Study finds coronavirus-related bat viruses in Thailand

 A team led by investigators in Thailand and Singapore has tracked down SARS-CoV-2-related coronaviruses, dubbed SC2r-CoVs, in bats from a cave in Thailand, highlighting the broad distribution and genetic diversity of potential progenitor viruses.

"Although the origin of the virus remains unresolved, our study extended the geographic distribution of SC2r-CoVs from Japan and China to Thailand over a 4,800-km range," co-senior authors Lin-Fa Wang and Thiravat Hemachudha, researchers with Chulalongkorn University's Thai Red Cross Emerging Infectious Diseases Health Science Centre, and their co-authors wrote in Nature Communications on Tuesday.

Starting with surveillance screening for SARS-related coronaviruses in rectal swab or blood samples from 100 Acuminatus horseshoe bats (Rhinolophus acuminatus) in Thailand and 10 pangolins at wildlife checkpoints in the country, Wang, Hemachudha, and their colleagues identified SC2r-CoV isolates in five bats from a wildlife sanctuary in eastern Thailand. Their subsequent whole-genome sequencing and phylogenetic analyses suggested that the Thai bats carried SC2r-CoVs with genetic ties to a viral isolate known as RmYN02 detected in R. malayanus bats from Yunnan in China.

"[T]he current study provides further experimental evidence to support the notion that the distribution of SC2r-CoVs is not limited to China," the authors reported. "Southeast Asia, due to its richness in both relevant bat species diversity and population density, may be more likely to be a hotspot for such viruses."

Using serological testing, meanwhile, the team detected SARS-CoV-2 neutralizing antibodies with activity against the receptor binding domain of SARS-CoV-2 in wild animals in Thailand — not only in R. acuminatus bats from the Thai cave, but also in at least one Malayan pangolin (Manis javanica) tested at a wildlife checkpoint station in southern Thailand.

The results are consistent with the notion that pangolins are prone to infection with viruses resembling SARS-CoV-2 or SARS-CoV. Indeed, prior studies have pointed to SARS-CoV-related viruses in bats and pangolins as clues to the potential reservoir for the virus behind the COVID-19 pandemic.

Even so, the authors of the current study cautioned that their work "is unable to differentiate the role of pangolins as a spillover host from a secondary reservoir host."

"Further investigation with more systemic and longitudinal sampling of animals in their natural habitat is required to better understand the role of pangolins in transmitting and/or maintaining [SARS-related coronaviruses]," the authors wrote, concluding that "rich diversity of SC2r-CoVs in the region suggests that there is a high probability to find the immediate progenitor virus of SARS-CoV-2 with intensified and internationally coordinated surveillance."

https://www.modernhealthcare.com/safety-quality/study-finds-coronavirus-related-bat-viruses-thailand

CRISPR-Based SARS-CoV-2 Test From UC Santa Barbara Shows High Sensitivity for Asymptomatic

 A new CRISPR-based molecular diagnostic for SARS-CoV-2 aims to make COVID-19 screening more equitable and broadly deployed.

As described Thursday in JAMA Network Open, the method — called Cas13-based, rugged, equitable, scalable testing, or CREST — showed high concordance with gold-standard testing.

CREST was used to evaluate self-collected oropharyngeal swabs from more than 1,800 students and staff at University of California, Santa Barbara in two test periods over late May and early July of last year.

The asymptomatic screening did not pick up any positive cases in a first cohort. In a second cohort of 1,000 people, however, the CREST method was able to detect eight out of nine positive samples also detected using gold standard RT-PCR testing — namely the US Food and Drug Administration Emergency Use Authorized-assay from the US Centers for Disease Control and Prevention.

The single discrepant test had positive results at the detection threshold for the N2 target in the CDC test. The authors concluded this represented a low viral copy number and further noted that the patient sample was not confirmed as positive by a separate diagnostic test performed in a CLIA-certified laboratory.

Carolina Arias, a microbiologist at UC Santa Barbara and lead researcher on the study, commented in an email that overall, CREST is "an equitable and accessible assay that could aid in bringing widespread testing to areas in need."

Arias and her team developed CREST out of the imperative for an alternative assay for COVID-19 that would not rely on standardized methods or add strain to the already overburdened supply chain.

The method was honed very early in the pandemic, Arias said, with a proof-of-concept study initially posted to bioRxiv in April of last year. The team was subsequently motivated to carry out its JAMA study by a need to track the prevalence of SARS-CoV-2 in the population at UCSB, she said.

