COVID-19 News and Discussions

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The Team Behind a Tree of 10 million Covid Sequences
by Rose Miyatsu
June 21, 2022

Introduction:

(UC Santa Cruz) 10 million sequences of COVID-19’s genomic code have now been organized into a phylogenetic tree in the UC Santa Cruz SARS-CoV-2 Browser, which is the largest tree of genomic sequences of a single species ever assembled. This accomplishment is impressive for both the computer engineering feat of processing such a massive amount of data and the incredible dedication and coordination of the researchers involved.

“It is an astounding thing that has happened there,” said Clay Fischer, Project Manager for the UCSC Genome Browser.

All of these sequences are assembled by the researchers into a phylogenetic tree that shows the evolutionary history of the virus, with different branches representing the lineages that have mutated throughout the pandemic. This tree is powered by a software tool called UShER that was developed at the UC Santa Cruz Genomics Institute and is hosted on the UCSC Genome Browser website.

Many hands from around the world have brought the Genomics Institute these 10 million sequences that live on the UShER tree. Clinicians worldwide have administered tests to be sent off to local labs, which then sent the samples on for sequencing. Once they are sequenced, they become digital files that are uploaded to databases for genomic information such as GISAID, GenBank, or the COG-UK database.

Angie Hinrichs, a senior software architect at the UCSC Genome Browser and self-described “data wrangler,” built a pipeline to pull these sequences into the UShER tree automatically. But this process was complicated as some databases, like GISAID, had restrictions that necessitated the manual download of sequences.

Read more here: https://news.ucsc.edu/2022/06/10-mill ... nces.html

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Covid-19 public health emergency extended in the US
Source: WSIL TV/CNN-Wire

The Biden administration on Friday extended the Covid-19 public health emergency for another three months. US Department of Health and Human Services Secretary Xavier Becerra officially renewed the declaration, extending it through October 13, 2022. The emergency declaration has been in place since January 2020, and the latest renewal comes as the Omicron offshoot BA.5, the most contagious variant yet, continues to stake its claim in the US.

Daily case rates, though vastly undercounted, are the highest they've been in months, as are Covid-19 hospitalizations and deaths. Data published this week by the US Centers for Disease Control and Prevention shows that more than half of the country's population lives in a county with a "high Covid-19 Community Level," where the health care system is at risk of becoming overburdened and universal indoor masking is recommended.

"The Public Health Emergency declaration continues to provide us with tools and authorities needed to respond to the highly transmissible COVID-19 subvariants that are currently circulating around the country," a Biden administration official told CNN. "The PHE provides essential capabilities and flexibilities to hospitals to better care for patients, particularly if we were to see a significant increase in hospitalizations in the coming weeks." Indeed, ensemble forecasts from the CDC published this week do predict that hospitalizations in the US will rise over the next month.

It's the first time in weeks that the forecasts have predicted an increase in hospitalizations, instead of a stable outlook. "Without the PHE in place, we would be limited in our ability to provide broad and equitable access to lifesaving treatments through our Test to Treat initiative, for example, which relies on flexibility for telehealth and operations," the official said. "Not renewing the PHE would leave us with fewer tools to respond and mean more Americans would get severely ill and end up in the hospital."

Read more: https://www.wsiltv.com/coronavirus/covi ... 616e6.html

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Vaccine protection against COVID-19 short-lived, booster shots important, new study says
https://medicalxpress.com/news/2022-07- ... shots.html
by Yale School of Public Health

Since COVID-19 vaccines first became available to protect against infection and severe illness, there has been much uncertainty about how long the protection lasts, and when it might be necessary for individuals to get an additional booster shot.

Now, a team of scientists led by faculty at the Yale School of Public Health and the University of North Carolina at Charlotte has an answer: strong protection following vaccination is short-lived.

The study is the first to quantify the likelihood of future infection following natural infection or vaccination by the Moderna, Pfizer, Johnson & Johnson, or Oxford-AstraZeneca vaccines. The findings are published in the Proceedings of the National Academy of Sciences.

The risk of breakthrough infections, in which a person becomes infected despite being vaccinated, depends on the vaccine type. According to the study, current mRNA vaccines (Pfizer, Moderna) offer the greatest duration of protection, nearly three times as long as that of natural infection and the Johnson & Johnson and Oxford-AstraZeneca vaccines.

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Long COVID affects 23% of positive cases, causing symptoms in 'long haulers' that may last for months
https://medicalxpress.com/news/2022-07- ... ptoms.html
by Leigh Hopper, University of Southern California

A new USC study finds that 23% of people infected with COVID will become "long haulers," and identifies predictors of who is likely to develop the sometimes-debilitating symptoms that can last for months.

The research, which appears in Scientific Reports, is unique because it accounts for preexisting symptoms such as fatigue and sneezing that are common to other conditions and may be mistaken for COVID symptoms.

