Dr Kenny Voon, virologist and lecturer at the International Medical University (IMU) explains the journey the coronavirus is on and how its variants affect us in the long run
THE MENTION of mutation is enough to give us nightmares of viruses that evolve with the sole aim of killing mankind and taking over the earth.
“But in reality, a virus’s main purpose of mutating is to seek coexistence with the human body. A virus mutates for survival, not to kill. It tries to adapt to the conditions of the human body,” explains Dr Kenny Voon.
“Humans are a reservoir for the virus. We help it to propagate more. It doesn’t want to kill us, the host. If the host dies, there is no co-existence. This is why its main aim is not to become more deadly,” he adds.
He explains that when a virus first jumps from one species to another, we often see a high death rate. This is because the virus has not learnt to live within its new host. “For example, the common cold was probably a virus that started infecting humans a long time ago and now it just coexists with us,” he says.
“Laboratory results, from a study that compared infectivity and virulence of emerging SARS-CoV-2 variants in Syrian hamsters, show that while the Covid-19 virus has become more contagious, it has not become more deadly,” he says, although he does warn that this is an inference made from laboratory testing. How the virus affects people in the real world can be different.
Case in point, the Delta (Indian) variant. This variant has been speculated to be more deadly because there have been more cases of death reported. However, in laboratory tests, the variant did not show up to be more deadly. “We will only know once we have more data from community samples,” explains Dr Kenny.
Roadmap of a virus
Dr Kenny also sheds some light on the journey of the Covid-19 virus from bats to humans. He explains that the original virus in a certain species is called an “ancestor virus”. When a virus jumps from another species into humans it is called an “outbreak virus”. For example, the Covid-19 virus is an outbreak virus while the ancestor virus has been found to be a coronavirus carried by bats.
However, in between the ancestor and outbreak viruses, there has to be a “progenitor virus” that has allowed the virus to make that jump. For example, in MERS, the link or progenitor virus came from camels, while the Nipah virus in Malaysia was passed through pigs.
In our current pandemic, the bat coronavirus (identified as RaTG13) carries 96.2% of the same genetic sequence as the Covid-19 virus (SARS-CoV2 Wuhan) in humans, leaving a significant four percent that is different. “The virus may have been propagating in another intermediate host before jumping into humans but we have not been able to identify that progenitor virus yet.”
Now that the virus has jumped into humans, next step is for it to mutate in order to adapt to our bodies.
There are two ways a virus can mutate. One is called point mutation, where at a certain point in the genetic sequence, the amino acid changes into another amino acid.
The other is through recombination. Recombination happens when a part of a virus joins up with a part of another virus. For example, with the MERS virus, it was found that a part of the MERS-CoV lineage 2 combined with the MERS-CoV lineage 4 to become another strain, namely the MERS-CoV lineage 5. “This can only happen if both virus strains infect one host,” ex-plains Dr Kenny.
Are there factors that make it more likely that a virus will mutate? “We cannot pinpoint what factors induce mutation as there are too many variables,” he says.
Concern vs Interest
Mutation causes changes in the genetic sequence which affect the behaviour of a virus. Unlike horror movies, the virus does not have a brain that tells it to mutate in one way or another. It is a process of trial and error that can sometimes make a virus stronger, or make it decrease in function.
According to Dr Kenny, when we analyse the behaviour of a virus, we are looking at three main areas: transmissibility, virulence and antigenicity. This translates to how contagious it is, how deadly it is and if the virus will escape the vaccines available.
You might have come across the term variants of concern (VOC) when reading about the virus mutation. A variant of concern is when the mutation has changed the way the virus behaves in one of the three areas. The Alpha, Beta, Gamma and Delta variants—or more commonly known respectively as the UK, South Africa, Brazil and Indian variants — are the current four variants of concern because enough data has been collected to show that the virus has changed behaviour in either transmissibility, virulence and antigenicity. Malaysia has now recorded three out of the four variants of concern.
