The C.D.C. significantly lowers its estimate of Omicron's prevalence nationwide

[BumRushDaShow]

8. Well you have red states refusing to timely report

(let alone correctly report) their data and blue states with wonky data systems that need a lot of care and feeding, where actually sequencing of the virus itself requires specific equipment, time and resources to do, then yeah, you are going to get "ballparks" based on what you have.

You then have the media and the public demanding to know what variant is circulating RIGHT NOW!!11!!!1!!!! and here we are.

The problem was ID'd back in February -

Biden administration is 'not where we want to be' on genetic sequencing of Covid-19 variants

By MJ Lee and Michael Nedelman, CNN

Updated 7:01 AM ET, Thu February 11, 2021

(snip)

The US has been ramping up its sequencing efforts and is on track to process at least 7,000 samples per week, Walensky previously said. But she has also echoed statements that more sequencing is needed to track the spread of variants across the country. A CDC official previously told CNN that the UK and some other countries have a more centralized system for doing sequencing. But in the US, several different types of labs -- federal, state, academic and private -- are doing the work.

Denmark, for example, launched an effort to sequence all positive samples starting January 12, a spokesperson for the government's public health institute told CNN last week. Before that, the institute, called Statens Serum Institut, fully sequenced about 20% of positive samples from the start of the pandemic.

Only eight states have genetically sequenced more than 1% of their total coronavirus cases during the pandemic, compared to a national average just under 0.4%, according to CDC data. Eighteen states have sequenced less than 0.1% of their confirmed cases. Experts have previously told CNN that the US should aim to sequence 5% to 10% of cases, in line with sequencing efforts in the UK. Given cases over the past seven days, this would amount to roughly 38,000 to 76,000 sequences in a week.

(snip)

https://www.cnn.com/2021/02/11/politics/biden-administration-covid-variants/index.html

Since then, there have been improvements -

The Omicron variant is putting America's coronavirus sequencing efforts to the test

By Jacqueline Howard, CNN

Updated 4:46 PM ET, Fri December 3, 2021


(snip)

Sequencing many more specimens than a year ago

Genomic sequencing involves examining and decoding the genetic material of a virus to identify how it has changed over time. These changes occur as mutations. Kelly Wroblewski, director of infectious disease at the Association of Public Health Laboratories, said in a written statement to CNN that sequencing can take just a couple days, but for many, it's longer. We generally say about a week," Wroblewski said. It's not as simple as a Covid-19 test with a swab. Only samples that are sent into laboratories for diagnostic testing can be sequenced to look for the genetic evidence to tell which variant of virus has infected someone.

The types of tests -- diagnostic and sequencing -- are done separately. Polymerase chain reaction or PCR testing makes the process easier. Quick antigen tests are not used to detect variants, nor are tests people take on their own at home. Earlier this year, in January, an international database showed the United States ranked 61st in how quickly virus samples were collected from patients, analyzed and then posted online -- taking about 85 days. Countries with far fewer resources, including Bangladesh, Sri Lanka and Suriname, processed samples more quickly than the United States.

As of November 24, based on data from the global science initiative GISAID, the United States appears to have moved up the list to rank 21st when it comes to the speed of collecting samples, sequencing and reporting results, taking a median of about 28 days. An analysis of GISAID data by the Broad Institute of MIT and Harvard also ranked the United States 21st in terms of how many sequences are performed per 1,000 Covid-19 cases, as of November 24.

"Back in January, the numbers were quite low. It was really I think under half a percent in terms of the Covid infections that were prevalent were getting sequenced," said Dr. Ingrid Katz, associate faculty director of the Harvard Global Health Institute and an associate professor at Harvard Medical School. The UK, for example, was sequencing around that time around 5%. Denmark was around 12%. Australia, they were doing like 60% of their detected viruses were getting sequenced," Katz said. "So, now we're in a better place, I would say, in turn, just because the federal government has infused more cash."

https://www.cnn.com/2021/12/03/health/coronavirus-genome-sequencing-omicron/index.html