The JAMA results were surprising in a few ways, she noted. The team "saw a complete shift in the prevalence of the virus" from the first cohort to the second one, Arias said, and was able to detect the leading edge of an outbreak.

It was also surprised to find asymptomatic individuals with very high estimated viral loads, and to discover that self-sampling was "equally robust," and could thus eliminate the need for skilled medical personnel to perform sample collection.

On the other hand, the team was unsurprised by the high concordance between CREST and RT-qPCR. "We designed CREST to be sensitive, yet accessible," Arias said.

CREST is a cousin of more standard CRISPR technologies, relying on Cas13, an RNA-guided RNA endonuclease that cleaves single-stranded RNA.

According to the bioRxiv proof-of-concept study, CREST addresses the hurdles of reagent accessibility, equipment availability, and cost that otherwise limit the scalability of Cas13-based testing through "taking advantage of widely available enzymes, low-cost thermocyclers, and easy-to-use fluorescent visualizers."

From sample to result, the reaction takes about two hours with minimal handling, and does not require AC power or a dedicated facility.

The proof-of-concept study also highlighted that the readout signal "saturates even at low input levels." Therefore, "CREST offers the added advantage of binary result interpretation, similar to lateral flow test strips, but at a fraction of the price as it does not require the costly antibodies or antibody-conjugates needed for lateral flow immunochromatography."

The authors of the original bioRxiv study noted that Cas13 is not yet commercially available. The team was able to purify enough protein from a 1-liter bacterial culture for more than 500,000 reactions, however, and the authors said they can provide aliquots of protein upon request.

Now, Arias and her team at USCB is modifying CREST for rapid identification of viral variants. It is also continuing to work on the portability of CREST, developing a "COVID-19 lab-in-a-backpack," she said, which contains all reagents and equipment required for the assay. Portability could potentially aid the team's collaborators in developing countries and bring the assay to remote areas to facilitate testing.

Going forward, the CREST method is "versatile by design," Arias also said, and so could be easily modified for other medical needs as well as applied areas like veterinary and agricultural applications.

Overall, the ongoing SARS-CoV-2 pandemic has accelerated development of CRISPR-based diagnostics. So far, these have included assays deploying Cas13 developed by researchers at UC Berkeley, and teams in Thailand and China. Assays using a similar protein, Cas12, are also being developed such as ones from Mammoth Biosciences and startup Caspr Biotech, as are assays using a variety of Cas proteins, such as the Emergency Use Authorized SARS-CoV-2 test from SHERLOCK Biosciences

https://www.360dx.com/molecular-diagnostics/crispr-based-sars-cov-2-test-uc-santa-barbara-shows-high-sensitivity

UK government in talks with IATA, US and Singapore on ‘vaccine passports’

 The UK’s transport secretary Grant Shapps has said that he is talking to his counterparts in the US and Singapore as well as international organisations such as ICAO about establishing an internationally recognised system that would indicate whether people had been vaccinated against Covid and the results of any tests for the virus.

Shapps, speaking on BBC Radio 4’s Today programme, would not be drawn on whether such a system would amount to the “vaccine passport” that had been much discussed in recent days. 

Today's presenters also revealed that airline body IATA was in discussions with the UK government about the use of its digital health passport and that talks with the UK were more advanced than with any other country.

Shapps’ comments come days after the UK’s vaccine minister Nadhim Zahawi said that the government was not looking into the concept because it would be "discriminatory".

Shapps said that the confusion came because the vaccine passport term is also being used when referring to domestic access to services, which he ruled out.

“Sometimes it is used as a casual term, for example, will you need a vaccine passport to go to the pub?” he said.

The transport secretary argued that the international system is just an extension of the existing yellow fever cards that are required by certain countries.

“I imagine there will be countries which will want to know if you have been vaccinated or have had tests,” he said.

Greece and Israel have recently agreed to remove quarantine for travellers between the countries who can prove they have been vaccinated or have had the disease in the past six months.

https://www.businesstravelnewseurope.com/Air-Travel/UK-government-in-talks-with-IATA-US-and-Singapore-on-vaccine-passports-

Fed aid at stake, Alaska Legislature fails to extend COVID state of emergency

 The Alaska Legislature on Friday failed to extend Alaska’s COVID-19 state of emergency, leaving the state on track to lose millions of dollars in federal aid and powers being used to coordinate the distribution of COVID-19 vaccines and treatment.

“The simple answer is we do not have a functional legislature right now,” said Senate President Peter Micciche, R-Soldotna.

Alaska has been in a COVID-19 emergency since March 2020, but the emergency is set to expire at midnight Sunday morning, and no legislative action is scheduled before then.