"Long COVID is a major public health concern. Twenty-three percent is a very high prevalence, and it may translate to millions of people," said first author Qiao Wu, a doctoral candidate at the USC Leonard Davis School of Gerontology. "More knowledge on its prevalence, persistent symptoms and risk factors may help health care professionals allocate resources and services to help long haulers get back to normal lives."

The work finds that obesity and hair loss at the time of infection are predictors of long COVID, but that other underlying conditions—such as diabetes or smoking status—have no discernable link to long-lasting symptoms.

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Boston City Leaders Say Mask Advisory Is Preemptive Strike to Keep COVID Hospitalizations Down
Source: NBC Boston

The Boston Public Health Commission says despite the increase, the number of severe cases is low, and they want to keep it that way, trying to pre-emptively reduce strain on the hospital system.

“We have a variant that is circulating, BA.5 that is highly transmissible. It evades immunity, and we are seeing a high rate of re-infections,” said Dr. Ojikutu.

Seventy-four percent of Boston residents are fully vaccinated, and 56-percent have received a booster.

Read more: https://www.nbcboston.com/news/local/bo ... n/2775792/

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Newly developed vaccine offers superior protection against omicron variants

by Bill Hathaway, Yale University

Yale scientists have developed a novel omicron-specific mRNA vaccine that offers superior immune protection against two viral subvariants than standard mRNA vaccines.

The new vaccine, called Omnivax, increased neutralizing antibody response against the BA.1 and BA.2.12.1 omicron subvariants in pre-immunized mice 19-fold and eight-fold, respectively, compared with standard mRNA vaccines. The improved response against the BA.1 subvariant was reported June 6 in the journal Nature Communications. The results of the study involving the BA.2 subvariant were published July 19 in the journal Cell Discovery.

"While standard mRNA vaccines still offer protection against infection from new variants, their effectiveness wanes over time and was compromised due to immune escaping mutations in emerging variants," said Sidi Chen, associate professor of genetics at Yale School of Medicine and senior author of both studies. "We wanted to see if we could develop variant-specific vaccines that offer additional protection against emerging subvariants."

The experimental vaccines, developed in Chen's lab by a team headed by postdoctoral associate Zhenhao Fang, use engineered lipid nanoparticles to deliver mRNA to cells with "instructions" to create spike proteins from mutating variants, which the virus uses to attach to and infect cells. The presence of these foreign viral fragments prompts the immune system to create antibodies against the virus. The rapid mutation of spike proteins on the surface of the virus over time has created a parade of subvariants and enabled them to blunt the protection of earlier generations of mRNA vaccines developed by Moderna and Pfizer-BioNTech.

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Effective Oxygen Treatment is Now Available for Millions Suffering from Long-term COVID-19 Symptoms
July 20, 2022

Introduction:

(EurekAlert)
• Researchers from Tel Aviv University exposed patients with long-term COVID-19 symptoms to intensive Hyperbaric Oxygen Therapy (HBOT) treatment, and found significant improvement in cognitive, neurological, and psychiatric functions.
• The treatments were accompanied by advanced MRI imaging of the patients' brains, identifying damage from the COVID-19 virus, and correlating the images with clinical findings, before and after HBOT treatment.

A groundbreaking new study from Tel Aviv University, the first of its kind in the world, found a promising treatment for long-term COVID-19 symptoms, based on advanced Hyperbaric Oxygen Therapy (HBOT). Long COVID, which affects up to 30% of patients infected by the COVID-19 virus, is characterized by a range of debilitating cognitive symptoms such as inability to concentrate, brain fog, forgetfulness and difficulty recalling words or thoughts - persisting for more than three months, and sometimes up to two years. To date, no effective therapy has been suggested, leaving many millions of sufferers around the world with no remedy. The researchers: "Our study is the first randomized controlled trial to demonstrate a real solution for long COVID. Patients exposed to an intensive protocol of HBOT treatments showed significant improvement compared to the control group. For millions suffering from long-term COVID-19 symptoms, the study provides new hope for recovery."

Read more here: https://www.eurekalert.org/news-releases/959362

For a technical presentation of the results of the study: [url] https://www.nature.com/articles/s41598-022-15565-0 [url]

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[Time_Traveller]

Public inquiry into UK Covid-19 response opens

Thu 21 Jul 2022 12.51 BST

Ministers will have a year to prepare before cross-examination at the UK’s Covid-19 public inquiry, its chair, Heather Hallett, announced, as she opened what is likely be one of the broadest statutory investigations in the country’s history.

The first cross-examinations of the government response to the pandemic, including decisions on lockdowns, maintaining public confidence and handling of scientific advice, will begin in summer 2023, two and a half years after the arrival of coronavirus, which has claimed more than 200,000 lives in the UK.

