Scientists Find 140,000 Virus Species in The Human Gut, And Most Are Unknown – ScienceAlert

The coronavirus pandemic has had the world fixated on viruses like no time in living memory, but new evidence reveals humans never even notice the vast extent of viral existence – even when it’s inside us.


A new database project compiled by scientists has identified over 140,000 viral species that dwell in the human gut – a giant catalogue that’s all the more stunning given over half of these viruses were previously unknown to science.

If tens of thousands of newly discovered viruses sounds like an alarming development, that’s completely understandable. But we shouldn’t misinterpret what these viruses within us actually represent, researchers say.

“It’s important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem,” explains biochemist Alexandre Almeida from the European Molecular Biology Laboratory’s Bioinformatics Institute (EMBL-EBI) and the Wellcome Sanger Institute.

“These samples came mainly from healthy individuals who didn’t share any specific diseases.”

The new virus catalogue – called the Gut Phage Database (GPD) – was complied by analyzing over 28,000 individual metagenomes – publicly available records of DNA-sequencing of gut microbiome samples collected from 28 countries – along with almost 2,900 reference genomes of cultured gut bacteria.

The results revealed 142,809 viral species that reside in the human gut, constituting a specific kind of virus known as a bacteriophage, which infects bacteria, in addition to single-celled organisms called archaea.


In the mysterious environment of the gut microbiome – inhabited by a diverse mixture of microscopic organisms, encompassing both bacteria and viruses – bacteriophages are thought to play an important role, regulating both bacteria and the health of the human gut itself.

“Bacteriophages … profoundly influence microbial communities by functioning as vectors of horizontal gene transfer, encoding accessory functions of benefit to host bacterial species, and promoting dynamic co-evolutionary interactions,” the researchers write in their new paper.

For a long time, our knowledge of this phenomenon was stalled by limitations in our understanding of bacteriophage species.

In recent years, new advancements in metagenomic analyses have significantly expanded our awareness of the viral variety we’re looking at here – and perhaps none more so than the Gut Phage Database, which the researchers describe as a “massive expansion of human gut bacteriophage diversity”.

“To our knowledge, this set represents the most comprehensive and complete collection of human gut phage genomes to date,” the study authors write.

“Having a comprehensive database of high-quality phage genomes paves the way for a multitude of analyses of the human gut virome at a greatly improved resolution, enabling the association of specific viral clades with distinct microbiome phenotypes.”


Already, the database is updating what we know about viral behavior.

The research shows over one-third (36 percent) of viral clusters identified are not restricted to infecting a single species of bacteria, which means they can create gene flow networks across phylogenetically distinct bacterial species.

In addition, the researchers found 280 globally distributed viral clusters, including one newly identified clade, called Gubaphage, which appears to be the second most prevalent virus clade in the human gut, following what is known as the crAssphage group.

Given certain similarities between the two, the researchers initially thought the Gubaphage might belong to a proposed family of crAssphage-like viruses, before determining the clades were, in fact, distinct.

There is still so much to learn, and not just on the Gubaphage – but about more multitudes of viruses than we ever dared to dream. Thanks to research efforts like this, though, tomorrow’s discoveries are closer, and new insights will come faster.

“Bacteriophage research is currently experiencing a renaissance,” says microbiologist Trevor Lawley from the Wellcome Sanger Institute.

“This high-quality, large-scale catalogue of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.”

The findings are reported in Cell.



Up to six cases of Manaus variant of coronavirus detected in UK – Reuters

LONDON (Reuters) – Up to six cases of a highly transmissible variant of coronavirus first identified in the Brazilian city of Manaus have been detected in Britain for the first time, English health officials said on Sunday.

FILE PHOTO: Medical workers move a patient between ambulances outside of the Royal London Hospital amid the spread of the coronavirus disease (COVID-19) pandemic, London, Britain, January 27, 2021. REUTERS/Toby Melville

Three cases were found in England and another three in Scotland.

Two of three cases found in England were from a household in the South Gloucestershire area that had a history of travel to Brazil. A third, currently unlinked, case has yet to be identified, Public Health England said.

