Why Does A Virus Mutate? Everything You Wanted To Know About Coronavirus Variants And Mutations

Mutations are a normal part of a viral life cycle. Viruses mutate all the time, and that’s how they survive various environments.  A virus that has a mutation makes it particularly deadly to its human host and kills the host within a few hours of infection. The virus needs a new, healthy host for its descendents to survive. If it kills its host before the host infects others, that mutation will disappear.

One way hosts protect themselves from a virus is to develop antibodies to it. Antibodies lock onto the outer surface proteins of a virus and prevent it from entering host cells.

Antigenic Drift

One way influenza viruses change is called “antigenic drift.” These are small changes (or mutations) in the genes of influenza viruses that can lead to changes in the surface proteins of the virus: HA (hemagglutinin) and NA (neuraminidase). The HA and NA surface proteins of influenza viruses are “antigens,” which means they are recognized by the immune system and are capable of triggering an immune response, including production of antibodies that can block infection. The changes associated with antigenic drift happen continually over time as the virus replicates.

Antigenic Shift

The other type of change is called “antigenic shift.” Antigenic shift is an abrupt, major change in an influenza A virus, resulting in new HA and/or new HA and NA proteins in influenza viruses that infect humans. Shift can result in a new influenza A subtype in humans. One way shift can happen is when an influenza virus from an animal population gains the ability to infect humans. Such animal-origin viruses can contain an HA or HA/NA combination that is so different from the same subtype in humans that most people do not have immunity to the new (e.g., novel) virus. Such a “shift” occurred in the spring of 2009, when an H1N1 virus with genes from North American Swine, Eurasian Swine, humans and birds emerged to infect people and quickly spread, causing a pandemic. When shift happens, most people have little or no immunity against the new virus.

Is Mutation bad news?

The novel coronavirus, SARS-CoV-2 that is continuing to spread around the world is not the same as the virus that emerged in Wuhan province of China in late 2019.

Like many other viruses, the genetic structure of coronavirus is also undergoing changes. This process is known as mutation. One of the most dominant variations of coronavirus common is called D614G. This variant had sparked the discourse around the mutation of coronavirus.

Mutations are a normal part of a viral life cycle, explains Akiko Iwasaki, PhD, a Yale immunobiologist and leading COVID-19 researcher. “Viruses mutate all the time, and that’s how they survive various environments,” she says.

Not only that but the mutation is actually key to how viruses spread, notes Nathan Grubaugh, PhD, a Yale School of Public Health epidemiologist. “Viruses mutate during each infection; what I’m worried about is ‘selection,’” he says. “Basically, selection is when mutations that help the virus survive get passed on to another host. Sometimes, selected mutations can help to make viruses more transmissible or evade immune responses.” Slowing transmission (through vaccination and other control measures) is key, he adds.

Emerging SARS-CoV-2 Variants

Source: CDC

  • In the United Kingdom (UK), a new variant of SARS-CoV-2 (known as 20I/501Y.V1, VOC 202012/01, or B.1.1.7) emerged with a large number of mutations. This variant has since been detected in numerous countries around the world, including the United States (US). In January 2021, scientists from UK reported evidence[1] that suggests the B.1.1.7 variant may be associated with an increased risk of death compared with other variants. More studies are needed to confirm this finding. This variant was reported in the US at the end of December 2020.
  • In South Africa, another variant of SARS-CoV-2 (known as 20H/501Y.V2 or B.1.351) emerged independently of B.1.1.7. This variant shares some mutations with B.1.1.7. Cases attributed to this variant have been detected in multiple countries outside of South Africa. This variant was reported in the US at the end of January 2021.
  • In Brazil, a variant of SARS-CoV-2 (known as P.1) emerged that was first was identified in four travelers from Brazil, who were tested during routine screening at Haneda airport outside Tokyo, Japan. This variant has 17 unique mutations, including three in the receptor binding domain of the spike protein. This variant was detected in the US at the end of January 2021.

Public health response

Source: WHO

The authorities in the affected countries are conducting epidemiological and virological investigations to further assess the transmissibility, severity, risk of reinfection and antibody response to new variants. As one of the mutations (N501Y) – found in both the SARS-CoV-2 VOC 202012/01 and 501Y.V2 variants – is in the receptor binding domain, the authorities are investigating the neutralization activity of sera from recovered and vaccinated patients against these variants to determine if there is any impact on vaccine performance. These studies are ongoing.