Hearings on the UK’s preparedness will start in late spring 2023, as Lady Hallett said she wanted to move as “speedily as possible so lessons are learned before another pandemic strikes”.

Boris Johnson had been repeatedly criticised by campaigners for the bereaved and Labour for delaying the launch of the inquiry. Hallett said it would scrutinise the “performance and effectiveness” of central government decision-making and its messaging – topics likely to expose current and former ministers.

The inquiry has powers to compel the production of evidence and appearances of witnesses.

https://www.theguardian.com/world/2022/ ... onse-opens

[Yuli Ban]

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International Study Identifies Risks for Long COVID in Children
July 22, 2022

Introduction:

(EurekAlert) Nearly 6 percent of children who presented to the Emergency Department (ED) with COVID-19 reported symptoms of long COVID 90 days later, according to a study conducted in eight countries and published in JAMA Network Open. Initial hospitalization of 48 or more hours, four or more symptoms at the initial ED visit, and age 14 years or older were associated with long COVID.

“We found that in some children, illness with COVID-19 is associated with reporting persistent symptoms after 3 months,” said Principal Investigator Stephen Freedman, MDCM, MSc, with the Cumming School of Medicine at University of Calgary, and Alberta Health Services. “Our results suggest that appropriate guidance and follow-up are needed, especially for children at high risk for long COVID.”

The study included 1,884 children with COVID-19 who had 90-day follow-up. Long COVID was found in nearly 10 percent of hospitalized children and 5 percent in children discharged from the ED.

“Reported rates of long COVID in adults are substantially higher than what we found in children,” said Co-Principal Investigator Nathan Kuppermann, MD, MPH, from University of California, Davis School of Medicine, Sacramento. “Our findings can inform public health policy decisions regarding COVID-19 mitigation strategies for children and screening approaches for long COVID among those with severe infections.”

The most reported persistent symptoms in children were fatigue or weakness, cough, difficulty breathing or shortness of breath.

Read more here: https://www.eurekalert.org/news-releases/959647

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In Brief: COVID-19 Vaccine Does Not Negatively Affect Placental Health
July 22, 2022

Introduction:

(EurekAlert) Vaccination against COVID-19 had no impact on the health of placentas in pregnant women, according to new research by pathologists at Weill Cornell Medicine and NewYork-Presbyterian. The findings ( https://www.ajog.org/article/S0002-937 ... /fulltext ), published June 27 as a research letter in the American Journal of Obstetrics & Gynecology , further emphasize the safety of vaccination during pregnancy for babies and pregnant women, the investigators note.

Most previous studies on the impact of COVID-19 vaccination during pregnancy have focused on maternal and infant outcomes. By contrast, for this study, the investigators examined 18 indicators of placental health, such as the presence of lesions, blood clots and inflammation associated with a higher risk of adverse health issues for babies and their mothers. They also collected data from clinical records on the babies’ birth weights and the score that assesses babies’ well-being at one minute and five minutes after birth, called the Apgar score.

The researchers analyzed findings for 431 women who gave birth to single babies at NewYork-Presbyterian/Weill Cornell Medical Center between April 2020 and July 2021 and compared results for 164 women who were fully vaccinated during pregnancy, defined as having received at least two doses of an mRNA COVID-19 vaccine (Pfizer or Moderna), with 267 unvaccinated women. All women included in the study had no evidence of current or prior SARS-CoV-2 infection. The investigators found no significant differences in placental health indicators, birth weights or Apgar scores between vaccinated and unvaccinated women.

As expected from previous research, 95 percent of babies born to vaccinated mothers had detectable antibodies against SARS-CoV-2 in umbilical cord blood. Other studies have shown that vaccinating mothers during pregnancy not only protects them from severe illness from COVID-19, but also helps protect their babies for several months after birth.

Overall, the findings add to the existing body of knowledge demonstrating that COVID-19 vaccines are safe during pregnancy, the authors concluded.

Read more here: https://www.eurekalert.org/news-releases/959633

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COVID Virus May Tunnel through Nanotubes from Nose to Brain

By Stephanie Pappas on July 20, 2022

As familiar to everyone as the COVID-causing coronavirus SARS-CoV-2 has become over the past two years, feverish research is still trying to parse a lingering puzzle. How, in fact, does the pandemic virus that has so changed the world cross over into the brain after entering the respiratory system? An answer is important because neurological complaints are some of the most common in the constellation of symptoms called long COVID. The mystery centers around the fact that brain cells don’t display the receptors, or docking sites, that the virus uses to get into nasal and lung cells.