The risk to the wider community from the Gloucestershire cases was considered low but as a precaution officials were moving quickly to deploy testing and increasing the sequencing of positive coronavirus samples from the area, PHE said.

The Scottish cases were not linked to the ones in England.

The P.1 variant detected in Manaus shares some mutations with a variant first identified in South Africa and it is possible that it might respond less well to current vaccines, PHE said.

Susan Hopkins, PHE’s strategic response director for COVID-19, said Britain’s advanced gene sequencing capabilities meant it was finding more variants and mutations than many other countries.

Late last year Britain detected a more transmissible variant of coronavirus that is believed to have originated near London and that led to a sharp rise in cases in the country and beyond.

“The important thing to remember is that COVID-19, no matter what variant it is, spreads in the same way. That means the measures to stop it spreading do not change,” Hopkins said.

PHE and test and trace officials system were following up with all passengers on Swiss Air flight LX318 from Sao Paulo to London via Zurich, which landed at London Heathrow on Feb. 10, to test them and their households.

All three of the Scottish cases were identified in people who returned to the country via Paris and London who self-isolated for the required period of 10 days.

“Due to the potential concerns around this variant other passengers on the flight used by the three individuals from London to Aberdeen are being contacted,” the Scottish government said.

Writing by William Schomberg; Editing by Jane Merriman and Frances Kerry


Our Chicago: Help UChicago Medicine researchers discover if vitamin D can reduce the risks of COVID-19 – WLS-TV

CHICAGO (WLS) — There has been some encouraging news this past week in the fight against COVID-19.

Illinois is administering more vaccines, even setting records.

The state’s test positivity rate remains low. And there’s more news about the vaccine from Johnson and Johnson.

Talking about these developments and what’s ahead is Dr. Michael Bauer, medical director at Northwestern Medicine Lake Forest Hospital.

WATCH: Our Chicago Part 1

And in our second half, Dr. David Meltzer, the Chief of Hospital Medicine at University of Chicago Medicine.

He’s leading research being done here looking at whether Vitamin-D supplements can reduce the risk and severity of COVID-19 particularly in Black and Latinx patients.

WATCH: Our Chicago Part 2

For information on the Vitamin D stud click here.

Copyright © 2021 WLS-TV. All Rights Reserved.


1,428 new COVID-19 cases, 52 additional deaths reported in Mass. – WCVB Boston

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Covid vaccine: More than 20 million people in UK have now received first dose – The Independent

More than 20 million people in the UK have now received their first dose of a Covid-19 vaccine, the health secretary has said.

Matt Hancock posted a video on his Twitter account with the announcement and thanked “every single person who’s come forward to get the jab”.

He said: “I’m absolutely delighted that over 20 million people have now been vaccinated across the UK – it’s absolutely fantastic.

“I want to thank every single person who’s come forward to get the jab because we know with increasing confidence that the jab protects you, it protects your community and it also is the route out of all of this for all of us.”

Nadhim Zahawi, the vaccines minister, also celebrated the news, tweeting: “BINGO! One score over 20,000,000 people have had the vaccination (1st dose). What an achievement for February 2021. What a team! Proud to be with you on this journey.”

The figure for the number of people getting their first dose of a vaccine on Saturday stood at 19.6 million.

NHS England has said that another two million people, aged between 60 and 63, are about to receive invitations for them to get vaccinated.

This next cohort will begin getting letters from Monday explaining how they can make an appointment to get a jab.

Professor Stephen Powis, the NHS national medical director, said: “The NHS vaccination programme, the biggest in the health service’s history and fastest in Europe, goes from strength to strength.

“I would like to thank my colleagues across the NHS, along with all the volunteers and others working on the programme, for their hard work which has seen more than 17 million jabs given in a matter of weeks.

“I would urge anyone who has been invited to take up the offer – it doesn’t matter when you were invited you can still come forward and protect yourself and others.”


Covid-19 Vaccines Yield Breakthroughs in Long-Term Fight Against Infectious Disease – The Wall Street Journal

The pandemic has opened a new era for vaccines developed with gene-based technologies, techniques that have long stumped scientists and pharmaceutical companies, suggesting the possibility of future protection against a range of infectious disease.

