N501Y mutation in SARS-CoV-2 Delta variant is key to breakthrough infections

A study in the Philadelphia area found that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants evolve to become more contagious and resistant to COVID-19 vaccines. In addition, depending on the sublineage, SARS-CoV-2 variants such as the Delta variant led to a three-fold increased risk for vaccine breakthrough cases.

The COVID-19 vaccines remain highly effective at preventing severe illness, hospitalization, and death. However, summer 2021 saw a spike in COVID-19 cases in both vaccinated and unvaccinated people.

In their analysis of SARS-CoV-2 samples, the researchers developed a new statistical method, the Bayesian autoregressive moving average logistic multinominal regression, that may be beneficial in evaluating the evolution of multiple viral variants. “We expect that these modeling methods will be useful in monitoring the effectiveness of vaccination programs going forward as novel variants of SARS-CoV-2 continue to emerge,” concluded the research team.

The study “SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021” is posted to the medRxiv* preprint server while awaiting peer review.

State of the pandemic in the Delaware Valley area

Several COVID-19 waves passed through Philadelphia, as noted with increases in positive COVID-19 tests and increased hospital admissions.

About 70% of Philadelphia residents were vaccinated by September 2021. During the 2021 vaccination campaign, the Alpha and Delta variants were most prevalent in the area.

The researchers collected 2,621 SARS-CoV-2 samples sequenced from individuals with COVID-19 infection from March 2020 to September 2021. Samples also came from 159 fully vaccinated patients with confirmed vaccine breakthrough cases.

Prevalence of Delta during the spike in COVID-19 cases

During the study period, multiple variants were circulating in the Delaware Valley area. The B.1 lineage dominated the region from March 2020 until Fall 2020 until it was usurped by B.1.2 and B.1.243 variants.

By the end of summer 2021, all SARS-CoV-2 variants in the region were from the Delta lineage.

Longitudinal data from the COVID-19 pandemic in the city of Philadelphia. The y-axis shows the daily test positivity rate (light grey) as a percent of the highest value (26.57% positivity on 4/13/2020), the hospitalization rate (dark grey) as a percent of the highest value (87 hospitalizations per day on 4/22/2020), the vaccination rate in adults 18 years old and older (black). The estimated percent of surveillance samples classified as alpha (green) or delta (red) variant was estimated from the sequence data presented in this paper. Other data is from the city of Philadelphia “Testing Data: Programs and Initiatives.”

Longitudinal data from the COVID-19 pandemic in the city of Philadelphia. The y-axis shows the daily test positivity rate (light grey) as a percent of the highest value (26.57% positivity on 4/13/2020), the hospitalization rate (dark grey) as a percent of the highest value (87 hospitalizations per day on 4/22/2020), the vaccination rate in adults 18 years old and older (black). The estimated percent of surveillance samples classified as alpha (green) or delta (red) variant was estimated from the sequence data presented in this paper. Other data is from the city of Philadelphia “Testing Data: Programs and Initiatives.”

Developing an alternative statistical model when faced with changing viral strains

Several issues arose when comparing SARS-CoV-2 samples from breakthrough infections with the rest of the infected community. For instance, the circulation of viral variants changed over time, with Delta being the predominant strain towards the end of the study period. For this reason, collecting samples of breakthrough infections during the study were uneven and heavily focused on the end of 2021.

To address these concerns, the researchers created a Bayesian analysis combining an autoregressive moving average model with multinominal logistic regression. The model accounted for uncertainty and random changes in viral circulation weekly.

“From this view, it is evident that several further lineages waxed and waned notably over the sampling period, including B.1.1.434 and B.1.526,” wrote the research team.

N501Y point mutation increases the risk of vaccine breakthrough cases

The presence of one Delta lineage, B.1.617.2, resulted in a three-fold increase in breakthrough infections.