Genomic data of the SARS-CoV-2 VOC 202012/01 and 501Y.V2 variants has been shared by the national authorities and uploaded to the Global Initiative on Sharing Avian Influenza Data (GISAID) and genomic surveillance of the virus continues, globally.

The following activities have been initiated:

  • National authorities that have reported virus variants are undertaking intensified sampling to understand how widely these new variants are circulating.
  • National scientific teams are studying the effect of the mutations on reinfection potential, vaccination, diagnostic testing, infection-severity and transmissibility.
  • Researchers and government authorities are working with WHO and collaborating with members of the WHO SARS-CoV-2 virus evolution working group to assess epidemiologic, modelling, phylogenetic and laboratory findings as results become available.
  • WHO is working with countries to identify how current surveillance systems can be strengthened or adapted to evaluate potential virus variations through ongoing systematic clinical and epidemiologic surveillance, establishment of genetic sequencing capacity where possible, and providing access to international sequencing services to send samples for sequencing and phylogenetic analysis.
  • Risk communication and community engagement activities scaled up to explain the public health implications of SARS-CoV-2 variants to the public and emphasize the importance of maintaining ongoing preventive measures to reduce transmission such as wearing face coverings, practicing hand hygiene and cough etiquette, keeping physical distance, ensuring good ventilation and avoiding crowded places.

WHO risk assessment

All viruses, including SARS-CoV-2, change over time, most without a direct benefit to the virus in terms of increasing its infectiousness or transmissibility, and sometimes limiting propagation. The potential for virus mutation increases with the frequency of human and animal infections. Therefore, reducing transmission of SARS-CoV-2 by using established disease control methods as well as avoiding introductions to animal populations, are critical aspects to the global strategy to reduce the occurrence of mutations that have negative public health implications.

Preliminary data suggest that the growth rate and effective reproductive number is elevated in areas of the United Kingdom with community circulation of the novel variant VOC-202012/01. In South Africa, genomic data highlighted that the 501Y.V2 variant rapidly displaced other lineages circulating, and preliminary studies suggest the variant is associated with a higher viral load, which may suggest potential for increased transmissibility; however, this, as well as other factors that influence transmissibility, are subject of further investigation.

Epidemiologic investigations are underway to understand the increase in cases in these communities and the potential role of increased transmissibility of these variants as well as the robustness of implementation of control measures. While initial assessment suggests that 202012/01 and 501Y.V2 do not cause changes in clinical presentation or severity, if they result in a higher case incidence, this would lead to an increase in COVID-19 hospitalizations and deaths. More intensive public health measures may be required to control transmission of these variants.

Further investigations are required to understand the impact of specific mutations on viral properties and the effectiveness of diagnostics, therapeutics and vaccines. These investigations are complex and require time and collaboration among different research groups. These studies are ongoing.

WHO advice

National and local authorities should continue to strengthen existing disease control activities, including monitoring their epidemics closely through ongoing epidemiological surveillance and strategic testing; conducting outbreak investigation and contact tracing; and where appropriate, adjusting public health and social measures to reduce transmission of SARS-CoV-2.

Prevention advice

  • Use appropriate personal protective equipment when caring for people suffering from an acute respiratory illness;
  • Practice frequent hand-washing, especially after direct contact with ill people or their environment
  • Practice cough etiquette (maintain distance, cover coughs and sneezes with disposable tissues or clothing, and wash hands)
  • Enhance standard infection prevention and control practices in hospitals, especially in emergency departments
  • Wear masks where appropriate, ensure good ventilation where possible and avoid crowded places

How Effective will be the Vaccines

The WHO’s Dr. Tedros explained at a recent press conference, “The bottom line is that we need to suppress transmission of all SARS-CoV-2 viruses as quickly as we can. The more we allow it to spread the more opportunity it has to change. Vaccines will help to end the pandemic but the effects of COVID19 will continue to be felt for many years to come. The pandemic has exploited and exacerbated the vulnerabilities and inequalities of our world but it has also shown that in the face of an unprecedented crisis we can come together in new ways to confront it, he said.

“None (of the mutations) has made a significant impact on either the susceptibility of the virus to any of the currently used therapeutics, drugs or the vaccines under development,” says WHO’s Dr. Soumaya Swaminathan.

However, it’s just a matter of time before new mutant strains will decrease that viral susceptibility.

Dr. Mike Ryan, Executive Director of WHO Health Emergencies Programme, stressed that while the new Covid mutations make the virus more readily transmitted, the pandemic can be controlled with more careful basic infection control measures—isolation, masking, and social distancing.

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