Johnson & Johnson’s Covid-19 vaccine, which was authorized Saturday for use in the U.S., is at the vanguard of a class of shots designed to mobilize a person’s immune defenses against the disease. It will be the first Covid-19 vaccine administered in the U.S. that uses viral-vector technology, which employs an engineered cold virus to ferry coronavirus-fighting genetic code to the body’s cells.

J&J’s vaccine is the third to be authorized in the U.S. after ones from Pfizer Inc. and its partner, BioNTech SE , and Moderna Inc. In a late-stage trial, J&J’s single-shot vaccine was 66% effective in preventing moderate to severe cases of the disease that has killed more than 500,000 people in the U.S. and about 2.5 million world-wide.

“This is one of those giant leap moments for us. These are fundamental shifts in how we will build vaccines for the future,” said C. Buddy Creech, director of Vanderbilt University’s vaccine research program. “I think this really ushers in a golden age of vaccinology.”

New vaccine technologies spurred by the pandemic are leading efforts to combat Covid-19 and herald a new arsenal of weapons for fighting lethal viruses in the future, infectious-disease researchers said, another example of how the fight against Covid has supercharged technological development.


N.J. reports 2,171 new COVID cases, 15 additional deaths –

New Jersey health officials announced 2,171 confirmed coronavirus cases on Sunday and 15 additional deaths as hospitalizations continued to fall and the state prepares to welcome sports fans back into arenas.

Continuing on a steady decrease, the number of people hospitalized with coronavirus as of Friday night dropped to 1,849 — the lowest it has been since Nov. 12, according to state data.

Gov. Phil Murphy announced the latest numbers on Twitter Sunday afternoon.

New Jersey’s sports and entertainment venues will be allowed to welcome fans for the first time in nearly a year on Monday, with 10% capacity limits on large indoor venues. Outdoor venues can have 15% capacity in fixed seats. In addition to professional sports, a limited number of people will be allowed to attend collegiate games.

There have been 1,960,629 coronavirus vaccine doses administered in New Jersey as of Saturday afternoon, including 1,295,891 first doses and 663,855 second doses.

That’s out of more than 2.47 million doses the state has received, according to a running tally by the federal Centers for Disease Control and Prevention. The state’s goal is to vaccinate 70% of its adult population — about 4.7 million people — within the next few months.

Previously, Murphy said New Jersey could get an initial shipment of 70,000 doses of the single-dose Johnson & Johnson vaccine next week. The vaccine was approved for emergency use on Saturday.

The positivity rate for tests conducted on Tuesday, the most recent day available, was 6.38% based on 53,495 tests. The statewide rate of transmission increased to 0.91, up from .89. Any rate below 1 means the outbreak is slowing.

New Jersey has now reported 701,725 confirmed coronavirus cases out of more than 10.56 million PCR tests in the nearly 12 months since the state reported its first case March 4, 2020. There have also been 87,631 positive antigen tests. Those cases are considered probable, and health officials have warned that positive antigen tests could overlap with the confirmed PCR tests because they are sometimes given in tandem.

CORONAVIRUS RESOURCES: Live map tracker | Newsletter | Homepage

The state, which has 9 million people, reported 23,253 residents have died from complications related to COVID-19 including 2,331 fatalities considered probable. That includes 1,589 confirmed coronavirus deaths reported in February.

New Jersey has identified 63 cases of the COVID-19 variant first identified in the U.K. with eight new cases reported Friday.


  • ATLANTIC COUNTY – 59,983 doses administered
  • BERGEN COUNTY – 223,170 doses administered
  • BURLINGTON COUNTY – 100,094 doses administered
  • CAMDEN COUNTY – 111,622 doses administered
  • CAPE MAY COUNTY – 28,118 doses administered
  • CUMBERLAND COUNTY – 26,231 doses administered
  • ESSEX COUNTY – 156,101 doses administered
  • GLOUCESTER COUNTY – 67,869 doses administered
  • HUDSON COUNTY – 91,200 doses administered
  • HUNTERDON COUNTY – 24,180 doses administered
  • MERCER COUNTY – 56,013 doses administered
  • MIDDLESEX COUNTY – 150,213 doses administered
  • MONMOUTH COUNTY – 143,805 doses administered
  • MORRIS COUNTY – 144,748 doses administered
  • OCEAN COUNTY – 119,072 doses administered
  • PASSAIC COUNTY – 88,570 doses administered
  • SALEM COUNTY – 12,438 doses administered
  • SOMERSET COUNTY – 74,233 doses administered
  • SUSSEX COUNTY – 29,418 doses administered
  • UNION COUNTY – 94,493 doses administered
  • WARREN COUNTY – 17,917 doses administered
  • UNKNOWN COUNTY – 84,776 doses administered
  • OUT OF STATE – 56,365 doses administered


