck cancers has over 100 strains referred to as genotypes. Most of these strains are harmless to people, but other specific genotypes are able to cause the diseases I listed.
The Hepatitis C virus (HCV) has six major strains, also referred to as genotypes. One of the most striking differences between these genotypes is their response to treatment. For example, when we used a drug called interferon to treat hepatitis C, patients with genotype 4 could expect to get cured by treatment whereas patients with genotype 1a or 1b were far less likely to experience such a benefit. Fortunately, we now have easy to take medicines that can cure all genotypes of HCV in most cases with just a couple months of treatment (more on this topic in the future).
So what about HIV? There is a lot of variation in HIV strains. First of all, you should understand that there are two major types of HIV: HIV-1 and HIV-2. For the most part, whenever you hear HIV, it is referring to HIV-1. It is by far the major virus that infects people all over the world. HIV-2 is only found in parts of West Africa.
HIV-2 is a deadly virus just as HIV-1 but it causes disease slower than HIV-1. It is also spread sexually, through birth and coming into contact with infected blood. It is possible for a person to be infected by both HIV-1 and HIV-2 butfortunately that isn’t very common. The biggest concern with HIV-2 is that there are some classes of HIV medicines that do not work against the virus. None of the drugs in the Non-nucleoside class (efavirenz, rilpivirine, etravirine, doravirne) can suppress HIV-2. Also, some protease inhibitors don’t work (e.g. atazanavir) while others do (e.g. darunavir).
For HIV-1 , the largest category of viruses are in group M and the different strains are referred to as subtypes. Subtypes are based on their genetic similarity and diversity. They are found in different geographical areas. What is amazing to observe is that most developed countries have the same HIV subtype. Throughout North America and Europe but also Latin America and the Caribbean, the predominant strain is HIV-1 subtype B.
This is quite significant because the most research has been done in subtype B virus. Diagnostic tests were developed to detect subtype B and all the drugs we used were developed for their effectiveness against subtype B virus. However, other subtypes predominate in developing countries. The most widespread strain of HIV is subtype C. It is found throughout Southern Africa, parts of east Africa, India and other parts of Asia. Approximately half of all HIV infections in the world are from subtype C virus. As I just mentioned, diagnostic tests early on were developed to detect subtype B virus and oftentimes were not able to recognize infections from other subtypes because of minor differences in their genetic makeup.
This created a problem where HIV infections were sometimes missed here in the US if the person had been infected with a different subtype and may have come from another country. I would say that in the last couple decades, the tests have been improved such that this is no longer a problem. There are differences between different subtypes in how easily they are transmitted sexually and through birth and also how aggressively they cause disease. For example, in the country of Uganda, most people have either subtype A or subtype D virus. But these two are NOT the same! Subtype A viruses have a significantly higher rate of heterosexual transmission than subtype D viruses.
However, in the absence of treatment, subtype D virus causes more damage to the immune system and progresses nearly twice as fast to AIDS as subtype A. The good news is that unlike the case for HIV-2, for HIV-1, all HIV medicines work in all subtypes for the most part.
Now back to the story at hand. The new subtype identified has been designated subtype L. It has been isolated from the Congo in central Africa. From what we can tell so far, all medicines should be
effective against this strain. We don’t think this strain is very widespread but we just don’t know yet because its discovery is so recent. There were specimens that had this virus that were from almost 20 years ago, but a new method of molecular genetic testing (called next-generation gene sequencing) allowed scientist to recognize the unique features of this virus and classify it as a new subtype.
HIV originated in Africa and spread to other parts of the world. Some scientists believe that HIV came into the human species from chimpanzees, yet HIV is very seldom found in wild chimpanzees. HIV-2 is found in a type of monkey called the Sooty mangabey, but it doesn’t cause disease in these monkeys. HIV doesn’t cause disease in most apes and monkeys because their bodies produce compounds which block infection by HIV.
These compounds are specialized proteins called restriction factors, and they can work in a variety of ways along with the immune system to fight HIV naturally. Humans also produce a variety of restriction factors which can seriously slow down the virus in our bodies and helps explain why HIV takes several years to progress to AIDS and cause death. Perhaps, by studying subtype L virus and people who are infected with that strain, we may discover new ways that our bodies can fight the virus through restriction factors or the immune system and possibly develop new treatments.
I’m sure we’ll be hearing more about subtype L HIV in the near future.
Dr. Crawford has over 25 years of experience in the treatment of HIV. While at Howard University School of Medicine, he worked in two HIV-specialty clinics at Howard University Hospital. He then did clinical research as a visiting scientist with the AIDS Clinical Trials Group (ACTG) at Johns Hopkins University School of Medicine. He served as the Assistant Chief of Public Health Research with the Military HIV Research Program where he managed research studies under the President’s Emergency Plan for AID Relief (PEPFAR) in four African countries.
He is currently working in the Division of AIDS in the National Institutes of Health. He has published research in the leading infectious diseases journals and serves on the Editorial Board of the journal AIDS. Any views and perspectives in his articles on blackdoctor.org are not representative of any agency or organization but a reflection of his personal views.
Posted on November 20, 2019By Dr. Keith Crawford, BDO HIV/AIDS Expert