For the U.S., Center for Disease Control (CDC) has posted that there are no "Variant of High Consequence" that defies current diagnostic capability or evades the vaccine-induced immunity or the EUA (Emergency Use Authorization) approved therapeutics.
For "Variants of Concern", it listed COVID-19 strains Alpha (B.1.1.7 first identified in U.K.), Beta (B.1.351 first identified in S. Africa), Gamma (P.1 first identified in Brazil/Japan), and Delta (B.1.617.2 first identified in India) that exhibit increased transmissibility and disease severity, interference with diagnostic test target, and significant reduction in neutralization by antibody-based therapeutics or vaccines.
For the "Variants of Interest", Iota (B.1.526 first identified in NY, U.S.), Epsilon (B.1.427 or B.1.429 first identified in Calif., U.S.), Kappa (B.1.617.1 or B.1.617.3 first identified in India), Zeta (P.2 first identified in Brazil), and Eta (B.1.525 first identified in NIgeria/U.K.) were listed with the potential impact on the above parameters. As for the latter, CDC further defined it as "variant with specific genetic markers that have been associated with changes to receptor binding" (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html ).
In the latest update provided by Moderna Inc. (research article preprint posted June 28, 2021 in bioRxiv), the efficacy of the originally devised mRNA-1273 vaccine against newly emerged COVID-19 variants was described (Choi et al., 2021). In the report, the ability of the sera containing antibodies from mRNA-1273 vaccinated individuals (1 week following 2nd dose) to neutralize the coronavirus was assessed. For the neutralization assay, the authors constructed multiple recombinant 'pseudoviruses' with each virus expressing the spike protein of different COVID-19 variants (instead of utilizing the true COVID-19 coronaviruses).
The pseudovirus was derived from Vesicular stomatitis virus (VSV) that has been engineered to lack its envelope glycoprotein G (mediates fusion with the host cell's plasma membrane), which cannot replicate in culture. VSV is a negative stranded RNA virus that normally infects various animals as well as humans, which can be maintained in a biosafety level 2 containment facilities. These properties have been exploited to allow VSV (lacking its G protein) to express the glycoprotein of high-risk viruses that require biosafety level 3 or 4 containment (COVID-19 may require level 3 facility) (Whitt, 2010). The recombinant VSV utilized in the assay has been engineered to expresses the spike protein of COVID-19 (also expresses the luciferase reporter gene (Choi et al., 2021). The construction of such pseudovirus has been previously described, allowing it to be used in biosafety level 1 facility (Zettl et al., 2020). Thus, by assaying the level of fluorescence emitted by the infected cells, the extent of neutralization afforded by the anti-COVID-19 antibody present in vaccinated individual's serum can be readily determined.
The neutralization results obtained with the variants were compared against the result obtained with D614G (changes residue 614 from Asp to Gly) mutant. The COVID-19 variant with D614G mutation (in spike protein) is currently the most widely circulating strain globally (Choi et al., 2021). Among the data reported, the vaccine's efficacy was reduced by 8.0 and 8.4 fold against A.VOI.V2 (1st detected in Angola, Africa) and B.1.351-v3 (Beta) variants, respectively. Against P.1 (Gamma) and B.1.617.2 (Kappa) variants, its efficacy was reduced by 3.2 and 2.1 fold, respectively. A 4.2 fold reduction was observed against B.1.525 (Eta) variant (1st detected in Nigeria, Africa). To counter the drop in efficacy, Moderna Inc. is currently testing the potential of using mRNA-1273.351 (targets the spike protein of Beta variant) as a booster for those who have been previously vaccinated. The mRNA-1273.211 multivalent booster vaccine is comprised of both the original mRNA-1273 vaccine and mRNA-1273.351 (50:50 mix) (research article preprint posted April 13, 2021 in bioRxiv) (Wu et al., 2021). Nevertheless, for the immunosuppressed individuals (ex. cancer patients undergoing chemotherapy), other forms of therapy than vaccines may be necessary.
The key to preventing epidemic is the ability to diagnose the infected early to preempt further propagation. For this, Bio-Synthesis, Inc. provides primers and probes (as well as synthetic RNA control) for COVID-19 diagnosis via RT-PCR assay. It specializes in oligonucleotide modification and provides an extensive array of chemically modified nucleoside analogues (over ~200) including bridged nucleic acid (BNA) in addition to mRNA synthesis. A number of options are available to label oligonucleotides (DNA or RNA) with fluorophores either terminally or internally as well as to conjugate to peptides or antibodies. It recently acquired a license from BNA Inc. of Osaka, Japan, for the manufacturing and distribution of BNANC, a third generation of BNA oligonucleotides. To meet the demands of therapeutic application, its oligonucleotide products are approaching GMP grade. Bio-Synthesis, Inc. has recently entered into collaborative agreement with Bind Therapeutics, Inc. to synthesize miR-21 blocker using BNA for triple negative breast cancer. The BNA technology provides superior, unequalled advantages in base stacking, binding affinity, aqueous solubility and nuclease resistance. It also improves the formation of duplexes and triplexes by reducing the repulsion between the negatively charged phosphates of the oligonucleotide backbone. Its single-mismatch discriminating power is especially useful for diagnosis (ex. FISH using DNA probe). For clinical application, BNA oligonucleotide exhibits lesser toxicity than other modified nucleotides.
Choi A, Koch M, et al. Serum Neutralizing Activity of mRNA-1273 against SARS-CoV-2 Variants. bioRxiv preprint doi: https://doi.org/10.1101/2021.06.28.449914; this version posted June 28, 2021.
Whitt MA. Generation of VSV pseudotypes using recombinant deltaG-VSV for studies on virus entry, identification of entry inhibitors, and immune responses to vaccines. J Virol Methods. 169:365-74. (2010). PMID: 20709108
Wu K, Choi A, et al. Variant SARS-CoV-2 mRNA vaccines confer broad neutralization as primary or booster series in mice. ioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439482; this version posted April 13, 2021.
Zettl F, Meister TL, et al. Rapid Quantification of SARS-CoV-2-Neutralizing Antibodies Using Propagation-Defective Vesicular Stomatitis Virus Pseudotypes. Vaccines (Basel). 8:386 (2020). PMID: 32679691