Effects of SARS-CoV-2 Subvariants on Vaccine Uptake and Patient Education

ContagionContagion, February 2023 (Vol. 08, No. 1)
Volume 8
Issue 1

"We made a mistake," said Wendy Wright, DNP, ANP-BC, FNP-BC, FAANP, FAAN, FNAP. "We needed to have a 3-dose primary series and not call these booster shots.”

You can watch this Peer Exchange here.

Educating the general public about the clinical significance of SARS-CoV-2 variants of interest and variants of concern and the importance of receiving the bivalent COVID-19 booster is important to increase vaccine uptake.

However, the advent of the Omicron variant and perceived reduction in the efficacy of COVID-19 vaccines for preventing infection has increased hesitancy about receiving the bivalent COVID-19 booster, according to experts who participated in a Contagion® Peer Exchange, moderated by Rodney E. Rohde, PhD, MS, SM(ASCP), MB(ASCP), SV(ASCP), FACSc.


Subvariants of SARS-CoV-2 are currently identified using nomenclature from the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN), a computational tool created to identify the most likely lineage of a SARS-CoV-2 genome based on what is known as the PANGO dynamic lineage nomenclature scheme.1,2 The PANGO nomenclature assigns a letter (A or B) to the 2 major lineages of SARS-CoV-2 based on the nucleotides at position 8782 in open reading frame (ORF)1ab and 28144 in ORF8.2 Descendant lineages are given a numerical value based on “phylogenetic evidence of emergence from an ancestral lineage into another geographically distinct population, implying substantial onward transmission in that population.”1,2

Although this nomenclature is used by researchers, remembering the scientific names for variants can be challenging for members of the media and general public.3 In May 2021, the World Health Organization (WHO) started to use letters from the Greek alphabet to help the general public track variants without associating them with the location in which they were first found. WHO recommends that national authorities, media outlets, and the general public use this naming system to standardize public communication and prevent stigmatization of places where the variants are first detected.3

“A lot of these viruses sometimes get named from their origin,” said Rohde. “We’ve tried to stop doing that so that we can quit [using] a geographic location or some other nomenclature that might be looked upon as a stigma.”


Although specific scientific names are generally not addressed in clinical practice, common circulating variants, such as BA.5, may be addressed when discussing coverage of the new bivalent COVID-19 vaccine, said Madeline King, PharmD, BCIDP, and Wendy Wright, DNP, ANP-BC, FNP-BC, FAANP, FAAN, FNAP. “We also use the variants to talk about how genetically different COVID-19 is today from what it was 2½ years ago, making it a little less recognizable by those native vaccines that we gave, which is why it’s so important that our patients get the booster shots that are targeted toward what we’re seeing today,” said Wright.

Wright also noted that many patients have the impression that the Omicron variant is associated with mild illness, but its extremely high transmissibility has led to high rates of hospitalization, particularly among individuals aged 4 and younger. “We use this to have a conversation about what we’re seeing so that I can push people to get a vaccine, particularly the boosters that are out,” she said.

Distinguishing between variants of concern and variants of interest is also important for educating community members about whether a variant is likely to actually have a clinically important effect on disease, said Jacinda C. Abdul-Mutakabbir, PharmD. “A variant of interest may have more mutations than seen in previous variants but [that] are not concerning as far as the COVID-19 disease itself,” she said. “I tell them that [the variant of interest] is something [researchers are] going to look for more in laboratory testing.”

She then explains to patients that the reason Omicron is considered a variant of concern is because the mutations have substantially increased its transmissibility compared with earlier variants; Omicron’s mutations were the impetus for developing the bivalent vaccines. “We’ve gone from a variant of interest to a variant of concern [with Omicron],” said Abdul-Mutakabbir. “This is a problem we have to deal with. It’s important that we continue to use these terms and that we make the folks we talk with stakeholders of what these terms mean and how serious they can be in terms of COVID-19 and how it’s changing.”


The Centers for Disease Control and Prevention defines a variant of interest as one with genetic markers that are associated with alterations in receptor binding, decreased neutralization by antibodies developed in response to prior infection or vaccination, lower treatment efficacy, or potential effects on diagnosis or increase in transmissibility or disease severity.4

A variant of interest may be upgraded to a variant of concern (eg, the Omicron variant) if there is evidence of increased transmission; greater disease severity; considerable reduction of neutralization by antibodies developed through prior infection or vaccination; or decreased effectiveness of treatments, vaccines, or diagnostic methods used for previous variants.4 A variant of high consequence, which has not yet been observed, has clear data to show that the effectiveness of preventive or treatment strategies is substantially reduced compared with prior variants.4

The emergence of multiple variants has presented growing challenges to vaccine uptake among patients, said Wright. Although the bivalent vaccine was an attempt to “get ahead of these variants,” patients are increasingly hesitant to receive it. “Those variants have made it tough for us to keep pushing people to continue to [receive a] booster,” she said. “We made a mistake when…we started giving the vaccines. We needed to have a 3-dose primary series and not call these booster shots. Many experts will say that we probably needed to give 1 [dose], give another a month later, and give a third 6 months later, as we do with many other vaccines.”

King also expressed concern that the perception of COVID-19 boosters becoming an annual need, much like the annual influenza vaccine, may increase reluctance regarding uptake among the general public, especially if vaccines are perceived to be ineffective for preventing infection. However, Wright noted that education around the COVID-19 vaccines and boosters has prompted changes in communication about how vaccines work in general.

“We aren’t saying that it’s going to protect you from the disease,” said Wright. “We’re saying that the efficacy of these vaccines is around hospitalizations and moderate to severe disease. That’s how we need to change our flu messaging as well. Maybe COVID-19 has set the stage for that.” Abdul-Mutakabbir added that being intentional in explaining the purpose of vaccinations and what the variants are and positioning trusted scientists as the experts are important for improving communication and increasing vaccine uptake. “As these subvariants occur, we need to have more protection and we need to make sure that we do what we can to build those antibodies back up,” she said. “It’s the conversation and the messaging. It’s how we package why these boosters are necessary. It’s important that we educate alongside these rollouts.”

Rohde concluded that although there is misunderstanding among the general public about the mRNA technology used in the COVID-19 vaccines, the technology has allowed scientists to readily adjust and pivot their strategy to optimize the effectiveness of the vaccine as variants arise. “We know all about some of the issues around vaccination and some of the hurdles people have to get them, but [evidence] shows that it’s critical to have them moving forward,” he said.


1. O’Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7(2):veab064. doi:10.1093/ve/veab064

2. Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5(11):1403-1407. doi:10.1038/s41564-020-0770-5

3. WHO announces simple, easy-to-say labels for SARS-CoV-2 variants of interest and concern. World Health Organization. May 31, 2021. Accessed December 29, 2022. https://www.who.int/news/item/31-05-2021-who-announces-simple-easy-to-say-labels-for-sars-cov-2-variants-of-interest-and-concern

4. SARS-CoV-2 variant classifications and definitions. Centers for Disease Control and Prevention. Updated April 26, 2022. Accessed December 29, 2022. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html#anchor_1632158885160.

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