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Three COVID-19 variants present globally, two currently identified in Virginia

Mutations in SARS-CoV-2 spike proteins have created more transmissible variants which may increase COVID-19 case numbers, including in the U.Va. community


SARS-CoV-2, the virus that causes COVID-19, has evolved to form new variants of itself. As of now, three variants of the virus have been identified around the world —  variant B.1.1.7, variant B.1.351 and variant P.1. Two of these variants were identified in Virginia last month. On Feb. 18, the Virginia Department of Health reported the first case of SARS-Cov-2 variant B.1.351 in the Northwest region of Virginia. Nine days later, the first case of SARS-Cov-2 variant B.1.1.7 was reported in the Southwest region of Virginia. 

These variants, caused by mutations in the genetic code of SARS-CoV-2, could potentially prolong the COVID-19 pandemic. The variants are believed to be more transmissible and recent data shows that current vaccines may be less effective against certain variants, contributing to calls for enhanced prevention measures. The first case of the B.1.1.7 variant was confirmed in the University community Feb. 12, but the University is not sharing the exact number of confirmed variant cases due to individual privacy concerns. 

Dr. Eric Houpt, the Jack M. Gwaltney Jr. professor of infectious diseases, explained how these mutations in the virus’s genetic code are created. 

“A virus, like a human, is not perfect,” Houpt said. “When it replicates, it can introduce errors in the genetic code which then lead to mutations in specific proteins. When you have a lot of COVID cases out in a community, there's a lot of virus replication. That provides a perfect incubator for variants to arise.”

Houpt explained that mutations within a genome are a natural occurrence and not unique to COVID-19. 

“Any virus, bacteria or organism may introduce errors during replication,” Houpt said. “This is nothing new to biology or to viruses … this is nothing surprising.” 

Assoc. Prof. of Biology Robert Cox emphasized this as well in an email to The Cavalier Daily. He noted that variants are to be expected, especially in large populations. 

“New virus variants occur all the time, and they are expected to arise in any virus population,” Cox said. “The larger the population size of the virus  — i.e., the greater the number of infected human hosts — the more chances there will be for new mutations to arise as the virus replicates.”

There have been over 122 million confirmed COVID-19 cases worldwide. It is possible that many of these recent cases have been caused by new COVID-19 variants.

Cox furthered that there are a couple ways mutations can affect fitness — the ability of an organism to pass its genetic material to its offspring. Some mutations may have no impact on the virus’s fitness while others are harmful. 

“Many of these mutations have little or no effect on the virus — they are selectively neutral,” Cox said. “Other mutations may alter the virus in a way that influences its fitness. In most cases, these mutations will probably disrupt the function of the virus and lower its fitness. These mutations will usually be eliminated from the viral population by natural selection, so we usually don’t even notice them.”

Cox continued that a select number of mutations are advantageous to the virus and increase the virus’s fitness, allowing it to spread more quickly amongst the population they infect. These mutations are seen in the prevalent SARS-CoV-2 variants B.1.1.7, B.1.351 and P.1. Specifically, these mutations have changed the virus’s spike proteins, making it easier for the variants to attach to and infect host cells compared to the original strain. 

“These mutations should increase in frequency because they lead to increased replication of viruses that contain the new mutations,” Cox said. 

While mutations in spike proteins have made the variants more transmissible, some evidence also suggests that these variants increase the risk of severe SARS-CoV-2 infection. 

The CDC currently reports over 6,600 cases of COVID-19 variant infection in the United States, but there are likely many more undetected cases. 

“What we know about these variants is really just scratching the surface,” Houpt said. 

He added that it is difficult to determine the amount of infections that have resulted from COVID-19 variants specifically — this would require thorough sequencing of the virus with specialized equipment and tests. Routine COVID-19 tests simply search for the virus’s presence and do not conduct in-depth sequencing of its genome. 

“We don’t know the full picture at this point,” Houpt said. 

Additionally, the presence of COVID-19 variants has raised some concerns regarding the effectiveness of the vaccines against the new variants. A recent study found that both the Pfizer-BioNTech and Moderna vaccines produced a similar antibody response against the B.1.1.7 variant and the original SARS-CoV-2 strain. However, the study found that both vaccines were less effective against the B.1.351 variant. The Moderna vaccine was 12.4 times less effective at producing neutralizing antibodies while the Pfizer vaccine was 10.4 times less effective. 

Houpt stressed that, although the vaccines are shown to be less effective against the B.1.351 variant, the vaccines should largely prevent severe infection, which often leads to hospitalizations. 

The emergence of new variants has also prompted a reevaluation of how quickly herd immunity can be achieved. In a U.Va. Health media briefing March 5, Costi Sifri, director of hospital epidemiology at the University, explained that herd immunity will likely require upwards of 80 percent of individuals to have immunity to COVID-19. Prior to the emergence of new variants, earlier estimates projected that between 60 to 70 percent of individuals would need to be immune against COVID-19 to achieve herd immunity. 

“What that number is exactly is not clear, but it's probably going to be a combination of both people that have had immunity due to COVID vaccination and people who have had immunity as a consequence of infection,” Sifri said. 

In order to help slow the spread of the virus, especially with the presence of new variants in the community, the University currently restricts indoor gatherings to six individuals and outdoor gatherings to 10 people. The University also requires students to attend weekly COVID-19 saliva prevalence testing. Moreover, indoor dining in dining halls is limited to groups of four individuals. 

Sifri emphasized the importance of continuing to wear masks and practicing social distancing in order to slow the spread of the virus, especially with the presence of new variants and recent loosening of statewide COVID-19 related restrictions. 

“If we can make a collective effort to do that, I think the spring and the summer will probably look a lot different than it looks like right now,” Sifri said.