”In just a few hours, UT Southwestern scientists can tell which variant has infected a COVID-19 patient – a critical task that can potentially influence treatment decisions but takes days or weeks at most medical centers…”Last year, pathologist Jeffrey SoRelle, M.D., and colleagues developed CoVarScan, a rapid COVID-19 test that detects the signatures of eight hotspots on the SARS-CoV-2 virus. Now, after testing CoVarScan on more than 4,000 patient samples collected at UT Southwestern, the team reports in Clinical Chemistry that their test is as accurate as other methods used to diagnose COVID-19 and can successfully differentiate between all current variants of SARS-CoV-2…“Using this test, we can determine very quickly what variants are in the community and if a new variant is emerging,” said Dr. SoRelle, Assistant Professor of Pathology and senior author of the study. “It also has implications for individual patients when we’re dealing with variants that respond differently to treatments.”…To test how well CoVarScan works, Dr. SoRelle’s team ran the test on more than 4,000 COVID-19-positive nasal swab samples collected at UT Southwestern from April 2021 to February 2022 – from patients both with and without symptoms. The tests were validated with the gold-standard whole genome sequencing, and the results were used by doctors to choose treatments in some critically ill COVID-19 patients.

Multiplex Fragment Analysis for Flexible Detection of All SARS-CoV-2 Variants of Concern



Fauci says he’s taking 2nd course of Paxlovid after experiencing rebound with the antiviral treatment

Fauci says he believes Paxlovid kept him out of the hospital, even though he tested positive again.


F.D.A. advisers recommend updated boosters that target forms of Omicron.

”…Despite all the uncertainties, the panel came down 19-2 in favor of redesigning booster shots to also target Omicron or its subvariants, rather than simply the original version of the virus.    The committee debated but did not specify which formulation might work best. The F.D.A. was clearly leaning toward a combination of the existing vaccine and one tailored to two subvariants of Omicron, BA.4 and BA.5.  According  to new estimates from the Centers for Disease Control and Prevention, those subvariants together now make up more than half of new cases in the country.   The meeting highlighted the scientific angst over how to combat a virus that is evolving faster than clinical trials involving humans can deliver results. The panel skipped over the divisive question of who should be eligible for a fall booster. Committee members argued for continuing to use the existing vaccines for people who have not yet gotten initial shots. “I don’t think we should lose the prototype,” Dr. Amanda Cohn, a top C.D.C. official, said. “I think it’s a known entity and it’s doing really well in its current job.”  …But some panelists questioned whether Moderna and Pfizer, along with its partner BioNTech, had proposed the best booster candidates. Several said that Novavax, a company whose vaccine is not yet even available for initial doses in the United States, presented more impressive data.

The F.D.A. recommends Covid boosters be retooled to target the Omicron subvariants BA.4 and BA.5.

(J. Harris: More of the same)


EXTENSIVE VACCINE UPDATE: Clarity for fall: We’re getting an Omicron booste

Patients treated with monoclonal antibodies during COVID-19 delta surge had low rates of severe disease

(J. Harris: Article sent to me by a reader who recently had Covid and took this medicine successfully.)


1. Duration of Shedding of Culturable Virus in SARS-CoV-2 Omicron (BA.1) Infection

Our data suggest that some persons who are infected with the omicron and delta SARS-CoV-2 variants shed culturable virus more than 5 days after symptom onset or an initial positive test.In this longitudinal cohort of participants, most of whom had symptomatic, nonsevere Covid-19 infection, the viral decay kinetics were similar with omicron infection and delta infection. Although vaccination has been shown to reduce the incidence of infection and the severity of disease, we did not find large differences in the median duration of viral shedding among participants who were unvaccinated, those who were vaccinated but not boosted, and those who were vaccinated and boosted.

(J. Harris: So 5 days hunkered down at home is not long enough. Try 10 days?)

2.  The Vaccine-Hesitant Moment

(J. Harris: Readable review.)


1. LONG COVID/PASC Researchers worldwide are investigating the potential causes of post-acute sequelae of SARS-CoV-2 infection (PASC), commonly known as long COVID. Blood clots, persistent virus, and immune system abnormalities—or a combination of those or other underlying mechanisms—are leading theories about what could be causing long-term symptoms following recovery from acute infection. To date, there is no agreement on how to define and diagnose long COVID, and estimates of its prevalence range from 5% to 50% of recovered patients. Recent data published by the US CDC, collected between June 1 and June 13, 2022, show that nearly 1 in 5 US adults who previously had COVID-19 continue to experience symptoms of long COVID, such as fatigue, rapid heartbeat, shortness of breath, muscle weakness, chronic pain, or cognitive difficulties. Overall, about 1 in 13 US adults, or 7.5% of the population, have symptoms lasting 3 or more months after COVID-19 recovery that were not experienced prior to infection. Women were more likely than men to currently have long COVID (9.4% vs. 5.5%), according to the data, findings that are supported by a review published June 20 in Current Medical Research and Opinion. …

 CDC data show that older adults are less likely to have long COVID than younger adults, but the symptoms are often overlooked in older individuals and some research suggests seniors are more likely to develop long-term symptoms. A study from Denmark published June 22 in The Lancet Child & Adolescent Health found that among children ranging in age from 0 through 14 years, those who previously tested positive for SARS-CoV-2 were more likely to experience at least 1 symptom for 2 months or more than children who never tested positive. Additionally, one-third of children who previously tested positive experienced at least 1 long-term symptom they did not have prior to infection, including mood swings, rashes, and stomach aches, memory and concentration problems, and fatigue. While any person of any age can experience long COVID, the question of why remains a mystery. But most scientists and public health officials agree that unraveling that mystery, including standardizing the condition’s definition and diagnosis and finding treatments, represents an urgent global emergency to prevent mass suffering.

