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How do you detect a mutated virus?

How do you detect a mutated virus?

Every time a human immunodeficiency virus (HIV) or hepatitis virus enters your body, it mutates. That’s 36.7 million mutations for HIV and 328 million mutations for hepatitis B and C together, according to the number of infections worldwide as estimated by the World Health Organisation (WHO).

Every time such a disease-causing virus mutates, we run the risk of not only being unable to treat it with our current medications, but also being unable to detect it in the first place. And if the presence of a virus in a person cannot be detected, not only can he or she continue infecting other people with it, but they will also not be treated properly as doctors would not know what they are ill from.

Dr Mary Rodgers is a senior scientist in the United States-based healthcare company Abbott and manages their Global Viral Surveillance Program.

“The surveillance programme exists because HIV and hepatitis viruses are continuously changing,” she says. “And when I say that they are changing, I mean that at the actual (genetic) sequence level, these viruses have new sequences in pretty much every person that they infect, which is a lot, considering that millions of people have these viruses.”

Speaking to Fit For Life via phone from Chicago where she is based, the biochemist adds that this is why it is crucial for diagnostic tests to keep pace with these viral changes. “We need to make sure that our diagnostic tests can keep pace and stay a step ahead of these viruses, so that we can ensure that we can detect an infection no matter where it is in the world and what strain is present.”

Types Of Tests

Diagnostic tests obviously rely on at least certain parts of the virus – the parts the test is designed to detect – remaining the same. Dr Rodgers explains that there are a few different types of tests for the three viruses.

Diagnostic test, HIV, Hepatitis B, Hepatitis C, hepatitis virus, Mary Rodgers, Abbott, surveillance programme, antigen, antibody, Star2.com

For HIV, she says: “The most common is an antibody test. That is the test that detects your immune response to the virus. So, if you’ve been infected, you’ll build antibodies against the virus, and that is what that kind of test can detect.

“There’s also the actual virus itself that can be detected, which is composed of the actual genome of the virus – the RNA (ribonucleic acid). And that can be detected by a nucleic acid-based test that determines how much virus is there.

“There is also the actual protein building blocks of the virus, like the P24 antigen, which is what your immune response is detecting with an antibody. And those two things, the RNA and the antigen, are the first things that can be detected in an infection.

“So you can usually detect them within two weeks of an actual infection, whereas an antibody can take much longer – sometimes two months depending on the person – to be of high enough of a level for a test to detect it.”

The window period – the time between the actual infection and when the body’s antibody levels have risen high enough to be accurately detected – is typically between three to 12 weeks for HIV.

For hepatitis B, Dr Rodgers says that the most common test is for the hepatitis B surface antigen, which is a protein on the surface of the virus.

“For hepatitis C, it’s generally the antibodies that people are testing for, although I think that as effective therapies become more widely available, people should really be testing for the viral building blocks (antigens) instead, because that’s really going to tell us who needs therapy or not,” she says.

A positive result for the hepatitis C antibody test means that the person has been infected by the virus at some point. It does not necessarily mean that they are currently having an active infection as their antibodies will remain present even after the virus has been cleared from their body.

So, if the virus mutates, meaning that their RNA, or DNA in the case of the hepatitis B virus, sequence changes, this can possibly render the test ineffective.

“Basically, if the sequence of the virus changes, then the building block (antigen) is going to change also,” says Dr Rodgers. “And so, if we have a test that is detecting the building block directly, and it has changed so that what we are using to detect it can’t bind to it anymore, then we’re not going to detect that as positive.

“Likewise with an antibody test; if we are trying to find an antibody in your body that has been raised against something that we don’t know is HIV, then it’s going to be kind of difficult to know whether or not it’s HIV for the test to detect it.”

Dr Rodgers explains: “Our reagents and our tests are made up of other antibodies that rely on the viral sequence to stay the same. What we’ve done to accommodate the diversity in the viral sequences is to have lots of different types of antibodies in our tests so that if there is a type of virus one antibody will miss, we have another antibody that can detect it.”

Multiple Viral Types

Dr Rodgers notes that there are actually five types of HIV, which all cause the same disease. These are Groups M, N, O and P of HIV-1, and HIV-2.

More importantly, she says: “They are able to recombine with each other, which means that if someone is infected with two different types of HIV, they can kind of merge together to form a new type of HIV, which would then be a challenge for a diagnostic test or treatment.”

For example, there are at least 90 known circulating recombinant forms of Group M, which are combinations of the various different viral subtypes of Group M.

Diagnostic test, HIV, history of HIV, types of HIV, SIV, Mary Rodgers, Abbott, surveillance programme, Star2.com

She notes that HIV diagnostic tests had to be modified at least twice since the virus was first identified in the early 1980s. First was when HIV-2 was identified in the late 1980s, and again in the 1990s, when Group O was first identified.

“At first, a lot of diagnostic tests missed Group O, so someone who was infected with it were being told they were not infected,” she says. “And so when we realised that was happening, we went back and changed our tests so that we had reagents in them that would allow us to detect these new strains that were coming up.”

She adds: “The same is pretty much true for hepatitis viruses – they are also able to recombine, and they are also able to evolve really quickly in an infected person and spread around the world. So when you have a different pandemic in different parts of the world, they’ll have really unique strains in that part of the world.”

The hepatitis B virus has 10 subtypes, with genotypes A, B and C most commonly found in Asia. The hepatitis C virus has six genotypes, with genotypes 1, 2, 3 and 6 found in Asia.

“Some of the different ways that HIV and hepatitis viruses have evolved in Asia, compared to Africa, have resulted in different strains that are present only in Asia,” she says. “So, if we want to make sure that our tests are working there, we need to be working in Asia with institutions like universities, hospitals and blood banks to make sure that what is being found in the population is something that we can detect.”

This is particularly important as, according to Dr Rodgers, Abbott’s diagnostic tests are used to screen over half of the world’s blood supply.

Being Prepared

This is the main function of the Surveillance Program. Dr Rodgers notes that they are currently actively collecting blood samples from 40 countries on six continents, including Laos, Thailand, Vietnam and the Philippines in South-East Asia.

“We have in our database over 60,000 samples that we’ve characterised, resulting in over 5,000 different viral sequences. And that is our resource for designing our tests.”

She adds that these samples allow them to identify which parts of the viral genome are the ones most susceptible to mutation, and which parts tend to stay the same, with the ones that tend to stay the same being the targets for diagnostic tests. In fact, after they modified their HIV diagnostic test to detect Group O, they also built it to accommodate future changes in the HIV genome.

“So when these other new strains arose called Group N (1998) and Group P (2009), we actually didn’t even have to change our test because we were able to detect these strains that had never been seen before anywhere due to our preparation from the Surveillance Program,” she says.

The blood samples are usually collected via collaborations with governments, medical institutions and universities, or even individual doctors or researchers.

“What we usually do is we get the leftover samples that would be thrown away after someone had their blood screened after they donated or after someone’s had a diagnostic test,” she explains. “And they’re just going to get rid of the sample anyway, so we ask them to send it to us and we then sequence what strains are present. We then publish together, so we are doing a collaborative research project with all these different institutions we have been partnering with.”

Some of these samples would have already been tested for either HIV or the hepatitis viruses, while some would be from voluntary testing for those viruses.

Dr Rodgers says that if a new diagnostic test were needed, they are poised to make the change within a year or so. “It depends on how extensive the change is and how much testing we need to do to prove that it works,” she says.

This usually involves adding to or modifying what is already in the current test as it should also still be able to identify the current strains it already does.

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