SARS-CoV-2, though, may have come up with an ingenious work-around. It may completely do away with the molecular maneuverings needed to attach to and unlock a cell membrane. Instead it wields a blunt instrument in the form of nanotube “bridges”—cylinders constructed of the common protein actin that are no more than a few tens of nanometers in diameter. These tunneling nanotubes extend across cell-to-cell gaps to penetrate a neighbor and give viral particles a direct route into COVID-impervious tissue. Researchers at the Pasteur Institute in Paris demonstrated the prospects for a nanotube-mediated cell crossing in a study in a lab dish that now needs to be confirmed in infected human patients. Given further proof, the findings could explain why some people who get COVID-19 experience brain fog and other neurological symptoms. Also, if the intercellular conduits could be severed, that might prevent some of these debilitating aftereffects of infection.

https://www.scientificamerican.com/arti ... -to-brain/

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Riverside, San Bernardino counties reach 'high' COVID level; no plans for indoor mask mandate
Source: ABC 7 Eyewitness News

Cotton credits vaccinations, booster shots and available therapies, but he cautions that people who are immune compromised still need to take precautions in public.

Orange County reached the "high" community transmission level last week. Health officials said the surge in cases is due to the highly transmissible omicron subvariants.

Leaders in Riverside, San Bernardino and Orange counties all say they have no plans to implement new mask mandates unless they are ordered to do so by the state.
L.A County is also in the "high" COVID transmission level, and has been since July 14.

If the county stays at the high category for two weeks straight, officials would bring back rules requiring the wearing of masks during most indoor public activities. At earliest that would be July 29.

Read more: https://abc7.com/riverside-county-covid ... /12067808/

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SARS-CoV-2 Hijacks Nanotubes Between Neurons to Infect Them
July 25, 2022

Extract:

(EurekAlert) COVID-19 often leads to neurological symptoms, such as a loss of taste or smell, or cognitive impairments (including memory loss and concentration difficulties), both during the acute phase of the disease and over the long term with "long COVID" syndrome. But the way in which the infection reaches the brain was previously unknown. Scientists from Institut Pasteur and CNRS laboratories have used state-of-the-art electron microscopy approaches to demonstrate that SARS-CoV-2 hijacks nanotubes, tiny bridges that link infected cells with neurons. The virus is therefore able to penetrate neurons despite the fact that they are lacking the ACE2 receptor that the virus usually binds to when infecting cells.

Further extract:

According to this new study, SARS-CoV-2 is also thought to be capable of inducing the formation of nanotubes between infected cells and neurons, as well as among neurons, which would explain how the brain is infected from the epithelium. The research team revealed multiple viral particles located both inside and on the surface of nanotubes. Since the virus spreads more rapidly and directly from within nanotubes than by exiting one cell to move to the next via a receptor, this mode of transmission therefore contributes to the infectious capacity of SARS-CoV-2 and its spread to neuronal cells.

But the virus also moves on the external surface of nanotubes, where it can be guided more quickly to cells that express compatible receptors. "Nanotubes can be seen as tunnels with a road on top," suggests Chiara Zurzolo, Head of the Institut Pasteur's Membrane Traffic and Pathogenesis Unit, "which enable the infection of nonpermissive cells like neurons but also facilitate the spread of infection between permissive cells."

Read more here: https://www.eurekalert.org/news-releases/959801

For a technical discussion of the study: https://www.science.org/doi/10.1126/sciadv.abo0171

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Coronavirus Jumped to Humans at Least Twice at Market in Wuhan, China
July 26, 2022

Introduction:

(EurekAlert) In a pair of related studies, published July 26, 2022 online via First Release in Science
( https://www.science.org/doi/10.1126/science.abp8337), researchers at University of California San Diego, with colleagues on four continents, show that the origin of the COVID-19 pandemic in 2019 was at the Huanan Seafood Wholesale Market in Wuhan, China, and resulted from at least two instances of the SARS-CoV-2 virus jumping from live animal hosts to humans working or shopping there.

The findings, first reported in February after the papers were posted online as preprints awaiting peer review, garnered international attention, primarily focusing on identifying the market as the early epicenter of the COVID-19 pandemic. The World Health Organization estimates that there have been more than 566 million confirmed cases of COVID-19 worldwide and 6.3 million deaths since the pandemic was declared in early 2020.

“It’s vital that we know as much about the origin of COVID-19 as possible because only by understanding how pandemics get started can we hope to prevent them in the future,” said Joel O. Wertheim, PhD, associate professor in the Division of Infectious Diseases and Global Public Health at UC San Diego School of Medicine, and a co-author on both papers.

Further extract:

(The findings undercut a circulating and persistent theory that the SARS-CoV-2 virus escaped from the Wuhan Institute of Virology, located a few miles from the market.)

Read more here: https://www.eurekalert.org/news-releases/959920

Edit: The study is also discussed in this article: https://www.sciencealert.com/scientists ... f-covid-19