There were 1,849 patients hospitalized with confirmed or suspected COVID-19 cases across New Jersey’s 71 hospitals as of Saturday night — 70 fewer than the previous night and the lowest since Nov. 12, according to the state’s dashboard.

That included 393 in critical or intensive care (11 fewer than the previous night), with 229 on ventilators (19 fewer).

There were also 245 COVID-19 patients discharged Saturday.

Hospitalizations peaked at more than 8,000 patients during the first wave of the pandemic in April.


New Jersey on Tuesday reported eight new in-school coronavirus outbreaks, bringing the total to 152 cases, which have resulted in 737 cases among students, teachers and school staff this academic year, according to the state’s dashboard.

New Jersey defines school outbreaks as cases where contact tracers determined two or more students or school staff caught or transmitted COVID-19 in the classroom or during academic activities at school.

School outbreaks have been reported in all 21 counties, according to the state.

Those numbers do not include students or staff believed to have been infected outside school or cases that can’t be confirmed as in-school outbreaks. Though the numbers keep rising every week, Murphy has said the school outbreak statistics remain below what state officials were expecting when schools reopened for in-person classes last summer.

There are about 1.4 million public school students and teachers across the state, though teaching methods amid the outbreak have varied, with some schools teaching in-person, some using a hybrid format and others remaining all-remote.


Broken down by age, those 30 to 49 years old make up the largest percentage of New Jersey residents who have caught the virus (31%), followed by those 50-64 (23.3%), 18-29 (19.5%), 65-79 (10.9%), 5-17 (8.4%), 80 and older (5%), and 0-4 (1.7%).

On average, the virus has been more deadly for older residents, especially those with preexisting conditions. Nearly half the state’s COVID-19 deaths have been among residents 80 and older (47.25%), followed by those 65-79 (32.76%), 50-64 (15.58%), 30-49 (4.02%), 18-29 (0.37%), 5-17 (0%), and 0-4 (0.02%).

At least 7,906 of the state’s COVID-19 deaths have been among residents and staff members at nursing homes and other long-term care facilities.

There are currently active outbreaks at 342 facilities, resulting in 6,413 active cases among residents and 6,538 among staffers.


As of early Saturday, there have been more than 113.89 million positive COVID-19 tests across the world, according to a running tally by Johns Hopkins University. More than 2.52 million people have died from coronavirus-related complications.

The U.S. has reported the most cases, at more than 28.5 million, and the most deaths, at more than 512,100.

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Katie Kausch may be reached at Tell us your coronavirus story or send a tip here.


Israel’s ahead-of-the-world vaccine rollout offers hope for countries lagging behind – The Washington Post

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Will Utahns wait their turn in line once vaccines open up for those with underlying conditions? – Salt Lake Tribune

The state will rely on the honor system for coronavirus protection, with no proof required that someone meets the new requirements for underlying conditions.

(Rick Egan | The Salt Lake Tribune) Julyn Shepherd fills syringes for Utah County residents to get their COVID-19 vaccinations in a former Shopko store in Spanish Fork, Wednesday, Jan. 27, 2021.

With the state now offering the COVID-19 vaccine to a large group of people with underlying health conditions, Utahns won’t be required to produce a doctor’s note or other proof they are eligible.

Instead, the state is relying on the honor system. It’s an effort to get shots into arms as quickly as possible, but it will almost surely result in abuse as people find there are relatively few obstacles that prevent them from skipping forward in line.

“It is possible for people to lie about whether or not they have one of these underlying health conditions,” Gov. Spencer Cox acknowledged at a news conference on Thursday, where he pleaded with Utahns to play by the rules.

