The COVID-19 Evolution—Variants and Vaccines

March 23, 2021 By: Quadax

Consensus among medical community is the virus will be around for some time.

Viruses are constantly changing, and this includes SARS-CoV-2, the virus that causes COVID-19. These genetic variations occur over time and can lead to the emergence of new variants that may have different characteristics.

As CDC and public health partners sequence more SARS-CoV-2 genomes, we will improve our understanding of which variants are circulating in the US, how quickly variants emerge, and which variants are the most important to characterize and track in terms of health.

According to the World Health Organization, SARS-CoV-2 tends to change more slowly than others such as HIV or influenza viruses. This could in part be explained by the virus’s internal “proofreading mechanism” which can correct “mistakes” when it makes copies of itself. Scientists continue to study this mechanism to better understand how it works.

How do variants occur?

Mutations are changes in the genetic code of a virus that naturally occur over time when an animal or person is infected. While a certain amount of genetic variation is expected to occur as SARS-CoV-2 spreads, it’s important to monitor circulating viruses for key mutation(s) that happen in important regions of the genome. Many mutations do not affect the virus’s ability to spread or cause disease because they do not alter the major proteins involved in infection; eventually these are outcompeted by variants with mutations that are more beneficial for the virus.

To find more information about the mutations and variants CDC is monitoring in the US and globally, go to the SARS-CoV-2 Variant page.

Icon-MicroscopeWhat is CDC doing to track SARS-CoV-2 variants?

In the United States, CDC tracks emerging variants through genomic surveillance with the following approaches:

Leading the National SARS-CoV-2 Strain Surveillance (NS3) system

Since November 2020, CDC regularly receives SARS-CoV-2 samples from state health departments and other public health agencies for sequencing, further characterization, and evaluation. On January 25, 2021, the NS3 system was scaled-up to process 750 samples per week. Notable strength of this system is the regular collection of numerous representative specimens from across the country and characterization of viruses beyond what sequencing alone can provide.

Partnering with commercial diagnostic laboratories

CDC is contracting with large commercial diagnostic labs to sequence samples across the United States. CDC has commitments from these laboratories to sequence 6,000 samples per week, with the capacity to scale up in response to the nation’s needs.

Collaborating with universities

CDC has contracts with seven universities to conduct genomic surveillance research in collaboration with public health agencies. The studies are meant to provide deeper insights into viral genomics and molecular epidemiology within the various regions across the country.

Icon-DNAWhy is genomic surveillance important for public health?

Routine analysis of genetic sequence data enables CDC and its public health partners to identify and characterize variant viruses—either new ones identified here or those already identified abroad—and to investigate how variants impact COVID-19 disease severity and how variants impact the effectiveness of vaccines and therapeutics.

Surveillance of emerging variants can help detect variant with:

. Ability to spread more quickly in people

. Ability to cause either milder or more severe disease in people

. Ability to evade detection by specific diagnostic tests
Many commercial nucleic acid amplification tests that use reverse transcription polymerase chain reaction (RT-PCR) have multiple targets to detect the virus, such that even if a mutation impacts one of the targets, the other RT-PCR targets will still work. However, there are some tests that rely on only one target, and mutations may impact their ability to work. FDA is using public health sequencing data to monitor mutations and their impact on confidential/proprietary diagnostic test designs.

. Decreased susceptibility to therapeutics that employ monoclonal antibodies
Such therapy involves specifically designed antibodies that target regions of the virus to block infection. Because these treatments are more specific than natural immune response-generated antibodies, they may be less effective against variants that emerge.

. Ability to evade natural or vaccine-induced immunity
Both natural infection with and vaccination against SARS-CoV-2 produce a “polyclonal” antibody response that targets several parts of the spike protein. The virus would need to accumulate significant mutations in the spike protein to evade immunity induced by vaccines or by natural infection.

Among these possibilities, the ability to evade vaccine-induced immunity would be the most concerning. There is no definitive evidence yet that this is occurring, but scientists are closely evaluating this possibility.

Icons-Yellow-VaccineWill the Vaccines Eradicate COVID-19?

No. So far, only one human disease -- smallpox -- has been officially eradicated; that is, reduced to zero cases and remained so long-term without continuous intervention measures. Smallpox was stamped out thanks to a highly effective vaccine and the fact that humans are the only mammals that are naturally susceptible to infection with the variola virus that causes the disfiguring, sometimes deadly disease. Humans are the only known reservoir of poliovirus, yet it still spreads in a few countries, causing paralyzing disease, despite the widespread use of effective immunizations and a 32-year-old global eradication effort.

SARS-CoV-2 is thought to persist in nature in horseshoe bats, and has been known to infect minks, cats, gorillas and other animals. Wiping out the virus would require banishing it from every susceptible species, which isn’t feasible. In countries that have successfully suppressed Covid-19 cases, disease elimination has been proposed instead.

David Heymann, chair of the WHO’s Strategic and Technical Advisory Group for Infectious Hazards, warned at the end of 2020, “it appears the destiny of SARS-CoV-2 is to become endemic.”

Viruses that are endemic continuously circulate in the community, often causing periodic spikes when disease characteristics and human behavioral patterns favor transmission.

Examples include norovirus, the notorious cause of gastroenteritis on cruise ships, and the myriad of viruses, including four coronaviruses, that cause the common cold, especially over the winter.

One study estimated that to stop transmission, 55% to 82% of the population would need to have immunity, which can be achieved either by recovering from an infection or through vaccination. Still, there’s reason to believe mass inoculations will have a more powerful effect because vaccines appear to elicit stronger and more durable protection than a prior infection.

The General Consensus

One model of the coronavirus’ transition to an endemic virus, developed by researchers at Emory University and Penn State University, predicts that it will eventually be just a minor childhood infection, no worse than the common cold. Adults would be protected from disease by immunity they acquired as kids.

Although none of the experts know exactly how COVID-19 will evolve or how the vaccines will affect the spread, it seems like there is a general consensus among the medical community that COVID-19 will be around for some time. 

Check your state’s health department website for more information on vaccine availability in your area, as well as eligibility for boosters, on the CDC site

We’re all in this together.

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