US ramping up Covid-19 genome sequencing to track variants, CDC director says

The US has ramped up its genome sequencing efforts in the hunt for coronavirus variants, US Centers for Disease Control and Prevention Director Dr. Rochelle Walensky said Monday.

“Over the last three weeks or so we’ve increased our sequencing about tenfold,” Walensky said during a White House briefing. “So as we look more, we certainly anticipate we might find more” variants.

The US effort in genetic sequencing lags far behind many other developed nations. One analysis ranked he US 33rd in the world for sequences per 1,000 cases of Covid-19.

Scientists search for coronavirus mutations by taking samples of the virus from patients’ nasal swabs and analyzing their genetic sequences.

Mutations are changes in the genetic code of a virus that naturally occur over time when an animal or person is infected — and such mutations can lead to the emergence of new variants.

“We anticipate that we’re probably going to be sequencing up to three to four more than we are already sequencing,” Walensky said Monday.

“I think once we have more sequencing that’s happening, we’ll have a better idea as to how many variants there are and what proportion are out there.”

Walensky said during the briefing that she was “reluctant” to provide an estimate of how many coronavirus variant cases there could be based on the current data. She also warned that variants and could reverse encouraging declines in Covid-19 statistics.

Walensky said an average of 119,900 new cases were reported between January 31 and February 6 — a drop of nearly 20% from the prior week. New Covid-19 hospitalizations dropped about 17% from the week prior, she said.

“The continued proliferation of variants remains of great concern and is a threat that could reverse the recent positive trends we are seeing,” she said.

Right now 699 variant cases have been confirmed across 34 states — 690 of the variant first discovered in the United Kingdom, she said. Other health officials have said there could easily be 10 times that number of variants in the country.

Experts say the highly contagious UK variant will likely soon become dominant in the US, and a new study found significant community transmission may already be occurring.

On Sunday, the US surpassed 27 million reported infections, according to Johns Hopkins University data. More than 31 million Americans have so far received at least their first dose of either the Pfizer or Moderna vaccine, according to CDC data, as officials work to ramp up vaccinations across the country. More than 9 million people have so far received both doses of a vaccine, according to the data.

And a third vaccine could be on its way to the US market soon: Johnson & Johnson asked the Food and Drug Administration for an emergency use authorization of its vaccine last week.

First sitting member of Congress dies of Covid

US Rep. Ron Wright has died after contracting coronavirus and being hospitalized, his congressional office said Monday.

Texas Republican Wright is the first sitting member of Congress to die after contracting Covid-19. In December, Congressman-elect Luke Letlow died after being diagnosed with the disease.

“Congressman Ron Wright passed away peacefully at the age of 67 on Feb 7, 2021. His wife Susan was by his side and he is now in the presence of their Lord and Savior,” the statement from his office said. “For the previous two weeks, Ron and Susan had been admitted to Baylor Hospital in Dallas after contracting COVID-19.”

What we know about variants and vaccines

Coronavirus variants have complicated things for some vaccines, but experts continue to encourage Americans to get vaccinated as soon as they can. Research published last month offered reassuring evidence that people who are vaccinated against the virus will also likely be protected against new variants.

Moderna previously said two doses of its vaccine are expected to protect against variants first detected in the UK and South Africa, but added it was planning to test booster shots out of an abundance of caution. Pfizer also said last month it was “laying the groundwork” to create vaccine boosters if a variant “shows evidence of escaping immunity by our vaccine.”

Due to uncertainty over the effect the Oxford/AstraZeneca vaccine has on hospitalizations, Abdool Karim, head of South Africa’s Covid-19 advisory board, said the country is pausing the widespread rollout of the vaccine after a study showed it offered reduced protection from the Covid-19 variant first identified there.

Instead the country will favor of a “stepped approach,” giving shots to 100,000 people to study its impact on severe disease and hospitalization. “If we find that the hospitalization rates are below the threshold that we are looking at, then we can be confident that the vaccine is efficacious and maintains its efficacy against hospitalization,” Karim told CNN’s Becky Anderson.

“And if so we can then proceed to continuing the rollout.”

Early data released Sunday suggested two doses of the vaccine provided only “minimal protection” against mild and moderate Covid-19 from the variant. The vaccine’s efficacy against severe Covid-19, hospitalization and death were not assessed.

An AstraZeneca spokesperson said in a statement, “We do believe our vaccine will still protect against severe disease” from the variant and added that “neutralizing antibody activity is equivalent to other COVID-19 vaccines that have demonstrated activity against more severe disease, particularly when the dosing interval is optimized to 8-12 weeks.”

Concerns over Super Bowl parties

Officials have continued to remind Americans it’s not just vaccines that will play a role in helping slow the pandemic in the coming months. It’s also the public health measures that have proved effective in curbing the spread of the virus: masks, social distancing, avoiding gatherings and regular hand washing.

But some opted to leave those suggestions at home over the weekend ahead of and following the Super Bowl. Images emerged out of Tampa, Florida, of crowded streets and venues as well as events with mask-less attendees and parties hosted by celebrities.

But Tampa Mayor Jane Castor said overall she is “very proud” of the level of compliance she has seen from people celebrating following Sunday night’s Super Bowl victory for the Tampa Bay Buccaneers.

During a news conference on Monday morning, Castor said the majority of the tens of thousands of people who were out celebrating the Buccaneers win over the Kansas City Chiefs did so responsibly.

There were “very few incidents” of people violating the mask mandate, she said.

When asked about the Super Bowl celebrations outside the stadium being a potential super spreader event after video of gatherings showing large crowds of unmasked revelers surfaced, Castor said the majority of people she saw were wearing masks.

What it will take to reopen schools

Mitigation measures will play an especially key role in helping schools safely reopen, two officials said Sunday, as the CDC is expected to soon release guidelines on how schools can open during the pandemic.

Dr. Scott Gottlieb, former FDA commissioner, told CBS that when it comes to reopening schools, “the prerequisite is putting in place mitigation steps … ”

He noted that when people wore masks and stayed socially distant, there was “very little transmission within the classroom.”

And while it would be good to prioritize teachers for vaccines, he said, “I don’t think it’s necessarily a prerequisite. I think schools have demonstrated that they can open safely if they’ve taken precautions in the classroom.”

Their recommendation comes amid an ongoing struggle in many parts of the country with how to safely resume classes.

About 62,000 New York City middle school students who opted for in-person learning will be returning to the classroom February 25, according Department of Education Deputy Press Secretary Danielle Filson. Teachers and staff will return the day before to prepare.

Those teachers returning to the classroom are being prioritized for vaccine access at city hubs from February 12 to 21 and over midwinter recess, NYC Department of Education Chancellor Richard Carranza said.