But Tom Hudachko, a spokesman with the Utah Department of Health, said in an email that the department has determined it’s more important to ensure the process is simple and efficient for the approximately 275,000 Utah residents who have qualifying medical conditions than it is to make it overly cumbersome just so “a few others don’t get in line early,” he said.

Requiring paperwork as proof of eligibility would not only “significantly slow the process of getting vaccines into these peoples’ arms,” Hudachko said, but it would also place an “unnecessary burden on health care workers who would be responsible for providing such documentation.”

This shift to more widespread vaccine access comes as Utah’s death toll from the coronavirus approaches 2,000. But the seven-day average for the rate of positive coronavirus tests has been dropping, under both the state’s traditional measure — which still stood above 10% last week — and its new methodology, which hovered around 6% last week. The number of Utahns who are fully vaccinated with two doses topped 225,000 midweek, with that total likely to top 250,000 over the weekend.

What’s happening elsewhere?

As states begin making larger groups of residents eligible for vaccinations, they’ve taken different approaches to the question of whether to require paperwork to vaccinate people in a priority group.

It can be difficult to find information on each state’s rollout, but Washington, New Jersey, Massachusetts and Alabama have so far reported using the honor system.
In Texas, health care providers have been told to look at people’s medical records to determine their status for the shots, when possible. In other circumstances, people can disclose their underlying health conditions and receive the vaccine with no paperwork required, according to the Dallas Morning News.
At vaccination clinics operated by New York state, residents are required to provide proof of eligibility for underlying conditions with a doctor’s letter, medical information that shows evidence of their health condition or a signed certification, according to the state’s coronavirus information website.

While it remains to be seen how well the honor system will be implemented here, Margaret Battin, a professor of philosophy at the University of Utah, said she wondered whether the community influence of The Church of Jesus Christ of Latter-day Saints could affect the success of the policy.

“The teachings of the church … I think would tend to discourage behavior like cutting in line,” said Battin, who is also an adjunct professor in the U.’s medical ethics and humanities program within the Department of Internal Medicine. “All that ‘do the right’ and ‘choose the right,’ that kind of moral teaching might well play a role in the behavior of many people in this state that might not be so true in a more heterogenous state like New York.”

Hudachko said the decision was made primarily based on feedback from vaccine and health care providers that requiring paperwork would create “significant bottlenecks.” He said he hasn’t been able to make comparisons on which approach is more effective and noted that several states haven’t yet started vaccinating people with underlying health conditions.

Who gets the vaccine next?

Utahns 16 and older with certain severe and chronic health conditions are now eligible to receive COVID-19 vaccine. Here is a list of those qualifying health conditions, according to the Utah Department of Health:

• Solid organ transplant recipients.

• Certain cancers.

• People who are immunocompromised (have a weakened immune system) from blood, bone marrow or organ transplants; HIV; use of corticosteroids long-term, or use of other immune-weakening medicines long-term.

• Severe kidney disease or dialysis, or with stage 4 or 5 chronic kidney disease.

• Uncontrolled diabetes.

• Severe obesity (body mass index over 40).

• Chronic liver disease, including chronic hepatitis B or C.

• Chronic heart disease (not including hypertension).

• Severe chronic respiratory disease (other than asthma).

• Neurologic conditions that impair respiratory function, including Down syndrome, multiple sclerosis, Parkinson’s disease, cerebral palsy, quadriplegia or hemiplegia.

• Stroke and dementia (Alzheimer’s, vascular, frontotemporal).

• Asplenia, including splenectomy or a spleen dysfunction, including sickle cell disease.

While the honor system poses its own problems, Jim Tabery, an associate professor of philosophy at the U., said he thinks the vaccine rollout as planned is the “ethically appropriate way to go.”

“Obviously when you’re thinking about something like this, your mind naturally goes to kind of the vaccine line jumpers or the freeloaders,” he said. “There might be some of that out there, but the question is: What system are you envisioning creating that would weed them out? And would it in fact be a better system?”

Requiring people to jump through hoops to prove they have an underlying health condition could be “terribly invasive” for people with disabilities he said, and it could also pose equity issues in gaining access to the vaccine. Individuals within hard-hit communities of color, for example, may not have access to a health care provider to obtain proof of their condition or might struggle to get work off to get an appointment.

