The Need for Vigilance: Novel Variants and Vaccine Breakthroughs

A little over a year ago, the World Health Organization officially declared COVID-19 a pandemic.1 Twelve months after that announcement, we witnessed the development and FDA Emergency Use Authorization issuance of two novel RNA vaccines and one adenoviral vector vaccine.2–4 This sparked a vaccination effort that has resulted in more than 275 million doses of vaccine administered in the United States as of 20 May 2021.5

The vaccination rate success, bolstered by the efficacy of the COVID-19 vaccines, has led the CDC to loosen mask guidance6 and states to move towards reopening. However, given the possibility of breakthrough infections—where fully-vaccinated individuals still contract SARS-CoV-2—it is important to remember that vaccines are not a silver bullet and diligence is still needed.

Two such breakthrough infections were recently identified at Rockefeller University following routine screening. In a recent publication,7 researchers used a targeted RNA-Seq panel to take a deeper look at these cases and examine potentially clinically significant variants.

Vigilance identifies breakthroughs

Rockefeller University began performing saliva-based SARS-CoV-2 qPCR tests on all employees and students in fall of 2020. Earlier this year, they monitored the testing of 417 people who had completed either the Moderna or Pfizer-BioNTech vaccine courses (defined as receiving the second dose at least two weeks prior to testing) and 1,491 unvaccinated people.

Through this screening effort, Rockefeller University identified two symptomatic individuals that tested positive for SARS-CoV-2. Neither individual had any risk factors for severe COVID-19. Patient 1, a 51-year-old woman, received the Moderna vaccine; while Patient 2, a 65-year-old woman, received the Pfizer-BioNTech vaccine.

Given these unusual histories, researchers opted to perform targeted RNA sequencing of both patients using the Agilent SureSelect CD Pan Human Coronavirus panel.8 This panel includes probes targeted towards not just SARS-CoV-2, but all human coronaviruses.

The Pan Human Coronavirus panel was designed in response to the COVID-19 pandemic by Professor Judith Breuer, Director of the Pathogen Genomics Unit at University College London and a member of the COVID-19 Genomics UK Consortium. More information on this panel and the benefits of using targeted NGS in pathogen genomics can be found in one of our earlier articles.

Breaking down the breakthroughs

Using the SureSelect CD Pan Human Coronavirus panel, researchers identified multiple mutations with potential clinical significance. Both patients carried variants with a D614G mutation, but only Patient 1 had a variant with an E484K mutation—previously shown to provide resistance to neutralizing antibodies.9,10 With further analysis of the variant from patient 1, researchers were able to determine that the variants found in Patient 1 were related to, yet distinct from, the B.1.526 (New York) and B.1.1.7 (UK) variants of concern.

The Need for Vigilance: Novel Variants and Vaccine Breakthroughs

Ensuring a response

To provide evidence that this was a genuine breakthrough rather than a lack of response to the vaccine, researchers used a pseudotype neutralization assay. 50% neutralizing testing titers (NT50) were significantly higher in vaccinated persons and unvaccinated persons at 1.3 months post-infection (NT50 = 451 and 401, respectively) than in unvaccinated persons at 6.2 months post-infection (NT50 = 78). However, the extremely high neutralizing antibody titers observed in Patient 1 post-vaccination and post-infection (NT50 = 3,209) are consistent with a vaccine-induced antibody response.

Given the previously observed antibody resistance conferred by the E484K mutant and similarity to the New York variant,9,10 researchers asked whether antibodies from Patient 1 were able to recognize these variants. NT50 values did not significantly vary between wild-type, E484K variant, and New York variant virus, suggesting that while the vaccine response was sufficient to recognize the tested variants, it was not enough to prevent subsequent infection.


Going forward, identifying SARS-CoV-2 variants that are able to evade protection from vaccines will be critical so that we can monitor their spread and potentially create vaccines that target them. While unwelcome news, the authors note that these findings do not diminish the importance of the ongoing vaccination efforts in the United States.

"In light of the virus' demonstrated ability to evolve clinically concerning variants, there is an ongoing need to identify them in order to mitigate disease spread and associated morbidity," said Robert B. Darnell, M.D., Ph.D. Heilbrunn Professor and Senior Physician, Rockefeller University.

These findings, particularly in light of the recently revised CDC mask guidelines,6 underscore the need for vigilance as we continue to navigate through the pandemic and work towards finally overcoming it.


  1. WHO Director-General's opening remarks at the media briefing on COVID-19 - 11 March 2020 (accessed May 25, 2021).
  2. Office of the Commissioner. Pfizer-BioNTech COVID-19 Vaccine (accessed May 25, 2021).
  3. Office of the Commissioner. Moderna COVID-19 Vaccine (accessed May 25, 2021).
  4. Office of the Commissioner. Janssen COVID-19 Vaccine (accessed May 25, 2021).
  5. CDC. COVID Data Tracker (accessed May 25, 2021).
  6. CDC. COVID-19 and Your Health (accessed May 25, 2021).
  7. Hacisuleyman, E.; Hale, C.; Saito, Y.; Blachere, N. E.; Bergh, M.; Conlon, E. G.; Schaefer-Babajew, D. J.; DaSilva, J.; Muecksch, F.; Gaebler, C.; Lifton, R.; Nussenzweig, M. C.; Hatziioannou, T.; Bieniasz, P. D.; Darnell, R. B. Vaccine Breakthrough Infections with SARS-CoV-2 Variants. N. Engl. J. Med. 2021, No. NEJMoa2105000.
  8. Agilent has not performed verification and validation on this panel. For Research Use Only. Not for use in diagnostic procedures.
  9. Wang, Z.; Schmidt, F.; Weisblum, Y.; Muecksch, F.; Barnes, C. O.; Finkin, S.; Schaefer-Babajew, D.; Cipolla, M.; Gaebler, C.; Lieberman, J. A.; Oliveira, T. Y.; Yang, Z.; Abernathy, M. E.; Huey-Tubman, K. E.; Hurley, A.; Turroja, M.; West, K. A.; Gordon, K.; Millard, K. G.; Ramos, V.; Da Silva, J.; Xu, J.; Colbert, R. A.; Patel, R.; Dizon, J.; Unson-O'Brien, C.; Shimeliovich, I.; Gazumyan, A.; Caskey, M.; Bjorkman, P. J.; Casellas, R.; Hatziioannou, T.; Bieniasz, P. D.; Nussenzweig, M. C. MRNA Vaccine-Elicited Antibodies to SARS-CoV-2 and Circulating Variants. Nature 2021, 592 (7855), 616–622.
  10. Weisblum, Y.; Schmidt, F.; Zhang, F.; DaSilva, J.; Poston, D.; Lorenzi, J. C.; Muecksch, F.; Rutkowska, M.; Hoffmann, H.-H.; Michailidis, E.; Gaebler, C.; Agudelo, M.; Cho, A.; Wang, Z.; Gazumyan, A.; Cipolla, M.; Luchsinger, L.; Hillyer, C. D.; Caskey, M.; Robbiani, D. F.; Rice, C. M.; Nussenzweig, M. C.; Hatziioannou, T.; Bieniasz, P. D. Escape from Neutralizing Antibodies by SARS-CoV-2 Spike Protein Variants. Elife 2020, 9.