Even on Friday, many legislators had left the state Capitol, missing a final opportunity for action. Meanwhile, the head of the state hospital and nursing home association said that the looming emergency declaration expiration would lead to disarray among agencies and organizations involved in the pandemic response, calling it “a mess.”

According to a list of impacts compiled by the state Department of Health and Social Services and public testimony from department officials:

• Food stamp payments will decline as the state loses $8 million per month in federal aid given to states with a disaster declaration.

• COVID-19 screening at airports will become optional, not mandatory, for travelers entering the state.

• Temporary housing will no longer be available for travelers who test positive for COVID and need to be quarantined, or for Alaska’s homeless who test positive.

• The state will be unable to set up emergency COVID-19 treatment centers in places like the Alaska Airlines Center.

• The state will be unable to manage the rationing of vaccines for small towns and boroughs without health powers.

The state House remained unorganized and unable to take action on Friday, one day after Rep. Louise Stutes, R-Kodiak, was named speaker of the House. Stutes said the House lacked a quorum to conduct business.

With the House unable to consider a Senate bill extending the emergency for 30 days, the state Senate shelved plans to approve the bill and instead passed a nonbinding resolution asking Gov. Mike Dunleavy to act unilaterally and issue a new emergency declaration.

A governor-declared and Legislature-extended emergency expired in November, and the governor has issued 30-day declarations of emergency three times since then.

“Please, for God’s sake, let’s tell the governor that we need him to create a new order,” Micciche said.

Thirty-five members of the state House have signed letters asking Dunleavy to take action and issue a fifth COVID-19 disaster declaration.

But Dunleavy has indicated he may not be willing to follow that request.

Earlier this week, he said an extension of the emergency was up to the Legislature and the Legislature’s own attorneys, analyzing an early version of the Senate resolution, said unilateral action by the governor “is likely not permitted by law.”

On Friday afternoon, Dunleavy issued a statement:

“In the absence of a declaration, my administration is fully prepared to manage the rollout and distribution of the vaccine to ensure anyone that wants a vaccination will be able to get one. We will also continue to respond to COVID-19 as we begin the process of getting back to normal as soon as possible by focusing on the economy and assisting Alaskans in staying healthy. As we move forward, we will notify Alaska and stakeholders of our plans.”

Jared Kosin, president and CEO of the Alaska State Hospital and Nursing Home Association, said that the potential expiration meant confusion and frustration for many entities in Alaska.

“What does the world look like without an emergency declaration? It’s not going to look any different to the general public, but for operators, for health care operators, for local governments, for even businesses, it’s going to look very chaotic,” Kosin said Saturday. “It’s going to be full of uncertainties. And it’s going to be full of analyses, trying to figure out what you’re about to lose.”

Kosin noted that an Alaska facility said, after consulting with its legal team, that it would have to shut down its COVID-19 testing site on Monday if the declaration lapsed Sunday.

“They don’t feel like they can reasonably operate without basically being in violation of requirements,” Kosin said. “And they’re going to try and restructure the deal so that the testing site can continue, but it’s completely thrown into the air.”

The ability for someone in Alaska to bypass travel and instead receive telehealth care from a cancer doctor or specialist in the Lower 48 under the arrangement would disappear, Kosin said.

That could potentially have a big effect on people who receive complex care. They might have their care disrupted or end up being forced to travel for care, he said.

There are still a lot of unknowns as expiration looms.

“It’s a mess,” Kosin said. “It’s a complete mess.”

https://www.adn.com/politics/alaska-legislature/2021/02/12/alaska-legislature-fails-to-extend-covid-19-state-of-emergency/

‘Universal Covid vaccine’ could be developed within a year

 A universal vaccine with the potential to be effective against all Covid-19 variants could be developed within a year, according to researchers.

The so-called second generation jab, developed by scientists at the University of Nottingham, targets the core of the virus as well as the surface spike protein.

If successful, the DNA vaccine could help protect against not only Covid-19 but also against any new strains of coronavirus that arise in the future.

It comes after AstraZeneca and the University of Oxford said their vaccine had been found to provide only limited protection against mild and moderate disease caused by the South African variant of Covid-19.

The Pfizer and AstraZeneca vaccines only target the spike protein, which enables the virus to gain entry into a cell, and so may lose effectiveness when it mutates.

However, researchers say the nucleocapsid (N) protein, which makes up the bulk of the virus particle, is "highly conserved" – meaning much less likely to mutate.

The Nottingham vaccine would also be relatively simple to manufacture and would not need to be stored in ultra-low temperatures, according to Scancell.

