What’s for Dinner?

Home-cooked 4-course Western Dinner

The Menu

Potato and Peapod Dressed with Anchovy

Sardine with Chicory, Japanese Orange, and Quesatilla

Spagehtti with Shirasu Fish and Cheese

Dessert – French Tarte Tatin

Quick Chicken Ragu

Ingredients

2 tablespoons extra-virgin olive oil
2 tablespoons unsalted butter
1 (1/4-pound) piece pancetta (Italian unsmoked cured bacon), cut into 1/4-inch dice (2/3 cup)
1 tablespoon finely chopped fresh sage
1-1/2 teaspoons finely chopped fresh rosemary
1-1/2 pounds skinless boneless chicken thighs, cut into 1-inch pieces
1 medium onion, chopped
1 medium carrot, chopped
1 celery rib, chopped
1 cup light dry red wine, such as Pinot Nair
1 (14- to 15-ounce) can diced tomatoes in juice, drained
coarse gray sea salt
coarsely ground black pepper

Method

  1. Heat oil and butter in a 12-inch heavy skillet (2 inches deep) over medium heat until hot but not smoking. Add pancetta and cook, stirring occasionally, 2 minutes.
  2. Add sage and rosemary and cook, stirring, 30 seconds.
  3. Add chicken and cook, stirring occasionally, until chicken is no longer pink on outside, 2 to 3 minutes.
  4. Add onion, carrot, and celery and cook, stirring occasionally, until softened, 5 to 7 minutes.
  5. Add wine and simmer, uncovered, stirring occasionally, until liquid is reduced to about 1 cup, about 10 minutes.
  6. Add tomatoes, 1/2 teaspoon sea salt, and 1/2 teaspoon pepper and simmer, stirring occasionally, until sauce is thickened, 5 to 10 minutes.
  7. Season with salt and pepper and serve over polenta.

Makes 4 servings.

Source: Gourmet Italian

COVID-19: Genetic Network Analysis Provides ‘Snapshot’ of Pandemic Origins

Researchers from Cambridge, UK, and Germany have reconstructed the early ‘evolutionary paths’ of COVID-19 in humans – as infection spread from Wuhan out to Europe and North America – using genetic network techniques.’

By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

“There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously,” said geneticist Dr Peter Forster, lead author from the University of Cambridge.

“These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is one of the first times they have been used to trace the infection routes of a coronavirus like COVID-19.”

The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct ‘variants’ of COVID-19, consisting of clusters of closely related lineages, which they label ‘A’, ‘B’ and ‘C’.

Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats – type ‘A’, the “original human virus genome” – was present in Wuhan, but surprisingly was not the city’s predominant virus type.

Versions of ‘A’ were seen in Chinese individuals, and Americans reported to have lived in Wuhan, and mutated versions of ‘A’ were found in patients from the USA and Australia.

Wuhan’s major virus type, ‘B’, was prevalent in patients from across East Asia. However, the variant didn’t travel much beyond the region without further mutations – implying a ‘founder event’ in Wuhan, or ‘resistance’ against this type of COVID-19 outside East Asia, say researchers.

The ‘C’ variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study’s Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on 27 January, and that another early Italian infection route was related to a ‘Singapore cluster’.

Importantly, the researchers say that their genetic networking techniques accurately traced established infection routes: the mutations and viral lineages joined the dots between known cases.

As such, the scientists argue that these ‘phylogenetic’ methods could be applied to the very latest coronavirus genome sequencing to help predict future global hot spots of disease transmission and surge.

“Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide,” said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as the University’s Institute of Continuing Education.

The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at http://www.fluxus-technology.com.

Variant ‘A’, most closely related to the virus found in both bats and pangolins, is described as ‘the root of the outbreak’ by researchers. Type ‘B’ is derived from ‘A’, separated by two mutations, then ‘C’ is in turn a “daughter” of ‘B’.

Researchers say the localisation of the ‘B’ variant to East Asia could result from a ‘founder effect’: a genetic bottleneck that occurs when, in the case of a virus, a new type is established from a small, isolated group of infections.

Forster argues that there is another explanation worth considering. “The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase.”

He added: “The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It’s like catching an incipient supernova in the act.”

