The omicron variant quickly took over the global coronavirus landscape after it was first reported in South Africa in late November, 2021. The U.S. became the 24th country to report a case of omicron infection when health officials announced on Dec. 1, 2021, that the new strain had been identified in a patient in California.
How do scientists know what versions of the coronavirus are present? How quickly can they see which viral variants are making inroads in a population?
Alexander Sundermann and Lee Harrison are epidemiologists who study novel approaches for outbreak detection. Here they explain how the genomic surveillance system works in the U.S. and why its important to know which virus variants are circulating.
Genomic surveillance provides an early warning system for SARS-CoV-2. The same way a smoke alarm helps firefighters know where a fire is breaking out, genomic surveillance helps public health officials see which coronavirus variants are popping up where.
Labs sequence the genome in coronavirus samples taken from patients COVID-19 tests. These are diagnostic PCR tests that have come back positive for SARS-CoV-2. Then scientists are able to tell from the viruss genome which coronavirus variant infected the patient.
By sequencing enough coronavirus genomes, scientists are able to build up a representative picture of which variants are circulating in the population overall. Some variants have genetic mutations that have implications for prevention and treatment of COVID-19. So genomic surveillance can inform decisions about the right countermeasures helping to control and put out the fire before it spreads.
For example, the omicron variant has mutations that diminish how well existing COVID-19 vaccines work. In response, officials recommended booster shots to enhance protection. Similarly, mutations in omicron reduce the effectiveness of some monoclonal antibodies, which are used both to prevent and treat COVID-19 in high-risk patients. Knowing which variants are circulating is therefore crucial for determining which monoclonal antibodies are likely to be effective.
The U.S. Centers for Disease Control and Prevention leads a consortium called the National SARS-CoV-2 Strain Surveillance (NS3) system. It gathers around 750 SARS-CoV-2-positive samples per week from state public health labs across the U.S. Independent of CDC efforts, commercial, university and health department laboratories sequence additional specimens.
Each type of lab has its own strengths in genomic surveillance. Commercial laboratories can sequence a high number of tests, rapidly. Academic partners can provide research expertise. And public health laboratories can supply insight into local transmission dynamics and outbreaks.
Regardless of the source, the sequence data is generally made publicly available and therefore contributes to genomic surveillance.
When a lab sequences a SARS-CoV-2 genome, it uploads the results to a public database that includes when and where the coronavirus specimen was collected.
The open-access Global Initiative on Sharing Avian Influenza Data (GISAID) is an example of one of these databases. Scientists launched GISAID in 2008 to provide a quick and easy way to see what influenza strains were circulating across the globe. Since then, GISAID has grown and pivoted to now provide access to SARS-CoV-2 genomic sequences.
The database compares a samples genetic information to all the other samples collected and shows how that particular strain has evolved. To date, over 6.7 million SARS-CoV-2 sequences from 241 countries and territories have been uploaded to GISAID.
Taken together, this patchwork of genomic surveillance data provides a picture of the current variants spreading in the U.S. For example, on Dec. 4, 2021, the CDC projected that omicron accounted for 0.6% of the COVID-19 cases in the U.S. The estimated proportion rose to 95% by Jan. 1, 2022. Surveillance gave a stark warning of how quickly this variant was becoming predominant, allowing researchers to study which countermeasures would work best.
Its important to note, however, that genomic surveillance data is often dated. The time between a patient taking a COVID-19 test and the viral genome sequence getting uploaded to GISAID can be many days or even weeks. Because of the multiple steps in the process, the median time from collection to GISAID in the U.S. ranges from seven days (Kansas) to 27 days (Alaska). The CDC uses statistical methods to estimate variant proportions for the most recent past until the official data has come in.
Earlier in 2021, the CDC and other public health laboratories were sequencing about 10,000 COVID-19 specimens per week total. Considering that hundreds of thousands of cases have been diagnosed weekly during most of the pandemic, epidemiologists considered that number to be too small a proportion to provide a complete picture of circulating strains. More recently, the CDC and public health labs have been sequencing closer to around 60,000 cases per week.
Despite this improvement, there is still a wide gap in the percentages of COVID-19 cases sequenced from state to state, ranging from a low of 0.19% in Oklahoma to a high of 10.0% in North Dakota within the past 30 days.