2. COVID-19 RECOVERY As world leaders drop the COVID-19 pandemic from their agendas, and US federal, state, tribal, and local governments roll back pandemic-related funding and mitigation efforts—such as mask mandates—local officials, grassroots organizations, and frontline community health workers continue to push for and implement piecemeal strategies to help increase vaccination rates, draw attention to the need for research into long COVID, and improve trust in and funding for public health systems. There is a need for the US to create “a sustainable infrastructure that can keep more people from getting COVID, regardless of their social circumstances,” writes Ed Yong in The Atlantic. Indeed, the US Government Accountability Office (GAO) last week released a report recommending that the US Department of Health and Human Services (HHS) prioritize the development of a real-time, public health situational awareness network to help raise public awareness to facilitate the early detection of and rapid response to future and potentially catastrophic disease outbreaks, such as COVID-19.

3. Effects of human mobility and behavior on disease transmission in a COVID-19 mathematical model

”…We perform simulations and analyze how distinct social behaviors and restrictive measures affect the dynamic of the disease within a population. The model proposed in this study revealed that the main focus on the transmission of COVID-19 is attributed to the “home” location setting, which is understood as family gatherings including relatives and close friends. Limiting encounters at work, school and other locations will only be effective if COVID-19 restrictions occur simultaneously at all those locations and/or contact tracing or social distancing measures are effectively and strictly implemented, especially at the home setting…”

4. First Reported Case of a Person Getting COVID From a Cat (Nature) A team in Thailand reports the first solid evidence of a pet cat infecting a person with SARS-CoV-2 — adding felines to the list of animals that can transmit the virus to people. Researchers say the results are convincing. They are surprised that it has taken this long to establish that transmission can occur, given the scale of the pandemic, the virus’s ability to jump between animal species, and the close contact between cats and people.

(J. Harris: Someone, please show this to my grandchildren.)


1. Pfizer’s modified vaccine is ‘substantially’ better against omicron

”Pfizer’s updated vaccine candidates, a monovalent and a bivalent option, both delivered a “substantially higher immune response” against omicron compared to its current version among study participants 56 and older when used as a fourth booster dose. ….In a phase 2/3 study, the monovalent vaccine targeting omicron resulted in a 13.5-times increase in neutralizing antibody titers with 30 micrograms and a 19.6-times increase with 60 micrograms. The bivalent vaccine, which targeted omicron and the original coronavirus strain, proved a 9.1- and 10.9-times increase, respectively, at the 30 and 60 microgram levels….”Based on these data, we believe we have two very strong omicron-adapted candidates that elicit a substantially higher immune response against omicron than we’ve seen to date,” Pfizer CEO Albert Bourla, PhD, said in a June 25 press release. …The research shows a stronger response against omicron’s BA.1 strain compared to “sister variants” BA.4 and BA.5. 

Novavax COVID vaccine surprisingly effective against all Omicron variants

”…The new data revealed by Novavax indicates its original vaccine formulation seems to generate broad immune responses, resulting in antibodies that display effective responses to all new Omicron variants, including the most immune-evasive BA.5 subtype. In particular, the data indicates a booster shot of Novavax’s vaccine generates neutralizing antibody responses to Omicron variants comparable to what was seen against the original strain of SARS-CoV-2 at the peak of its initial Phase 3 trial….”

(J. Harris: Company release. This might make a good “mix and match” vaccine alternative in the future if the data hold up.”

The genetic and evolutionary determinants of COVID-19 susceptibility

(J.Harris: This article will be of interest to those with a great knowledge of modern genetics; others of us can follow parts of it. I think I almost understand the Neanderthal information.)

”… the genetic legacy of ancient admixture with Neanderthals around 50,000 years ago still affects the health of humans today, even in the specific context of the COVID-19 pandemic.”…One of the most remarkable aspects of such outbreaks is the stunning interindividual variability observed in the course of infection… Predispositions to many infections have since been shown to be controlled by a narrow set of core genes, specific to each type of infection. For example, since 2015, it has been shown that life-threatening influenza pneumonia is linked to inborn errors of TLR3-, IRF7-, and IRF9-dependent type I interferon (IFN) immunity [14, 15]. These groundbreaking discoveries paved the way for the first breakthrough in dissecting the genetic basis of susceptibility to severe COVID-19….it is now estimated that ~20% of patients with critical COVID-19 over 80 years of age, and ~20% of patients of all ages who died from the disease, carried autoantibodies neutralizing type I IFNs…a meta-analysis including 125,584 cases and over 2.5 million controls across 60 studies from 25 countries conducted by COVID-19 HGI, has identified 23 loci significantly associated with disease severity or susceptibility to infection [33]….these observations lend further support to the notion that Neanderthal introgression has had profound consequences for the adaptation of our species to viral challenges, and that such past adaptation events can affect the present-day health status of individuals infected with SARS-CoV-2….”



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