A summary of presentations from the weekly Summit partner webinars
January 5, 2023 – The latest Summit Summary
COVID Surveillance Update – Clinton R. Paden (CDC)
Clinton R. Paden, Ph.D., Bioinformatics Co-Lead, COVID-19 Coordination Unit, CDC, gave an update on COVID-19 surveillance.
Genomic Surveillance Update, U.S., through December 2022
Genomic surveillance is the most effective way to monitor the strains in a quickly moving epidemic. The CDC system aims to generate baseline surveillance sequence data to give an understanding of what’s circulating in the general population from collected samples. This builds a library of viruses that can be selected for isolation and characterization.
Sources of CDC Genomic Data
- U.S. states send specimens to CDC for sequencing at CDC
- 200–500 sequences/week
- CDC partners with national commercial diagnostic labs to sequence specimens
- 10,000 sequences/week
- State/local public health labs, academic labs, and medical labs deposit sequences labeled as “Baseline Surveillance” into public repositories
- 2,000–4,000 from direct submissions from local labs
Data Lag and Nowcasting
- Data lag
- There is a variable lag time from collection to sequence availability
- Most of the CDC data takes 2–3 weeks from collection to be available to analyze
- For weeks with a complete data set, can take a number or positive SARS-CoV-2 strains or variance lineages to see what variants are growing or receding
- Uses a multivariant model to estimate the current proportion of variants, based on weeks-old data
- 21 weeks of data to project those variant proportions into the current week
- Recent weeks provided in reporting in the Nowcasts are not based on actual data that has been collected and observed because the data is not available
- Nowcasting is reliable but projecting further into the future gets noisy and unreliable
- CDC: Genomic Surveillance of SARS-CoV-2 Circulating in the United States
- MMWR: Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021 (6/11/21)
- MMWR: Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022 (2/11/22)
Estimates of Variant Proportions in the U.S. (COVID Data Tracker)
- This interactive dashboard displays hundreds of defined lineages using the Pango lineage system, a hierarchical system
- Smaller, minor lineages are broken up when they exceed 1% nationally and have a potentially impactful change in the spike protein
- These fall under their parent lineage name and are collapsible in the dashboard
- Looking at the data, BQ.1 and BQ.1.1 are B.A.5 family members and have become dominant over the last two months
- Continue to dominate new cases in all regions except for the NE regions
- Responsible for the majority of cases in the week ending December 31, 2022
- XBB.1.5 variant is rapidly emerging in the last week at between 23–61% of cases (95% prediction interval)
- Large regional bias and comprises over 70% of cases in the NE regions
- Primary lineage increasing in proportion in the U.S.
Additions to COVID Data Tracker on Genomic Surveillance
- Wastewater surveillance system monitors sewer sheds for copy number of virus and for reporting the dominant variant in a region
- Wastewater doesn’t vary with the testing rate of a region
- May provide a better advanced warning of future ways of disease
- Traveler-based genomic surveillance program has partners at several U.S. international airports conducting voluntary screening of passengers arriving from outside the country
- Can provide advanced notice of new variants that are coming into the country
- More rapid access to specimens
Cases, Hospitalization, and Deaths, U.S., through December 2022
Weekly Trends in Reported COVID-19 Cases and Test Percent Positivity (7-Day Moving Average), U.S.
- Around country seeing an uptick in cases as well as the percent positivity of tests
- XBB.1.5 variant is all over the country
Weekly Trends in COVID-19-Associated Hospitalization Rates by Age Group – COVID-NET, March 2020–December 24, 2022
- There was a second wave this fall of hospitalizations, especially in individuals age 65+
COVID-19 Weekly Deaths per 100,000 Population by Age Group – United States, March 1, 2020–December 24, 2022
- There is an increased recent risk of death for those age 65+, and especially in those age 75+
COVID-19 Deaths by Vaccination Status, April 2022–October 2022
- Vaccination provides an overall 18.6-fold reduction in the risk of dying from COVID-19
- Vaccination provides a 3-fold lower chance of testing positive
- Data shows 15.1% of people age 5+ have received a bivalent booster
Q: An article suggested that there was a correlation between increased frequency of vaccination with COVID-19 vaccines and a higher risk of infection with the currently surging XBB strain. Is that something that is real?
See also: WSJ: Are Vaccines Fueling New COVID Variants? (1/1/23)
Clinton R. Paden: I cannot speak to that. It’s important to note that vaccines used internationally are not made using the same formulation of strains in the U.S. bivalent booster. There’s a complex landscape of the variables that are out there.
Q: What’s the significance of the burden of COVID-19 in community-acquired pneumonia?
Carolyn Bridges (Immunize.org): We will have a future call in the next few weeks with an update on this regarding hospitalization data.
Q: We have this bivalent vaccine that is designed to make antibodies against the BA.4/5. Can you talk more about the antigenic vs. genetic distances between these B.A.4/5-related variants and the new variants you mentioned?
Clinton R. Paden: There are pseudo-virus studies that are out now, one from Beijing, that are comparing the neutralizing antibody after BA5 and other infections and that neutralizes XBB1 and XBB1.5 and concluded that the strains are not well neutralized. XBB is also not well neutralized, and there are several other B.A.2 viruses that are not well neutralized. The B.Qs were intermediate. Pseudo-virus neutralization is not always the whole story. With live viruses there is a significant improvement in the neutralization of B.Q.1 and B.Q.1.1; however, the XBB-derived viruses are still at the lower end of the assay. It’s not worse in the parental XBB, but it is a lower neutralization than the currently circulating BA.5s.
Q: Is the newer variant still fitting under the same subgroup of Omicron?
Clinton R. Paden: They are all from the same parent, Omicron, at this point. XBB is a recombinant of two branches of the Omicron BA.2 family so it still fits into the BA.2 subgroup but got combined from two branches that had been mutating independently.
Q: There’s more news about countries who want to screen travelers from China coming into the country. Are there any variants they are looking for that are coming in from China?
Clinton R. Paden: Most of the concern is due to the complete unknown. China has not shared much data in the past couple of months. They are starting to share more now, but the information is in slow coming. What we’ve seen are mostly BA.5 derivatives, things we have seen in other places like BF.7, BA.5.2, and a smaller number of XBB sequences.
Q: Is other surveillance being done on borders as well and is that something that you typically report publicly and separately so that people can identify domestically acquired versus not domestically acquired?
Clinton R. Paden: The only surveillance that the CDC is doing at the borders goes through several international airports, and it’s voluntary except for what they may be doing with this new screening with China.
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