Moreover, the U.S. overall sequences a much smaller percentage of COVID-19 cases compared to some other countries: 2.3% in the U.S. compared to the 7.0% in the U.K., 14.8% in New Zealand and 17% in Israel.
Imagine if researchers collected COVID-19 tests from only one neighborhood in an entire state. The surveillance data would be biased toward the variant circulating in that neighborhood, since people are likely transmitting the same strain locally. The system might not even register another variant that is gaining steam in a different city.
Thats why scientists aim to gather a diverse sample from across a region. Random geographically and demographically representative sampling gives researchers a good sense of the big picture in terms of which variants are predominant or diminishing.
There are a few reasons patients are generally not informed about the results if their specimen gets sequenced.
First, the time lag from specimen collection to sequence results is often too long to make the information clinically useful. Many patients will have progressed far into their illness by the time their variant is identified.
Second, the information is often not relevant for patient care. Treatment options are largely the same regardless of what variant has caused a COVID-19 infection. In some cases, a doctor might select the most appropriate monoclonal antibodies for treatment based on which variant a patient has, but this information can often be gleaned from faster laboratory methods.
As we begin 2022, it is more important than ever to have a robust genomic surveillance program that can capture whatever the next new coronavirus variant is. A system that provides a representative picture of current variants and fast turnaround is ideal. Proper investment in genomic surveillance for SARS-CoV-2 and other pathogens and data infrastructure will aid the U.S. in fighting future waves of COVID-19 and other infectious diseases.
From delta to omicron, here's how scientists know which coronavirus variants are circulating in the US - The Conversation US
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- Coronavirus Roundup: One Year of the Biden COVID-19 Response - GovExec.com - January 19th, 2022
- Thousands in Hong Kong volunteer to adopt hamsters amid COVID-19 fears - Reuters - January 19th, 2022
- Coronavirus spreading like never before in Americas, health agency says - Reuters Canada - January 19th, 2022
- Here are the latest COVID-19 numbers for Wednesday, January 19 - WNEP Scranton/Wilkes-Barre - January 19th, 2022
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- Is headache a symptom of the omicron COVID variant? - FOX31 Denver - January 19th, 2022
- Omicron won't be the last COVID-19 variant, WHO says - WXYZ - January 19th, 2022
- The cGAS-STING pathway drives type I IFN immunopathology in COVID-19 - Nature.com - January 19th, 2022
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- With many wondering whether Omicron means we're approaching the endemic phase of Covid-19, Fauci cautions it's still too soon to tell - CNN - January 18th, 2022
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- Preparing for the endemic stage of COVID-19: What this looks like - KOIN.com - January 18th, 2022
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- COVID tests, other public service events on MLK Day in L.A. - Los Angeles Times - January 18th, 2022
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- Novel coronavirus - Wikipedia - January 16th, 2022
- Virus Outbreak: Covid (Coronavirus) News and Analysis From Jan. 15 - Bloomberg - January 16th, 2022
- Corona Virus SalzburgerLand.com - January 16th, 2022
- Protest in Netherlands against coronavirus measures - Reuters - January 16th, 2022
- For Coronavirus Testing, the Nose May Not Always Be Best - The New York Times - January 16th, 2022
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- Encouraging signs plan B Covid measures may soon be lifted in England - The Guardian - January 16th, 2022
- Experts warn against using Benadryl and milk to treat COVID, despite NC lawmakers post - KXAN.com - January 16th, 2022
- What do we know about the 175,000 people who died of Covid in the UK? - The Guardian - January 16th, 2022
- Coronavirus Data for January 12, 2022 | mayormb - Executive Office of the Mayor - January 16th, 2022
- How The mRNA Vaccines Were Made: Halting Progress and Happy Accidents - The New York Times - January 16th, 2022
- Brazil registers 48520 new cases of coronavirus and 175 deaths-health ministry - Reuters - January 16th, 2022
