DNA sleuths read the coronavirus genome, tracing its origins and looking for dangerous mutations

Stat ^ | JANUARY 24, 2020 | SHARON BEGLEY

[aquila48]

As infectious disease specialists and epidemiologists race to contain the outbreak of the novel coronavirus centered on Wuhan, China, they’re getting backup that’s been possible only since the explosion in genetic technologies: a deep-dive into the DNA of the virus known as 2019-nCoV.

Analyses of the viral genome are already providing clues to the origins of the outbreak and even possible ways to treat the infection, a need that is becoming more urgent by the day: Early on Saturday in China, health officials reported 15 new fatalities in a single day, bringing the death toll to 41. There are now nearly 1,100 confirmed cases there.

Reading the DNA also allows researchers to monitor how 2019-nCoV is changing and provides a roadmap for developing a diagnostic test and a vaccine.

“The genetics can tell us the true timing of the first cases” and whether they occurred earlier than officials realized, said molecular biologist Kristian Andersen of Scripps Research, an expert on viral genomes. “It can also tell us how the outbreak started — from a single event of a virus jumping from an infected animal to a person or from a lot of animals being infected. And the genetics can tell us what’s sustaining the outbreak — new introductions from animals or human-to-human transmission.”

Scientists in China sequenced the virus’s genome and made it available on Jan. 10, just a month after the Dec. 8 report of the first case of pneumonia from an unknown virus in Wuhan. In contrast, after the SARS outbreak began in late 2002, it took scientists much longer to sequence that coronavirus. It peaked in February 2003 — and the complete genome of 29,727 nucleotides wasn’t sequenced until that April.

[AdmSmith]

Beijing Municipal Health Commission, in an announcement on Jan. 26, stated that three of its doctors had tested positive for 2019-nCoV.

https://www.theepochtimes.com/novel-coronavirus-live-updates-confirmed-cases-in-10-countries_3215641.html

Live updates at the link

[AdmSmith]

We currently do not know where 2019-nCoV falls on the scale of human-to-human transmissibility. But it is safe to assume that if this virus transmits efficiently, its seemingly lower pathogenicity as compared with SARS, possibly combined with super-spreader events in specific cases, could allow large-scale spread. In this manner, a virus that poses a low health threat on the individual level can pose a high risk on the population level, with the potential to cause disruptions of global public health systems and economic losses. This possibility warrants the current aggressive response aimed at tracing and diagnosing every infected patient and thereby breaking the transmission chain of 2019-nCoV.

https://www.nejm.org/doi/full/10.1056/NEJMp2000929

[tired&retired]

Thanks for the updates

[MarMema]

Of the original 41 infected not one had any compromising illness and they were healthy middle aged men. This rumor about the elderly only needs to be squashed.

[MarMema]

Of the original 41 infected 2/3 had been to that market.

[AdmSmith]

“It is unclear at the current time whether this outbreak can be contained within China,” said Dr Neil Ferguson, an infectious disease specialist at Imperial College London who co-led one of the studies.

Dr Ferguson’s team suggest as many as 4,000 people in Wuhan were already infected by Jan 18 and that on average each case was infecting two or three others.

A second study by researchers at Britain’s Lancaster University also calculated the contagion rate at 2.5 new people on average being infected by each person already infected.

“Should the epidemic continue unabated in Wuhan, we predict (it) will be substantially larger by Feb 4,” the scientists wrote.

They estimated that the central Chinese city of Wuhan where the outbreak began in December will alone have around 190,000 cases of infection by Feb 4, and that “infection will be established in other Chinese cities, and importations to other countries will be more frequent”.

https://www.todayonline.com/world/studies-show-person-infected-wuhan-virus-passes-it-2-3-others

i.e. R0 = 2 - 3 or similar to influenza
https://en.wikipedia.org/wiki/Basic_reproduction_number

[MarMema]

Visited a Chinese forum last night via Twitter and there are a lot of reports about a family member being rapidly cremated without testing....but fever,etc

Originally they put the Ro at 3.8 then backed it down to 2.8.

Still too early but Beijing stopped all ground traffic from outside the city. And of course we are airlifting us citizens from Wuhan.

[AdmSmith]

A Novel Coronavirus from Patients with Pneumonia in China, 2019



Although 2019-nCoV is similar to some betacoronaviruses detected in bats, it is distinct from SARS-CoV and MERS-CoV. The three 2019-nCoV coronaviruses from Wuhan, together with two bat-derived SARS-like strains, ZC45 and ZXC21, form a distinct clade in lineage B of the subgenus sarbecovirus. SARS-CoV strains from humans and genetically similar SARS-like coronaviruses from bats collected from southwestern China formed another clade within the subgenus sarbecovirus. Since the sequence identity in conserved replicase domains (ORF 1ab) is less than 90% between 2019-nCoV and other members of betacoronavirus, the 2019-nCoV — the likely causative agent of the viral pneumonia in Wuhan — is a novel betacoronavirus belonging to the sarbecovirus subgenus of Coronaviridae family.

https://www.nejm.org/doi/full/10.1056/NEJMoa2001017

[AdmSmith]

A good background: TWiV 582: This little virus went to market
http://www.microbe.tv/twiv/twiv-582/

Later today there will be a new podcast I guess they will talk about it again

http://www.microbe.tv/twiv/

[Fury]

Ahh, bats. Are known reservoir species for other virii.