“We don’t necessarily claim it will be a pan-coronavirus vaccine, but it has got the potential to be so simply because of where it is targeted," Dr Gillies O’Bryan-Tear, the chief medical officer of the immunology company Scancell which collaborates with the University of Nottingham, told the Daily Telegraph.

Dr O'Bryan-Tear said that the vaccine candidate needed a big pharmaceutical partner and hundreds of millions of pounds to put it through the clinical trials process.

If this funding is in place then it could be developed within a year.

"There is no reason why, if we get a partner, we shouldn't be able to do it as quickly as the others have done it," Dr O'Bryan-Tear told the Telegraph.

"I think the pandemic will be around for two or three more years, because of supply, because of not being able to vaccinate developing countries. During that time, the virus will mutate, so there are plenty of opportunities for new entrants to try their hand."

https://www.independent.co.uk/news/health/covid-vaccine-variant-universal-nottingham-scancell-b1801966.html

Mexico gets AstraZeneca doses from India, expects more Pfizer

 Mexico received a shipment of 870,000 doses of AstraZeneca’s COVID-19 vaccine from India on Sunday, the government said, as the country prepares to prioritize older adults in the next phase of its vaccination campaign.

Mexico is also expecting shipments of Pfizer’s vaccine to resume, with 494,000 doses due to arrive on Tuesday, Foreign Minister Marcelo Ebrard told a news conference.

Sunday’s shipment amounts to about 42% of the two million doses of the AstraZeneca and Oxford University vaccine the country plans to import from India, in addition to packaging it locally, the government said.

Mexico and Argentina have an agreement with AstraZeneca to produce the vaccine for eventual distribution of 250 million doses in Latin America, with financial support from the foundation of Mexican billionaire Carlos Slim.

Mexico, which has one of the world’s highest coronavirus death tolls, started vaccinating healthcare workers in December but struggled to hit its targets amid global shortages and delays of Pfizer’s vaccine.

Mexico will next vaccinate adults over the age of 60, a group representing 12% of Mexico’s 126 million people, between February and April.

“The vaccines are already available.... and they will not stop arriving so that the national vaccination plan does not stop,” President Andres Manuel Lopez Obrador said at the news conference in the southwestern state of Oaxaca.

Latin America’s no. 2 economy has so far received just 1,636,350 vaccine doses, according to government data, but has agreements for millions more, including for China’s CanSino and the Russian Sputnik V. Mexico received the active ingredient for 2 million doses of the CanSino vaccine on Thursday.

Additionally, Mexico has secured enough vaccines to cover 20% of its population through the global COVAX facility, led by the GAVI vaccines alliance and the World Health Organization, though shipments have yet to begin.

https://www.reuters.com/article/us-health-coronavirus-mexico-vaccines/mexico-gets-astrazeneca-doses-from-india-expects-more-pfizer-as-it-prepares-for-next-phase-idUSKBN2AE0HW

Learning how to lose

 

On the surface, it seems like a strange idea:  We become winners when we learn how to lose.  It's when we can't accept losing that we hold onto trades long after they've gone against us.  It's when we can't accept losing that we play small ball and never pursue meaningful rewards.  It's when we can't accept losing that we become frustrated during drawdowns and lose our focus and discipline.  It's when we can accept losing that the good entry in a trade is never good enough and we miss opportunity.

So many of the challenges of trading psychology are rooted in our inability to lose.

When we can accept--truly accept--that trading is a probabilistic game, that losing is part of those probabilities, and that we can trade well and lose, our egos no longer become attached to our P/L.  If we go to a Vegas casino and bet large when we hold two pair, we can lose when someone around the table comes up with three Kings.  We were right to bet large and, over time, that bet is likely to pay off.  If we can't accept losing, however, we will not just lose but be defeated.  That will prevent us from placing the next solid bet, or it could frustrate us and place us in revenge mode, betting even larger on a poor hand.

Learning how to lose means losing in a planned manner.  It means knowing when our trade has been proven wrong and exiting at a point that we have rehearsed and accepted.  It means sizing our bets so that the probabilities going against us won't take us out of the game.  If we run a 60% win rate with our trades over time--which would be quite good--the reality is that we will lose several times in a row many times during the year if we trade often, simply by random chance.  If we can't accept that kind of losing, can we truly hang in there to win?

Traders work on improving their trading and that is necessary for success.  Working on losing is equally important.  A great topic for a trading review is:  Did I do a good job of losing?  The odds can never work in our favor if we don't fully embrace those odds.

http://traderfeed.blogspot.com/2021/02/learning-how-to-lose.html