- 3 big Covid misconceptions people still have, according to infectious disease experts - CNBC - January 16th, 2022
- High demand for COVID testing calls Kauai War Memorial Convention Hall to action - KHON2 - January 16th, 2022
- The Covid Race to Watch: Vaccines vs. Variants - The Wall Street Journal - January 16th, 2022
- Hacking a home COVID test by adding a throat swab is a hot topic on Twitter : Goats and Soda - NPR - January 13th, 2022
- Coronavirus Data for January 11, 2022 | mayormb - Executive Office of the Mayor - January 13th, 2022
- Shawnee County Covid Indicator shows cases of coronavirus rising by more than 25% - KSNT News - January 13th, 2022
- Coronavirus in Ohio Thursday update: More than 19,000 new cases reported - NBC4 WCMH-TV - January 13th, 2022
- England cuts coronavirus isolation to 5 days - POLITICO Europe - January 13th, 2022
- COVID-19 in South Dakota: 2,584 total new cases; Death toll rises to 2,544; Active cases at 24,796 - KELOLAND.com - January 13th, 2022
- The Real Reason Americans Aren't Isolating - The Atlantic - January 13th, 2022
- China: Over 20 million in COVID-19 lockdown ahead of 2022 Olympics - NPR - January 13th, 2022
- Coronavirus in Arkansas: another record as over 10,000 new cases reported, 14 more deaths - KNWA - January 13th, 2022
- Utah surge ongoing with 12,990 new COVID-19 cases Thursday - fox13now.com - January 13th, 2022
- Increasing demand for coronavirus tests in Southern Oregon - KDRV - January 13th, 2022
- The Mood in the Capitol Was Already Dark. Then Came Omicron. - The New York Times - January 13th, 2022
- Information for travellers in regards to the corona virus ... - January 10th, 2022
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- Coronavirus in Ohio Sunday update: Just over 19,000 new cases and less than 100 new hospitalizations - WKBN.com - January 10th, 2022
- Coronavirus Briefing: A Pandemic of the Forgotten - The New York Times - January 10th, 2022
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- Coronavirus: should the UK make vaccination mandatory? - The Guardian - January 10th, 2022
- COVID-19: UK records 141,472 new cases and further 97 coronavirus-related deaths - Sky News - January 10th, 2022
- Flu and Covid at the Same Time? Your 'Flurona' Questions, Answered - The New York Times - January 10th, 2022
- States are scrambling to keep up with an increase in Covid-19 hospitalizations and the demand for testing - CNN - January 10th, 2022
- Health experts want to focus on 'new normal' with the coronavirus | TheHill - The Hill - January 10th, 2022
- Chicago's COVID-19 fight with teachers hangs over a 2nd week - KMTV - 3 News Now - January 10th, 2022
- From delta to omicron, heres how scientists know which coronavirus variants are circulating in the US - KRQE News 13 - January 10th, 2022
- Coronavirus Watch: Oregon breaks COVID-19 case record for the third day running - KDRV - January 7th, 2022
- Understanding flurona: person has the flu and the coronavirus simultaneously - fox2now.com - January 7th, 2022
- Rapid nasal COVID tests feared to be returning false negatives - Axios - January 7th, 2022
- COVID infections hit another daily record in Louisiana as hospitalizations rise - The Advocate - January 7th, 2022
- Coronavirus Data for January 4, 2022 | mayormb - Executive Office of the Mayor - January 7th, 2022
- If you give yourself a COVID test, who tracks the results? - Los Angeles Times - January 7th, 2022
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- COVID-19 testing in Massachusetts impacted due to snow - WWLP.com - January 7th, 2022
- Washington to expand access to coronavirus tests, to help contain spread of COVID-19 - KOMO News - January 7th, 2022
- Coronavirus Omicron variant, vaccine, and case numbers in the United States: Jan. 7, 2022 - Medical Economics - January 7th, 2022
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- COVID-19: Did Omicron evolve in mice? - Medical News Today - January 7th, 2022
- Hogan says 10 new hospital-based COVID testing sites to open in Maryland - WTOP - January 7th, 2022
- Outbreak hits Rhode Island hospital after COVID-positive staff called in to work - fox4kc.com - January 7th, 2022
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- Omicron estimated to be 95.4% of coronavirus variants in U.S. - CDC - Reuters - January 5th, 2022
- US COVID cases are on the rise, but this doctor sees hope on the horizon : Coronavirus Updates - NPR - January 5th, 2022
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