COVID-19 Emerging Variants
MUTATIONS AND VARIANTS
Mutations are defined as changing a gene, resulting in a variant form transmitted to subsequent generations. Mutations are common in viruses. The capacity of viruses to adapt to the host and environment is dependent on the ability of the virus to generate diversity in a short period of time. In terms of viral mutation rates among the different types of viruses, RNA viruses can mutate faster than DNA viruses, and there is a negative correlation in mutation rate versus the size of the genome. These viral mutation rates are normally represented as the rate of substitution per nucleotide per cell infection cycle (s/n/c).6 Coronaviruses are the exception to the rapid viral mutation rate seen in other smaller RNA viruses such as influenza.
Coronaviruses such as SARS-CoV-2 contain within their large(>30 kb) genome a region to encode for an RNA-dependent RNA-polymerase, a proofreading mechanism to reduce the mutation rate and stabilize the genome. Betacoronaviruses accumulate around 10-6 (s/n/c) mutations in each round of replication compared to the 14 kb influenza virus, which has a mutation rate of approximately 10-5 (s/n/c) or 10 times the mutation rate for coronavirus.7
Although most of the mutations found on the SARS-CoV-2virus are benign, specific mutations on the spike protein can enhance the adaptability and transmissibility of the virus. More importantly, mutations on the spike protein can be concerning considering that this region houses the receptor-binding domain (RBD) — the contact region to the host cellular entry receptor. Mutations are represented by an amino acid residue number indicating the location of the amino acid sequence. The location for the RBD for SARS-CoV-2 is between amino acid residues 319 and 541, with the receptor-binding motif located between amino acid residues 437 and 508.8
The first recognized mutation that altered the fitness of the SARS-CoV-2 virus was the D614G mutation found on the spike protein, which enhanced the infectivity and stability of the virions. Before May 2020, the D614G mutation was rare but quickly became the dominant circulating strain of SARS-CoV-2, occurring in more than 74 percent of all published sequences by June 2020. Nearly all specimens sequenced today contain the D614G mutation.9
VARIANTS OF INTEREST AND VARIANTS OF CONCERN
Monitoring variants is essential to containing the COVID-19 pandemic. As an example, the genomic database GISAID is an international collaboration of genetic data aggregation and identification. The most significant value is the ability of these databases to identify and monitor emerging variants with criteria from organizations such as the WHO and CDC. Unfortunately, the sharing of SARS-CoV-2 genome data continues to lag. As an example, the United States only uploaded 1.6% of COVID-19 cases to GISAID in March 2021.10
As of spring 2021, there were more than a dozen circulating variants of SARS-CoV-2. Three classifications of these variants are closely monitored by the CDC and WHO. Variants of interest are variants with genetic markers associated with changes in the RBD, reduced neutralization by antibodies, reduced efficacy of treatments, predicted increase in transmissibility or disease severity, or potential diagnostic impact. Variants of concern demonstrate significant increase in transmissibility, more severe disease, reduction in neutralization by antibodies, reduced effectiveness of vaccines, or diagnostic failure. Fortunately, none of the current variants meet criteria for the third classification, variant of high consequence. The variant of high consequence classification is reserved for viral variants with clear evidence that prevention measures or medical countermeasures have significantly reduced effectiveness.
Globally, per the WHO, in May 2021, there were four primary variants of concern: B.1.1.7, B.1.351, P.1, and B.1.617.2 (Figure 2). The variant B.1.1.7 was initially detected in the United Kingdom in September 2020. The B.1.351 and P.1 variants are similar but have different origins. B.1.351 emerged from South Africa around September 2020, and P.1 was detected in early December 2020 in travelers from Brazil to Japan. The B.1.351 and P.1 have three mutations on the RBD (N501Y, E484K, and K417N/T). Of note, the mutation at the E484K position appears in three of the SARS-CoV-2 variants of concern — a pattern of convergent evolution where the trait emerges in different independent lineages over time as the virus adapts to similar environments. There is evidence that the mutation improves the virus fitness in some way by either evading neutralizing antibodies or reducing the efficacy of vaccines.
The other emerging variant of concern, B.1.617.2, was first discovered in India in December 2020 and quickly spread throughout the country. It contains two key mutations, L452R and T478K. These two mutations were not discovered together before being identified in the B.1.617.2 variant. The L452R mutation is the same mutation found in the B.1.427 and B.1.429 strains, which demonstrate an approximately 20 percent increase in transmissibility compared to the original Wuhan strain, along with a twofold increase in viral shedding.11 The B.1.617.2 variant has mutations associated with an increase in transmissibility and ability to evade the immune responses. Early studies suggest that convalescent sera from patients infected with SARS-CoV-2 was 50 percent less effective against B.1.617.2. Antibodies from participants vaccinated with the Pfizer vaccine were 67 percent less potent against the B.1.617.2.12 Figure 2 summarizes the WHO variants of concern and important mutation characteristics.