Amazing how bats have adopted/evolved to essentially be symptomless carriers of a virus.Its already been shown that flying increases many species’ temperature due to increased metabolism. Could be such increased temperature causes immune response that keeps the virus from making such a bat symptomatic?

[AdmSmith]

Yes, that could be the case:

bats are reservoirs for more than 60 viruses that can infect people, according to a 2013 study. The animals host more viruses per species than rodents.

When they fly, bats increase their energy expenditure (metabolic rate) and body temperature, resulting in body temperatures similar to those seen in other mammals that have a fever (100 to 105 degrees Fahrenheit), the researchers said. This suggests that flight protects bats from infection in the same way that fever protects mammals — by boosting their immune response, the researchers said.

If the high metabolic rates and high body temperatures that accompany flight activate the immune system, then flight could be the ultimate explanation “for the evolution of viral infections without overt signs of illness in bats,” the researchers wrote in a paper in the May issue of the journal Emerging Infectious Diseases.

https://www.livescience.com/44870-bats-viruses-flight.html

[musicman]

BTTT!!!

[MarMema]

There was an intermediate host however. They’re speculating it was civets cats.

[AdmSmith]

yes, according to BBC:
Sars started off in bats and then infected the civet cat, which in turn passed it on to humans.

Some people were infected by direct contact with civet cats.
https://www.bbc.com/news/world-asia-china-51176409

[AdmSmith]

Suggested reading about epidemiology models

https://institutefordiseasemodeling.github.io/Documentation/general/model-si.html

http://www.mtholyoke.edu/~ahoyerle/math333/ThreeBasicModels.pdf

[AdmSmith]

oops:

China’s National Health Commission (NHC) said on Sunday that the new coronavirus is contagious even in its incubation period, which lasts up to 14 days, and that the virus’ ability to spread is getting stronger.

Ma said that unlike Sars (severe acute respiratory syndrome) the new coronavirus was infectious during its incubation period. He also reiterated earlier reports that people infected with the virus might not immediately show any symptoms.

https://www.scmp.com/news/china/society/article/3047701/coronavirus-contagious-even-incubation-stage-chinas-health

[21twelve]

“More than 1,350 medics had already arrived in the city to help battle the epidemic and a further 1,000 would follow, he said.”

With the “official” total of about 1500 cases, I guess each one is getting their own doctor!

I wonder what the average case load for a doctor/medic might be. Maybe see a person every half hour? Or every 15 minutes during a critical event? Lets say 2/hour. And a 12-hour shift during an emergency. That’s 24 patients. Times 2,350 medics = 56,000 patients. (Plus the normal number of doctors in the city times 24 patients each).

Maybe I’m overestimating. Would have medics for entrance, some for triage, some for support, etc.

[Fury]

Hopefully, the response will be to not start to depopulate the civet cats on large scale. Bats can infect other species and depending on the challenge response, the virus can find a new host species.

[AdmSmith]

Perhaps a good idea to skip the next dinner with “bat soup”

[AdmSmith]

Usually coronavirus illnesses are fairly mild, affecting just the upper airway. But the new virus, as well as both SARS and MERS, are different.

Those three types of betacoronaviruses can latch onto proteins studding the outside of lung cells, and penetrate much deeper into the airway than cold-causing coronaviruses, says Anthony Fauci, director of the U.S. National Institute of Allergy and Infectious Diseases in Bethesda, M.D. The 2019 version is “a disease that causes more lung disease than sniffles,” Fauci says.

Damage to the lungs can make the viruses deadly. In 2003 and 2004, SARS killed nearly 10 percent of the 8,096 people in 29 countries who fell ill. A total of 774 people died, according to the World Health Organization.

MERS is even more deadly, claiming about 30 percent of people it infects. Unlike SARS, outbreaks of that virus are still simmering, Fauci says. Since 2012, MERS has caused 2,494 confirmed cases in 27 countries and killed 858 people.

Bats are often thought of as a source of coronaviruses, but in most cases they don’t pass the virus directly on to humans. SARS probably first jumped from bats into raccoon dogs or palm civets before making the leap to humans. All the pieces necessary to re-create SARS are circulating among bats, though that virus has not been seen since 2004 (SN: 11/30/17).

MERS, meanwhile, went from bats to camels before leaping to humans (SN: 2/25/14).

https://www.sciencenews.org/article/how-new-wuhan-coronavirus-stacks-up-against-sars-mers