Multitude of coronavirus variants found in the US — but the threat is unclear

‘For the scientists who have spent the past year poring over hundreds of thousands of coronavirus genomes, the United States has been an enigma. Despite having world-leading genome sequencing infrastructure and experiencing more COVID infections than any other country, the United States has until recently lagged far behind in sequencing coronavirus genomes and spotting worrisome variants.

‘But in recent weeks, US researchers have identified a host of new variants, including in California, New York State, Louisiana and elsewhere. And they are continuing to ramp up SARS-CoV-2 sequencing efforts.

‘That has brought another challenge: making sense of the variants that are discovered. They carry potentially worrying mutations and might be becoming more common, but a dearth of data on how the variants are spreading means the threat they pose is unclear.’

Read here (Nature, Mar 6, 2021)

Protein behind corona’s slow Asia spread: Study

‘Deficiency in a particular human protein, which is more common in Europe and the United States than in Asia, could explain why coronavirus is not spreading as fast in Asian countries. A team of scientists from the National Institute of Biomedical Genomics in Kalyani, West Bengal, have found a biological reason for the slower spread of a mutant of coronavirus in Asia compared to the West. The team has explained how higher levels of a human protein — neutrophil elastase — helps the virus to enter the human cell, multiply and also spread faster from infected individuals... 

“However, some naturally-occurring mutations in the AAT-producing gene results in deficiency of the AAT protein. This deficiency is known to be much higher in the Caucasians of Europe and America than among Asians,” said Majumder. “While we used AAT deficiency data from East Asia, along with North America and Europe, for the study, considering the pace at which the coronavirus is spreading, the numbers are representative of other Asian regions too, including India.”... 

‘As per their data, AAT deficiency is the least in East Asian countries — 8 per 1,000 individuals in Malaysia, 5.4 per 1,000 in South Korea, 2.5 in Singapore. On the other hand, 67.3 in per 1,000 individuals in Spain are AAT deficient, 34.6 in the UK and 51.9 in France and in the US it is prevalent in 29 individuals among 1,000.’

Read here (Times of India, Feb 9, 2021)

Research finds 5 genes linked to severest form of Covid-19

‘A study found five key genes central to many severe cases of COVID-19 and pointed to some existing drugs that could be repurposed to treat those at risk of getting critically ill from the disease...

‘Five key genes are linked with the severest form of COVID-19, scientists said on Friday, in research that also pointed to several existing drugs that could be repurposed to treat people who risk getting critically ill with the pandemic disease.

‘Researchers who studied the DNA of 2,700 COVID-19 patients in 208 intensive care units across the United Kingdom found that five genes involving in two molecular processes – antiviral immunity and lung inflammation – were central to many severe cases.’

Read here (Aljazeera, Dec 11, 2020)

The wisdom of pandemics

‘Viruses are active agents, existing within rich lifeworlds. A safe future depends on understanding this evolutionary story...

‘Researchers since then have uncovered evidence that pathogens exert ‘the strongest selective pressure to drive the evolution of modern humans’. Among the drivers, look to evidence that prehistoric pandemics played a role in selecting for ancestral traits and behaviours that we recognise as human today. Scientists following another thread in this evolutionary narrative describe viral nucleic acids insinuating themselves into our genetic codes. The biologist David Enard at Stanford University in California and colleagues have concluded that ‘viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes’...

‘As we become more deft at exploring the nested, dynamically complex relationships among viruses, bacteria, fungi and ourselves, we’ll come closer to grasping how pandemics emerge from a rupturing and rearranging of these relationships. From this deep linking of Aion with Chronos, we can already see the outlines of the wisdom that pandemics offer us. What we’re beginning to faintly understand is this: if we wish to survive as a species, we must gather all of our knowledge from multiple perspectives – however fragmented and partial – and actively engage in conversations with the world we inhabit and that gives us life. Only then will we begin to understand ourselves, and live up to our name, the wise ones, Homo sapiens sapiens.’

Read here (Aeon, Nov 3, 2020)

A supercomputer analysed Covid-19 — and an interesting new theory has emerged: A closer look at the Bradykinin hypothesis

‘Earlier this summer, the Summit supercomputer at Oak Ridge National Lab in Tennessee set about crunching data on more than 40,000 genes from 17,000 genetic samples in an effort to better understand Covid-19. Summit is the second-fastest computer in the world, but the process — which involved analyzing 2.5 billion genetic combinations — still took more than a week.

‘When Summit was done, researchers analyzed the results. It was, in the words of Dr. Daniel Jacobson, lead researcher and chief scientist for computational systems biology at Oak Ridge, a “eureka moment.” The computer had revealed a new theory about how Covid-19 impacts the body: the bradykinin hypothesis. The hypothesis provides a model that explains many aspects of Covid-19, including some of its most bizarre symptoms. It also suggests 10-plus potential treatments, many of which are already FDA approved. Jacobson’s group published their results in a paper in the journal eLife in early July...

‘Covid-19 is like a burglar who slips in your unlocked second-floor window and starts to ransack your house. Once inside, though, they don’t just take your stuff — they also throw open all your doors and windows so their accomplices can rush in and help pillage more efficiently...’

