The latest on the Covid-19 pandemic as Olympics approach

The Delta Covid-19 variant first detected in India now accounts for 83.2% of Covid-19 cases in the US, and 90% of cases in Missouri, according to estimates updated Tuesday by the US Centers for Disease Control and Prevention. 

CDC Director Dr. Rochelle Walensky told a Senate Committee on Health, Education, Labor, and Pensions hearing about the 83% projection earlier on Tuesday. “This is a dramatic increase, up from 50% for the week of July 3rd,” she said.

The Delta variant, also known as B.1.617.2,  now accounts for nearly 90% of cases in Missouri, the CDC says.

The B.1.1.7 or Alpha variant first detected in the UK accounted for 8.3% of cases in the US as of July 17, the CDC estimates. The P.1 or Gamma variant first seen in Brazil accounts for 3.3% of cases. Other variants account for very few cases, the CDC estimates show. 

The CDC used data collected in the two weeks ending in July 17. It creates estimates by sequencing samples taken from some people and modeling what that might mean for the whole country.

Researchers say they’ve found some evidence that people who got the single-dose Johnson & Johnson coronavirus vaccine might benefit from a booster dose to better protect them from new variants of the virus.

The study was done in the lab and does not reflect real-world effects of the vaccine – and it’s published online as a preprint, meaning it was not subject to careful peer review. 

But Nathaniel Landau of the New York University Grossman School of Medicine and colleagues said their tests of blood taken from vaccinated volunteers shows that at least some of the newly emerging variants may evade the protection offered by a single dose of Johnson & Johnson’s Janssen vaccine.

They tested the blood using lab-engineered versions of the key parts of coronavirus variants. It’s an approach many labs are using to approximate what might happen in real life.

They found that, as other studies have shown, two doses of the Pfizer/BioNTech and Moderna vaccines provide a strong and broad immune response against the variants, with enough of a cushion to protect people even if the variant does evade the immune system somewhat.

But a single dose of the J&J vaccine did not provide the same degree of protection, they wrote. Johnson & Johnson published similar research in the New England Journal of Medicine last week that showed a single dose of its vaccine protected well against the Delta variant, with protection lasting at least eight months. Tuesday’s study contradicts this finding.

The variants Landau’s team tested includes the Delta or B.1.617.2 variant, which has been shown to be more transmissible than older lineages, as well as Beta (B.1.351), Epsilon (B.1.427/B.1.429), Iota (B.1.526), Delta plus (AY.1) and Lambda (C.37).

“Several reports have shown partial resistance of SARS-CoV-2 variants of concern to vaccine-elicited antibodies. The data shown here extend those findings to the Delta plus and Lambda variants,” the researchers wrote. 

Lambda is so far barely showing up in the US, while the Delta variant represents 83% of newly diagnosed cases that are sequenced, according to the US Centers for Disease control and Prevention. Each variant carries a slightly different cluster of mutations that affect how well the immune system can recognize them. 

The tests the Landau team ran showed a single dose of Johnson & Johnson’s vaccine did not produce an overwhelming antibody response against the Beta, Delta, plus and Lambda variants. It was reduced by five-fold to seven-fold compared to older lineages, they said. This “according to mathematical modeling, could result in decreased protection against infection,” they wrote.

“While a single dose vaccination has advantages, the benefit provided by a second immunization may be well worth the inconvenience,” Landau’s team wrote.

“The data presented here emphasize the importance of surveillance for breakthrough infections with the increased prevalence of highly transmissible variants. If an increase in breakthrough infections accompanied by severe COVID-19 is found following adenovirus vector or mRNA vaccination, this would provide a rationale for public health policy-makers and manufacturers to consider booster immunizations that would increase protection against the variants of concern and Lambda variant.”

UPDATE: Some information in this story has been removed as it was under embargo.

About 22% of the US population – nearly 73 million people – lives in a county considered to have “high” Covid-19 transmission, according to data published Monday by the US Centers for Disease Control and Prevention.

This is about 10 times what it was in early June, when less than 3% of the population lived in a county with “high” Covid-19 transmission.

The CDC considers a county to have “high” transmission if there have been 100 or more cases of Covid-19 per 100,000 residents or a test positivity rate of 10% or higher in the past seven days. 

The number of people living in a county with “low” community transmission has been cut in half since in early June. 

According to the latest CDC data, about 5% of the US population – some 16 million people – lives in a county considered to have “low” transmission, defined by the CDC as less than 10 new Covid-19 cases per 100,000 residents and a test positivity rate of less than 5% in the past seven days, down from about 10% of the population and about 32 million people. 

And now, about half of the US population lives in a county with “moderate” community transmission. 

Test positivity rate is one of two indicators used by the CDC to assess community transmission levels. But the number of daily Covid-19 tests have dropped off — down 34% from a month ago – according to data from the US Department of Health and Human Services. The CDC did not respond to CNN’s requests to learn more about this metric.

Washington Regional Medical Center in Fayetteville, Arkansas, posted a video to its Facebook Page featuring a doctor pleading with the public to get vaccinated as cases worsen among younger people.

In the video, Dr. Michael Bolding said he’s seen a dramatic rise in Covid-19 cases in unvaccinated 20- and 30-year-olds who are young and healthy.

“The regret and remorse on their face, and fear, I can’t show you. I can’t describe it. It certainly will be with me forever,” Bolding said. “That look on a patient’s face would be more motivating than anything to go ahead and get your vaccine if you have not already."