Since today’s PNAS study was conducted, the research team has extended its analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans of COVID-19 occurred between mid-September and early December.

The phylogenetic network methods used by researchers – allowing the visualisation of hundreds of evolutionary trees simultaneously in one simple graph – were pioneered in New Zealand in 1979, then developed by German mathematicians in the 1990s.

These techniques came to the attention of archaeologist Professor Colin Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to establish one of the first archaeogenetics research groups in the world at the University of Cambridge.

Source: University of Cambridge

False-negative COVID-19 Test Results may Lead to False Sense of Security

Jay Furst wrote . . . . . . . . .

As COVID-19 testing becomes more widely available, it’s vital that health care providers and public health officials understand the limitations of COVID-19 testing and the impact that false results can have on public safety and efforts to curb the pandemic.

A special article published in Mayo Clinic Proceedings calls attention to the risk posed by over-reliance on COVID-19 testing to make clinical and public health decisions. The sensitivity of reverse transcriptase–polymerase chain reaction (RT-PCR) testing and overall test performance characteristics have not been reported clearly or consistently in medical literature, the article says.

As a result, health care officials should expect a “less visible second wave of infection from people with false-negative test results,” says Priya Sampathkumar, M.D., an infectious diseases specialist at Mayo Clinic and a study co-author.

“RT-PCR testing is most useful when it is positive,” says Dr. Sampathkumar. “It is less useful in ruling out COVID-19. A negative test often does not mean the person does not have the disease, and test results need to be considered in the context of patient characteristics and exposure.”

Even with test sensitivity values as high as 90%, the magnitude of risk from false test results will be substantial as the number of people tested grows. “In California, estimates say the rate of COVID-19 infection may exceed 50% by mid-May 2020,” she says. “With a population of 40 million people, 2 million false-negative results would be expected in California with comprehensive testing. Even if only 1% of the population was tested, 20,000 false-negative results would be expected.”

The authors also cite the effects on health care personnel. If the COVID-19 infection rate among the more than 4 million people providing direct patient care in the U.S. were 10% — far below most predictions ­­— more than 40,000 false-negative results would be expected if every provider were tested.

This poses risks for the health care system at a critical time. “Currently, CDC (Centers for Disease Control and Prevention) guidelines for asymptomatic health care workers with negative testing could lead to their immediate return to work in routine clinical care, which risks spreading disease,” says Colin West, M.D., Ph.D., a Mayo Clinic physician and the study’s first author. Victor Montori, M.D., a Mayo Clinic endocrinologist, also is a co-author.

While dealing with the enormity of the growing COVID-19 pandemic, it’s important for public health officials to stick to principles of evidence-based reasoning regarding diagnostic test results and false-negatives. Four recommendations are outlined in the Mayo Clinic article:

  • Continued strict adherence to physical distancing, hand-washing, surface disinfection and other preventive measures, regardless of risk level, symptoms or COVID-19 test results. Universal masking of both health care workers and patients may be necessary.
  • Development of highly sensitive tests or combinations of tests is needed urgently to minimize the risk of false-negative results. Improved RT-PCR testing and serological assays — blood tests that identify antibodies or proteins present when the body is responding to infections such as COVID-19 — are needed.
  • Risk levels must be carefully assessed prior to testing, and negative test results should be viewed cautiously, especially for people in higher-risk groups and in areas where widespread COVID-19 infection has been confirmed.
  • Risk-stratified protocols to manage negative COVID-19 test results are needed, and they must evolve as more statistics become available.

“For truly low-risk individuals, negative test results may be sufficiently reassuring,” says Dr. West. “For higher-risk individuals, even those without symptoms, the risk of false-negative test results requires additional measures to protect against the spread of disease, such as extended self-isolation.”

At Mayo Clinic, RT-PCR testing is “one of many factors we take into account in deciding whether the patient meets criteria for COVID-19,” Dr. Sampathkumar says. If the RT-PCR test is negative but chest X-ray or CT scan results are abnormal, or there has been close contact with a person who has confirmed COVID-19, the recommendation is to continue caring for the patient as if he or she has COVID-19.

“We need to continue to refine protocols for asymptomatic patients and exposed health care workers,” says Dr. Sampathkumar.

Source: Mayo Clinic


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