Read here (Elemental Medium, September 1, 2020)

Genes may leave some people more vulnerable to severe Covid-19

‘Variations at two spots in the human genome are associated with an increased risk of respiratory failure in patients with Covid-19, the researchers found. One of these spots includes the gene that determines blood types. Having Type A blood was linked to a 50 percent increase in the likelihood that a patient would need to get oxygen or to go on a ventilator, according to the new study...

‘The coronavirus triggers an overreaction of the immune system in some people, leading to massive inflammation and lung damage — the so-called cytokine storm. It is theoretically possible that genetic variations influence that response.’

Read here (New York Times, June 3, 2020)

Genetic engineering could make a Covid-19 vaccine in months rather than years

‘The established approach is to grow weakened viruses in chicken eggs—or more recently in mammalian or insect cells—and extract the desired pieces. The process can take four to six months to get the right antigens for familiar viruses that change every year, such as influenza. It can take multiple attempts over years for a new germ. That is far too slow to combat a virus that has already spread to pandemic proportions.

‘Instead labs are turning to gene-based vaccines. Scientists use information from the genome of the virus to create a blueprint of select antigens. The blueprint is made of DNA or RNA—molecules that hold genetic instructions. The researchers then inject the DNA or RNA into human cells. The cell’s machinery uses the instructions to make virus antigens that the immune system reacts to. Cells respond to the instructions as a normal part of their daily existence. This is the same trait infectious viruses exploit; they cannot reproduce on their own, so they use a cell’s machinery to make copies of themselves. They burst out of the cell and infect more cells, widening the infection.’

Read here (Scientific American, May 14, preview of June 1, 2020 issue)

Covid-19 and the harsh reality of empathy distribution

‘Empathy has a substantial genetic contribution, about half as much as height, a group of researchers found in 2018. Inevitably, some individuals inherit more pro-empathy genes than average. Moreover, since they are likely to be born from empathic parents, such children will also witness empathic behaviors and be rewarded for performing them. Thus, learning and family values reinforce the pro-social neural circuitry. Such individuals are likely to become professional caregivers.’

Read here (Scientific American, May 2, 2020)

US launches SPHERES consortium to monitor, conduct genomic research and share information on the Coronavirus

CDC is leading the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES), a new national genomics consortium to coordinate SARS-CoV-2 sequencing across the United States. Large-scale, rapid genomic sequencing of the virus that causes COVID-19 will allow public health experts to:

• Monitor important changes in the virus as it continues to circulate.
• Gain important insights to support contact tracing.
• Provide crucial information to aid in identifying diagnostic and therapeutic targets.
• Advance public health research in the areas of transmission dynamics, host response, and evolution of the virus.

Read here (US CDC, April 30, 2020)

Inside a COVID-19 lab and why more people return inconclusive tests

The head of NSW’s busiest COVID-19 testing lab says rising numbers of people will return undefined coronavirus results as the testing blitz picks up cases that shed the virus weeks ago. According to Professor Bill Rawlinson, director of Serology, Virology and OTDS Laboratories (SAViD), NSW Health Pathology based at Prince of Wales Hospital, “We are at the stage when individuals may only be positive for one of the several targets that PCR tests pick up,” he said, referring to the molecular testing performed samples collected by the nasal and throat swabs at COVID clinics. “These indeterminate results are going to increase because there will be people who had [the virus] a long time ago and still have some residual RNA [ribonucleic acid].”

Read here (The Sydney Morning Herald, April 25, 2020)

First case of Covid-19, presumably Type A, occurred ‘no earlier than September 13, 2019 and no later than December 7, 2019’

‘Peter Forster, a geneticist at the University of Cambridge, has identified three distinct strains of COVID-19. Forster and his team traced the origins of the epidemic by analysing 160 genomes from human patients and found that the strain in #Wuhan mutated from an earlier version.’

View here (CGTN, Youtube, April 11, 2020)

Genomic study points to natural origin of COVID-19, says NIH Director’s blog. Two scenarios suggested

‘In the first scenario, as the new coronavirus evolved in its natural hosts, possibly bats or pangolins, its spike proteins mutated to bind to molecules similar in structure to the human ACE2 protein, thereby enabling it to infect human cells. This scenario seems to fit other recent outbreaks of coronavirus-caused disease in humans, such as SARS, which arose from cat-like civets; and Middle East respiratory syndrome (MERS), which arose from camels.

‘The second scenario is that the new coronavirus crossed from animals into humans before it became capable of causing human disease. Then, as a result of gradual evolutionary changes over years or perhaps decades, the virus eventually gained the ability to spread from human-to-human and cause serious, often life-threatening disease.

‘Either way, this study leaves little room to refute a natural origin for COVID-19. And that’s a good thing because it helps us keep focused on what really matters: observing good hygiene, practicing social distancing, and supporting the efforts of all the dedicated health-care professionals and researchers who are working so hard to address this major public health challenge.’

Read here (NIH Director’s Blog, March 26, 2020)

Read here too on ‘The proximal origin of SARS-CoV-2’ (Nature Medicine, March 17, 2020)