COVID-19 News and Discussions

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caltrek
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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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