“If you’re dealing with someone [in that situation] who’s got diabetes and you’re saying, ‘In order to get the vaccine, we also need some sort of confirmation that you have diabetes,’ you’re essentially asking them to kind of go see a health care provider that they don’t have access to,” he said. “And so most likely what you’re doing is guaranteeing someone is not going to get access to a vaccine.”

Up to this point, it’s been “relatively simple” for vaccination providers to determine eligibility in Utah, Hudachko noted.

The first round of inoculations was largely based on employment, and it was easy for health care workers, teachers, first responders and long-term care facility staff to prove they qualified based on pay stubs or badges. And older adults have been able to “easily provide proof of age with a government-issued ID or similar document with their birth date listed,” he said.

Even so, Salt Lake County Health Department spokesman Nicholas Rupp said there have been a few instances where people have tried to “cheat the system” and have been turned away at a vaccination site.

“Fortunately, it isn’t a widespread problem,” he said. “We’ve had more people genuinely misunderstand their eligibility, but even those aren’t widespread.”

The county has not taken a position on the use of an honor system, but Rupp said the health department will follow the directions of the state and governor “and encourage people to be honest so vaccine goes first to those truly at the greatest risk of serious illness.”

(Rick Egan | The Salt Lake Tribune) A socially distance waiting area for Utah County residents to get their COVID-19 vaccinations in a former Shopko store in Spanish Fork, Wednesday, Jan. 27, 2021.

In announcing Thursday that the vaccines would be open to people with underlying conditions immediately, rather than the March 1 date previously planned, Cox noted that those who now qualify are at the highest risk for hospitalization and death because of COVID-19.

And he urged Utahns who aren’t eligible not to schedule appointments.

“We have so many more vaccines coming and they’re coming soon but we’re prioritizing these individuals — again based on age and these underlying comorbidities — because they are at the greatest risk of hospitalization or death,” he said. “So if you jump ahead in line, that means there is someone else who won’t get the vaccine as soon as they could have and it’s very possible that they could end up hospitalized, or even worse, dying.”

Those who follow the rules “can sleep well at night by knowing you didn��t cheat the system, that you were willing to give it to those who needed it the most,” he added.

Hudachko noted that every Utahn who is 16 and older who wants one is expected to have the opportunity to receive a vaccination by the end of May. People who are considering gaming the system to get their shot a few weeks early, he said, need to consider that “the person you are skipping ahead of is far more likely than you are to become seriously ill or even die if they were to become infected with COVID-19.”

As the state opens vaccines up to more people, Tabery said the most ethical thing those who aren’t eligible for one yet can do is wait their turn.

There are legitimate questions about fairness within the vaccine rollout, he noted. But if, say, a grocery store employee felt like he or she should have been included in the latest round of inoculations, the way to deal with that is to contact state leaders to voice that concern — not for someone to take matters into their own hands.

The exception to that rule, Tabery said, is a scenario in which there are excess doses that need to be used and will go bad if they aren’t. Both the Pfizer and Moderna vaccines must be stored at freezing temperatures and, once unthawed, have to be used within a certain time frame.

“If somebody were to find themselves in a situation where they just so happened to be at the hospital or at the pharmacy and the pharmacist or the nurse says, ‘Hey, we’ve got an extra dose. This is going to go to waste if you don’t use it,’ then it would be it would be wrong not to take that,” he said.

It’s likely many people will make these ethical calculations during this phase of the state’s rollout, but Battin indicated that social stigma and disapproval of people who do cut the line will be the primary defense against that behavior.

Tabery said he anticipates there will be times where people cut the vaccine line and that those instances, when identified, will make the news.

But he’s confident most Utahns will “play by these rules.”

“I do think there’s a kind of underlying communal mentality to the state of Utah, which serves it well in situations like this,” he said. “And so I’m sure there will be line cutters. I’m sorry that they found themselves in a situation where they felt like they had to or could do that. But I think they’re certainly going to be the exception — not the rule.”


Texas is diverting thousands of COVID-19 vaccine doses away from Dallas County, Judge Jenkins says –

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