A summary of presentations from the weekly Summit partner webinars
May 6, 2021
CDC Update on Emerging SARS-CoV-2 Virus Variants – Adam MacNeil (CDC)
Adam MacNeil, PhD, of the Respiratory Viruses Branch at CDC and Co-lead of the SARS-CoV-2 Response Epidemiology Task Force, provided a presentation on emerging SARS-CoV-2 virus variants.
Overview of CDC SARS-CoV-2 Genomic Surveillance
The CDC is collecting genomic data from two main streams, one of which is the National SARS-CoV-2 Strain Surveillance (NS3), a program that represents baseline sequence data that is received from jurisdictional and state laboratories. This program collects around 750 random samples per week and plans to keep collecting data for an extended period of time. With the emergent variants late last year, sequencing data jumped to around 20,000 sequences a week from a number of commercial laboratory contracts.
Weighted survey methods are used to account for potential biases in sampling to generate representative data. This data has grown exponentially since the beginning of the outbreak and can be found on CDC’s national genomic surveillance program COVID Data Tracker webpage.
There are three levels of classification of SARS-CoV-2 variants which are established by the SARS-CoV-2 Interagency Group (SIG). To be classified as a variant, there are certain characteristics that they look for such as higher rates of transmission, greater disease severity, reduction in antibody neutralization among individuals of previous infection or vaccination, and reduced effectiveness of treatments/diagnostics.
A variant of interest is associated with reduced efficacy of treatment and vaccine protection and could have a potential increase in transmissibility or disease severity. Variants of interest include B.1.526 (from New York) and B.1.617 (from India).
A variant of concern causes more serious disease, greater hospitalizations and deaths, a significant reduction in the efficacy of vaccination or antibodies generated by previous infection, and reduced effectiveness of treatments. There are several variants of concern right now in the U.S.
- The B.1.1.7 (from U.K.) variant rapidly increased in late 2020 and became the dominant virus circulating in the U.K and the U.S. There is substantial evidence that this variant has increased transmissibility and severity.
- The P.1 (from Japan/Brazil) variant seems to have reduction in neutralization from antibody prior illness or vaccination
- The B.1.351 (from South Africa) variant has increased transmission and significant reduction in neutralization by antibodies from prior illness or vaccination.
- Two variants identified in California, B.1.427 and B.1.429, show significant reduction in neutralization by some prior illness or vaccine-related antibody and have slight increased transmissibility.
A variant of high consequence is defined as a variant that has significantly reduced effectiveness to prevention measures or medical countermeasures (MCMs) than do previously circulating variants. To date there are no variants of high consequence that have been identified in the U.S.
It may be more important to pay attention to specific mutations than to the variants themselves. These variants have different mutations within the spike protein; however, some mutations are showing up in multiple variants with separate virus lineages. This suggests convergent evolution of some of these mutations. The most concerning is the E484K mutation; in vitro evidence suggests that the mutation affects neutralization withing the receptor-binding domain. The D614G mutation, which increases transmissibility, exists in almost all of the viruses in circulation now.
National Prevalence of SARS-CoV-2 Variants
As of April 10, the B.1.1.7 variant is the predominant viral lineage circulating in the U.S, representing around 60% of all variants. Other notable variants of high prevalence are B.1.526 (prevalence steady at 8.7%), B.1.427 and B.1.429 (prevalence continuing to decrease for both), P.1 (prevalence steadily increasing to 3.7%), and B.1.351 (prevalence increased to 1%).
The increase in the P.1 variant is concerning and being monitored closely as it seems to be increasingly transmissible, with the ability of break-through infection. Currently there is evidence that most people are still protected from the P.1 variant through vaccination or previous infection.
The increase in B.1.351 is also of concern and being monitored.
The CDC is working to provide regional-level estimates of variant prevalence.
COVID-19 Variant Forecasting
The CDC has developed methodologies for variant forecasting to predict variant trends over time that are called “nowcasting.” Because of the lag in sequencing data, the weighted prevalence is dated back a series of weeks, so nowcasting allows projections to the present with an obvious degree of confidence uncertainty.
Vaccine Selection Pressure
Further tests will need to be conducted to determine if the population will need additional vaccinations to account for new variants. One of the key components in determining this will be to data from global virus surveillance networks, much like is done with the flu.
If this coronavirus becomes like the other four common seasonal coronaviruses that cause minor colds where we get re-infected from year to year, then we may require boosters of the COVID-19 vaccine.
Announcements – L.J Tan (IAC)
The Summit will conduct a virtual meeting, Maintaining Influenza Prevention During the Ongoing COVID-19 Pandemic, on May 20 from 2–4:30 pm ET. This webinar will be held in place of the usual in-person Summit meeting held each spring. The agenda will include updates on influenza surveillance, influenza vaccine uptake, communications planning for the upcoming season, and presentations from vaccine manufacturers on their estimated vaccine supply for the 2021–22 influenza season. Registration information is available on the Summit website.