Variants of interest (VOI) on the other hand are those that we have not collected enough data to conclude behavioural changes in the virus. “It is just speculation now. But it is probable that these are variants that have experienced a decrease in function because there are not as many cases reported,” Dr Kenny says. At the time or writing, there are currently seven variants of interest that have popped up on the global radar.
How do these variants affect us?
Dr Kenny says that the situation on the ground remains the same. “The current SOPs still apply. Washing hands, wearing masks and practising social distancing will still give you the same level of protection as before. That hasn’t changed at all. The virus may become more infectious but using the same SOPs will still help to protect us,” Dr Kenny says. According to him, vaccinations remain as important as they have been shown to still be effective against the variants.
The new knowledge that the virus is airborne should also help us to enhance certain habits such as double masking and washing out air conditioner’s filters more often.
“When we talk about the virus being airborne, it is because both the virus and water vapour are so small, they can bind to particles in the air. These particles are less than 2.5 microns and this is what makes it airborne,” explains Dr Kenny. According to him, swab tests on air conditioner’s filters have found presence of virus. “So, you actually should wash it more often, if not daily then weekly,” he advises.
Sequencing strains
While Malaysians around the country line up to get their vaccinations, a number of re-infections have surfaced and there is talk that there may be a local strain that has escaped the vaccines.
“Yes, there are suspicions that there is a local strain but we can only be sure if we do intensive genetic sequencing. We do have some data on last year’s strain, but this year it could be different,” Dr Kenny says.
The cost of sequencing is prohibitive, as the cost for one sample can be anything between ten to 20 times more than a RT-PCR test. This is why Malaysia does not have as much sequencing data as the UK, China and the US. “We have to maximise our limited resources,” says Dr Kenny, explaining that we do need to focus on the vaccination programme and economic recovery. “At the moment, in Malaysia, we use sequencing only if it is required,” he says.
However, it remains important to trace and discover different strains as this will allow us to determine if the vaccines are still working, as well as to help ensure future vaccines remain effective.
Post-vaccination infections
Variants are not the only possible reason people are getting infected after vaccination. “After the first and second doses, you still have to protect yourself. It takes about four to six weeks on average to build up antibodies. During this time your body will be focusing on the vaccine and this can leave you more vulnerable to infections,” says Dr Kenny.
Can the vaccines help us to stop transmission? Some data shows that the vaccine reduces virus shedding — i.e., the virus seems to replicate less in vaccinated people — but there is not enough information to determine if this reduction is enough to reduce transmission.
“We don’t actually know how much of the virus is needed in one person for it to pass on to others. So even if there’s only a little amount of virus, it may still pass on. It’s hard to detect because every human’s immune system is different,” Dr Kenny explains, adding that even as we continue to gain data from the community there are still too many variables that we cannot control such as an individual’s immune system and different environmental factors such as climate. To conduct a controlled study of humans subjected to the virus would be unethical, he adds.
Further down the road
Scientists continue to study the virus and work goes on to come up with better vaccines. “There is work to come up with a universal vaccine that can vaccinate against the three coronaviruses, i.e., MERS, SARS and COVID-19. This would be important to fight against variants as well as other coronavirus outbreaks in the future. But it’s not easy and I don’t know if we will ever be successful,” says Dr Kenny.
So far tests have shown that the antibodies we produce from the current vaccinations can last up to a year. “We haven’t been able to collect data further than that.” He foresees that we will need vaccinations every few years and, he says, it would all depend on how fast the virus mutates and whether the vaccine will be able to protect us from the variants.
Will we ever be able to stop zoonotic diseases? “Human behaviour is such that we cannot control it. Look at how long we have been fighting dengue. We educate people about how mosquitoes reproduce, yet we still find that people leave rubbish everywhere which are cause stagnant water pools.”
“Similarly with zoonotic diseases, it boils down to human behaviour. As long as we continue to urbanise and the forest barrier is encroached, as long as we have a lot more contact with the wild, the exposure to these viruses will continue to increase and with it the risk of zoonotic viruses. Just by being in the same area as wildlife for a long period, we will be exposed,” Dr Kenny says, adding, “And vice versa. Don’t forget that we are also releasing our viruses to the animals!”
