A closer look at the nature of SARS-CoV-2 strains

When a viral genome has one or more mutations distinct from the original virus, it is identified as a variant.

The circulation of SARS-CoV-2 variants in late 2020 prompted an increased risk to global public health. As we continue to hear collections of strange letters and numbers from the news, the disheartening reality we face is that new strains of the COVID-19-causing virus are still emerging.

Last year on November 24th, South African geneticists first reported to the World Health Organization (WHO) the detection of the B.1.1.529 or the Omicron variant. Shortly after, epidemiologists sounded the alarms due to the variant’s potentially concerning mutations. With this in mind, one is prompted to ask: where exactly do these variants come from?

Tracing the evolutionary tree

Viruses gradually change via mutation as they replicate and make copies of their genomes—the collection of their DNA. In this process, however, errors could be introduced to their genetic codes. This risk of alteration that exists every time a virus replicates is neither new nor unexpected. Dr. Cynthia Saloma, executive director of the Philippine Genome Center, elaborates that these genetic changes could also occur as a response to “changes in the environment or the host’s immune response.”

As these mutations accumulate, they may lead to new lineages of the virus. When a viral genome has one or more mutations distinct from the original virus, it is identified as a variant. Generally speaking, however, these variants “come and go,” Saloma posits. In fact, most mutations have little to no effect on the virus’ properties. “Just because they are new variants does not mean they possess the characteristic of increased transmissibility,” Saloma expounds. Due to this condition, a variant only gains a specific designation from WHO when it has potentially concerning mutations or characteristics.

In laboratories, the various SARS-CoV-2 variants are designated by name in a technical manner. Saloma shares that the COVID-19 Genomics UK Consortium developed the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) for this reason. PANGOLIN involves a system that names the variants based on their viral genome sequences; it uses the letters A, B, C, and D, followed by appointed numbers.

We briefly heard of the names B.1.617.2 and the recent B.1.1.529, for example. As these are difficult for common people to remember, WHO assigns important variants new names using letters of the Greek alphabet. This way, these variants are easier to say and to remember. Thus, the B.1.617.2 and B.1.1.529 variants are more commonly known as the “Delta” and “Omicron” variants, respectively.

With more than 30 mutations in its spike protein—the portion which attaches to human cells—and 50 mutations in total, the recent Omicron variant possesses characteristics never seen before.

While findings are currently limited, recent studies show that Omicron could be about two times more transmissible than the Delta variant; the reason behind this behavior has yet to be identified. On top of this difference in transmissibility, Omicron was found to attack the upper respiratory more so than the lungs, which explains why it has been found to show “milder” symptoms.

Enlightening the masses

With new SARS-CoV-2 variants cropping up all the time, the public has gotten warier. While Saloma states that not all variants are necessarily harmful or increase the severity of the symptoms, she elaborates that variants with higher transmissibility or immune escape mutations are classified as Variants of Concern (VOCs) or Variants of Interest (VOIs). Thus, reporting on unmonitored or unverified VOCs and VOIs not only contributes to panic but also to confusion.

Sensationalism is a strategy employed by journalism companies that is prevalent today to hook the public into reading articles and watching the news. Even without any official findings, especially regarding new VOCs or VOIs, COVID-19-related materials are released for the sake of clicks.

However, this tactic stirs up mass panic among the general public, on top of the stress of living through a pandemic. For the sake of profits, misinformation is bred when more important information could instead be reported on.

Among these is the concept of immune evasion, or the process by which a disease—in this case, a viral disease—develops mechanisms to slip past the body’s immune system. Escape mutations, meanwhile, are the individual mutations that help facilitate immune evasion.

The circulation of new immune-evasive variants poses a great threat not only to the general public but to our healthcare system as well. As a result, vaccines against COVID-19 have become even more important, especially now that booster doses are more widely available. Thus, it is paramount that health authorities gain confidence among the masses and stimulate change in public health policies in the fight against COVID-19.

Can we keep hope alive?

Most of the vaccines currently available—like the mRNA vaccines made by Pfizer-BioNTech and Moderna—were created from the remnants of the original SARS-CoV-2 virus first observed in Wuhan, China. Additionally, these mRNA vaccines were designed according to the sequence of the spike proteins in this original strain. These spike proteins help viruses latch onto cells and infect the host.

“Early studies reveal that some synthetic antibodies which worked against the original virus and even with the Delta variant seem to be ineffective in neutralizing the Omicron variant in laboratory studies,” Saloma explains. She elucidates that sera accumulated from vaccinated individuals show declining antibody levels over time—as well as a reduction in neutralization against the Omicron variant.

In the process of recovery when antibody presence is low, the Omicron variant first gets past the immune system. Furthermore, when COVID-19 patients recover, they have lower immunity because of an impaired immune system. Hence, patients who have recovered from COVID-19 are still at risk of reinfection.

With this in mind, booster doses have been highly recommended. “Vaccine designers are tweaking the [composition] of their vaccines in the face of the highly mutated Omicron variant,” Saloma notes. She also adds that vaccinologists are currently developing a vaccine that is able to protect us against all variants. Researchers, as well as vaccine scientists, also recommend the acceleration of global vaccination and booster shots to prevent the rapid spread of SARS-CoV-2 VOCs.

COVID-19 has undeniably modified our way of living. We currently live in an era where new variants continue to emerge and quickly spread, emphasizing the great need for vaccines and booster shots. While scientists continue working on new treatments, we must keep in mind that SARS-CoV-2 and its variants will remain a part of our lives—now and for the foreseeable future.

Arianne Joy Melendres

By Arianne Joy Melendres

Jericho Zulueta

By Jericho Zulueta

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