Comparison of viral genome sequence data from surveillance samples (A, B) to spike target gene failures (C) and vaccine breakthrough samples (D). A) Longitudinal stacked bar graph depicting the SARS-CoV-2 variants present in surveillance samples from the Delaware Valley, shown as the proportion of genomes classified as each variant lineage within each week. The numbers of genomes sampled each week are shown above the graph. Variants are colored according to the key at the bottom of the figure. B) Markings are the same as in A), but showing the proportions of variants estimated from the count data in A) using Bayesian autoregressive moving average multinomial logistic regression. C) Markings as in A), but showing counts of spike target gene failures samples. D) Markings as in A), but showing the counts of vaccine breakthrough samples.

Comparison of viral genome sequence data from surveillance samples (A, B) to spike target gene failures (C) and vaccine breakthrough samples (D). A) Longitudinal stacked bar graph depicting the SARS-CoV-2 variants present in surveillance samples from the Delaware Valley, shown as the proportion of genomes classified as each variant lineage within each week. The numbers of genomes sampled each week are shown above the graph. Variants are colored according to the key at the bottom of the figure. B) Markings are the same as in A), but showing the proportions of variants estimated from the count data in A) using Bayesian autoregressive moving average multinomial logistic regression. C) Markings as in A), but showing counts of spike target gene failures samples. D) Markings as in A), but showing the counts of vaccine breakthrough samples.

A common element in SARS-CoV-2 variants involved in breakthrough infections is the N501Y substitution. The N501Y mutation is observed in Alpha, Beta, and Gamma variants.

Prior research on the N501Y substitution has linked it to increased spike protein binding affinity with the ACE2 receptor and decreased binding of human antibodies to the spike protein.

Frequencies of individual variants estimated using Bayesian autoregressive moving average multinomial logistic regression. Time is shown along the x-axis and estimated proportions of the surveillance population along the y-axis. The grey bars indicate raw proportions from the count data shaded by the number of observations observed in a given week (darker indicating more samples) while the colored lines indicate the proportion estimated by the Bayesian model. The light colored envelopes around each line show the 95% credible intervals for the proportion. Only lineages achieving an estimated proportion of >10% in any given week are shown.” height=”1244″ src=”https://d2jx2rerrg6sh3.cloudfront.net/image-handler/picture/2021/10/F3.large_(8).jpg” srcset=”https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/1280/picture/2021/10/F3.large_(8).jpg 1280w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/1250/picture/2021/10/F3.large_(8).jpg 1250w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/1050/picture/2021/10/F3.large_(8).jpg 1050w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/850/picture/2021/10/F3.large_(8).jpg 850w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/650/picture/2021/10/F3.large_(8).jpg 650w, https://d2jx2rerrg6sh3.cloudfront.net/image-handler/ts/20211025101200/ri/450/picture/2021/10/F3.large_(8).jpg 450w” sizes=”(min-width: 1200px) 673px, (min-width: 1090px) 667px, (min-width: 992px) calc(66.6vw – 60px), (min-width: 480px) calc(100vw – 40px), calc(100vw – 30px)” title=”Frequencies of individual variants estimated using Bayesian autoregressive moving average multinomial logistic regression. Time is shown along the x-axis and estimated proportions of the surveillance population along the y-axis. The grey bars indicate raw proportions from the count data shaded by the number of observations observed in a given week (darker indicating more samples) while the colored lines indicate the proportion estimated by the Bayesian model. The light colored envelopes around each line show the 95% credible intervals for the proportion. Only lineages achieving an estimated proportion of >10% in any given week are shown.” width=”1280″/></p>
<p><span style=Frequencies of individual variants estimated using Bayesian autoregressive moving average multinomial logistic regression. Time is shown along the x-axis and estimated proportions of the surveillance population along the y-axis. The grey bars indicate raw proportions from the count data shaded by the number of observations observed in a given week (darker indicating more samples) while the colored lines indicate the proportion estimated by the Bayesian model. The light colored envelopes around each line show the 95% credible intervals for the proportion. Only lineages achieving an estimated proportion of >10% in any given week are shown.

Another spike protein substitution, P681H, was also increased in breakthrough infection samples.

Other enriched mutations not found on the spike protein include the P199L substitution on the nucleocapsid.

*Important Notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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