Bolding said patients are ending up on ventilators, high flow oxygen and are sicker than at any time in this pandemic.

In Washington County where the hospital is, there’s currently 626 active cases of Covid-19, according to Arkansas’ Department of Health.

Only 41% of people 12 and older in Washington County are fully immunized, according to the state’s health department.

“If the Delta variant is affecting 20- and 30-year-olds, I don’t want to know what the next variant is going to look like and that’s not a scare tactic. That is how viruses work,” Bolding said.

The United States is facing a “collision” of rising overdose deaths and fatalities from Covid-19, US Centers for Disease Control and Prevention Director Dr. Rochelle Walensky said Tuesday. 

“There have been two things in the last decades that have decreased life expectancy in this country. One is Covid-19 and the second is overdose,” she said in a Senate Committee on Health, Education, Labor, and Pensions hearing. 

Walenksy said CDC was continuing to work to understand the rise in opioid deaths and to develop preventative measures. 

“We are actively working to not only study this issue and not only study the overdose deaths, but the overdose hospitalizations, to look at surveillance, to look at the infectious diseases associated with injection drug use, to promote syringe services programs, naloxone programs,” she said, “as well as to provide services and toolkits around the country for not just substance use disorders but for mental health.” 

Some more context: According to provisional numbers from the CDC, more than 93,000 people are predicted to have died from a drug overdose last year, the deadliest year on record for drug overdoses. Overdose rates have been increasing since 1999, according to the NCHS. In 2019, there were 70,630 deaths, and compared with that year's rate, deaths in 2020 increased by almost 30%. According to the CDC data, three-fourths of all fatal overdoses last year involved opioids. 

Downing Street has reiterated that people should isolate if they are notified or "pinged" by a Covid app used by the national health service to trace possible contacts of those who test positive for Covid-19. 

The confirmation comes after UK business minister Paul Scully suggested that it was down to individuals and employers to follow the instructions or to ignore them. 

“You legally have to isolate if you are contacted by the NHS in terms of contact tracing or if you’re claiming self-isolation payments,” he told British media. “But the app is there to allow you to make informed decisions. It should be there for the employer and employee to have those sorts of conversations.”

According to the government rules, people who are told to self-isolate by the NHS app do not have to do so legally; whereas those who are contacted by the NHS Test and Trace system, in which they have been named as a close contact of someone who has tested positive, must do so.

Scully’s comments come as the NHS released its latest figures showing over half a million people in the UK were contacted and told to self-isolate between July 1 to 7, forcing disruption to businesses and pubs which were subsequently short staffed.

On Monday Prime Minister Boris Johnson said that critical workers would be exempt from the requirement to self-isolate, and would use regular testing instead, provided they are fully vaccinated. The mixed messaging has caused further criticism of the UK’s Covid-19 response, particularly as England has dropped all restrictions as of Monday despite a continuing rise of Delta variant cases.

President Biden urged all Americans to remain vigilant in the fight against Covid-19, especially with the rise of the Delta variant, during his second full Cabinet meeting of his administration.

While acknowledging that Covid-19 deaths are “down dramatically” since he took office six months ago, Biden warned that unvaccinated Americans are still at great risk of getting seriously sick because of the variants. 

“We have to stay vigilant, especially with the Delta variant that’s out there. While Covid-19 cases are rising, virtually all of the Covid deaths, virtually all of the Covid deaths and hospitalizations are from unvaccinated people,” Biden said during the Cabinet meeting, taking place in the Cabinet Room for the first time during his presidency.

The first Cabinet meeting he convened was held in the East Room of the White House to allow for social distancing.

“That means the safest thing to do is to get vaccinated, get vaccinated. And that's why we're focusing on our next phase on getting the unvaccinated vaccinated. I know it seems like a constant uphill climb, but gradually we're making progress, but we've got a way to go yet,” he added.

White House deputy press secretary Karine Jean-Pierre defended the Biden administration's effort to convince Americans to get vaccinated today when pressed by CNN's Alisyn Camerota on why they had fallen off their aim to vaccinate 70% of Americans by July 4.

"What we are seeing now is certainly something that we are very aware of, that we are paying very close attention to, and that's why our message has been clear on Covid, that people need to get vaccinated," said Jean-Pierre, when Camerota pointed out that cases are once again rising.

"We have seen some successes here," Jean-Pierre continued. "Many would have said, I would argue Alisyn, that a year ago or six-months ago, they wouldn't have thought we would be as successful as we are now."

Jean-Pierre then said that the administration still planned to hit the 70% vaccination mark despite a myriad challenges.

"We are going to hit that goal," she said. "...We're doing everything that we can and we have seen successes. We have seen Americans go out there and get vaccinated which is so critical."

It is “very likely” that data about Covid-19 vaccines in children under 12 may be available by early winter, National Institute of Allergy and Infectious Diseases Director Dr. Anthony Fauci said Tuesday.

“Very likely when you do the age de-escalation study, so we've gone from 12 to 9, 9 to 6, 6 to 2 and then 6 months to 2 years, likely by late fall, early winter, we'll have enough data,” Fauci said in a Senate Committee on Health, Education, Labor, and Pensions hearing. 

“But that doesn't mean that then it's all of a sudden going to be allowed to happen, that will be a regulatory decision that the FDA will have to make,” he cautioned.