VACCINE EFFICACY ACROSS DIFFERENT VARIANTS
The adenovirus-vector vaccine ChAdOx1 from AstraZeneca only found 10% protection against mild-to-moderate disease from the B.1.351 variant, but demonstrated 75 percent protection against the B.1.1.7variant, demonstrating the importance of understanding vaccine efficacy with respect to circulating variants.13 Another adenovirus-vector vaccine from Janssen also showed differing efficacy based on the region and associated circulating variants.14
Moderna and Pfizer vaccines are both authorized mRNA vaccines with greater than 90 percent efficacy against SARS-CoV-2 observed in the clinical trials.15,16 However, SARS-CoV-2 variants have changed over time, and the currently circulating predominant variant differs compared to the time period of the phase 3 clinical trials; in vitro studies suggested a four- to sixfold reduction in neutralizing antibody response against variants with the E484K mutation.17,18,19
VACCINE DEVELOPMENT AND VARIANTS
Public health and nonpharmaceutical interventions remain two of the most effective ways to control the spread of the SARS-CoV-2 virus and its variants. Vaccines remain the greatest hope at stopping the pandemic, and booster vaccination will likely be required to help protect against emerging variants.
Vaccine manufacturers are employing different strategies to evaluate booster doses of COVID-19 vaccines. Pfizer-BioNTech is evaluating a booster dose of the same vaccine against the variants, hoping that the increase in antibody production and associated immune system priming will be effective at preventing infection from the variants, while Moderna is exploring booster vaccine candidates based on the B.1.351 genetic sequence.
Unlike the traditional vaccine platforms, the mRNA vaccines are agile in terms of adaptability and speed of development. Additionally, mRNA vaccines have inherent adjuvant properties that enhance the response of the antigen-presenting cell. Once the target vaccine antigen is identified, the genetic information is sequenced and converted to an mRNA sequence that encodes the target antigen. The process from antigen identification to mRNA vaccine candidate can occur in just eight days.20
Indeed, several questions remain on the first-generation COVID-19 vaccines and their efficacy against the variants. The immune response, along with which elements are associated with protection against infection, remains incompletely understood. The correlates of protection from the different vaccines still need to be determined.
The WHO recently proposed a framework for expediting new vaccine development. One intriguing proposal is using pooled safety data on products sharing the same platform, to avoid the need for lengthy, costly, and challenging clinical studies. The proposal is in line with European Medical Association guidance on adapting the second generation of vaccines to the variants.
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- Coronaviridae Study Group of the International Committee on Taxonomy of V, et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol 2020;5:536-44, 2020. doi. org/10.1038/s41564-020-0695-z.
- V’Kovski et al. Coronavirus biology and replication.
- Hamming I, Timens W, Bulthuis ML, et al. Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis. J Pathol 2004 Jun;203(2): 631-37. doi: 10.1002/path.1570.
- V’Kovski et al. Coronavirus biology and replication.
- Sanjuan R, Domingo-Calap P. Mechanisms of viral mutation. Cell Mol Life Sci 2016;73(23):4433-48. doi: 10.1007/s00018-016-2299-6.
- Sanjuan R, Nebot MR, Chirico N, et al. Viral mutation rates. J Virol 2010 Sep;84(19):9733-48. doi: 10.1128/JVI.00694-10.
- Hu B, Guo H, Zhou P, Shi ZL. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol 2021 Mar;19(3):141-54. doi: 10.1038/s41579-020-00459-7.
- Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 2021 Apr;592(7852):116-21. doi: 10.1038/s41586-020-2895-3.
- Maxmen A. Why US coronavirus tracking can’t keep up with concerning variants. Nature 2021;592: 336-37. doi.org/10.1038/d41586-021-00908-0.
- Deng X, Garcia-Knight MA, Khalid MM, et al. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021. doi.org/10.1016/j. cell.2021.04.025.
- Hoffman M, Hofmann-Winkler H, Kruger N, et al. SARS-CoV-2 variant B. 1.617 is resistant to Bamlanivimab and evades antibodies induced by infection and vaccination. Posted at bioRxiv, May 5, 2021. https://doi.org/10.1101/2021.05.04.442663.
- Madhi SA, Baillie V, Cutland CL, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 variant. N Engl J Med 2021 Mar 16;NEJMoa2102214. doi: 10.1056/NEJMoa2102214.
- Sadoff J, Gray G, Vandebosch A, et al. Safety and efficacy of single-dose Ad26. COV2.S vaccine against Covid-19. N Engl J Med 2021 Apr 21. doi: 10.1056/NEJMoa2101544.
- Polack FP, Thomas SJ, Kitchin N, et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N Engl J Med 2020;383:2603-15. doi: 10.1056/NEJMoa2034577.
- Baden LR, El Sahly HM, Essink B, et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N Engl J Med 2021;384:403-16. doi: 10.1056/NEJMoa2035389.
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- Sanjuan, Domingo-Calap. Mechanisms of viral mutation.
- Dagan N, Barda N, Kepten E, et al. BNT162b2 mRNA Covid-19 vaccine in a nationwide mass vaccination setting. N Engl J Med 2021;384:1412-23. doi: 10.1056/NEJMoa2101765.
- Hekele A, Bertholet S, Archer J, et al. Rapidly produced SAM(®) vaccine against H7N9 influenza is immunogenic in mice. Emerg Microbes Infect 2013 Aug;2(8):e52. doi: 10.1038/emi.2013.54.