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.

[Mariner]

Consider this: Just 3 days ago the Chinese government was saying there is no human-human transmission.

[tired&retired]

Read Richard Preston’s book “Hot Zone,” a true story of an Ebola virus going airborne in a Reston Virginia primate clearing house.

[Pelham]

The Hot Zone incident involved “Reston virus” rather than Ebola. It isn’t particularly dangerous to humans.

[Long Jon No Silver]

‘earlier than officials realised’. Cover for the commie cover up

[Natty Bumppo@frontier.net]

The genome of the 24 available samples are very similar, indicating a single source for transmission to humans that occurred no earlier than 30 Oct 2019, and no later than 29 Nov 2019.

The virus has an incubation period of 14 days.

China reported the first case on 8 Dec 2019, and provided the complete sequence of the virus genome on 10 Jan 2020. The genome is 29,903 bases long. That 33 days shattered all previous records for sequencing a genome this long. A single mutation was all that was required for the virus to be able to infect humans.

It took more than 6 months to sequence the SARS virus from Oct 2002 to Apr 2003, which is 29,727 bases long.

Note that China has two large, sophisticated biological weapons research facilities within 20 miles of the city of Wuhan.

Coincidence? I think not. The Chinese had the novel coronavirus genome sequence all along, since they developed it.

[justa-hairyape]

Kinda like a doomsday bomb if the castle is surrounded and the food is running out.

[null and void]

Bring Out Your Dead

Post to me or FReep mail to be on/off the Bring Out Your Dead ping list.

The purpose of the “Bring Out Your Dead” ping list (formerly the “Ebola” ping list) is very early warning of emerging pandemics, as such it has a high false positive rate.

So far the false positive rate is 100%.

At some point we may well have a high mortality pandemic, and likely as not the “Bring Out Your Dead” threads will miss the beginning entirely.

*sigh* Such is life, and death...

If a quarantine saves just one child's life, it's worth it.

[MarMema]

A great read. Thanks for posting this.

[tired&retired]

Thanks.

At the time they did not know... per Wiki:

Reston virus (RESTV) is one of six known viruses within the genus Ebolavirus. Reston virus causes Ebola virus disease in non-human primates; unlike the other five ebolaviruses, it is not known to cause disease in humans, but has caused asymptomatic infections.

Reston virus was first described in 1990 as a new “strain” of Ebola virus (EBOV).

It is the single member of the species Reston ebolavirus, which is included into the genus Ebolavirus, family Filoviridae, order Mononegavirales.

Reston virus is named after Reston, Virginia, US, where the virus was first discovered.

Following the test at the CDC campus in DeKalb County, two of the monkeys who had survived Reston virus infection were infected with a very large dose of the Ebola virus in an effort to produce an Ebola vaccine. One of the two monkeys remained resistant; the second died.

The physical building in which the outbreak occurred was demolished on 30 May 1995 and a daycare center was constructed in its place.

[Brooklyn Attitude]

“...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.”

Corona viruses have no DNA, only a single strand of RNA. However they can use the Reverse Transcriptase enzyme to convert the RNA strand to DNA.

[Brooklyn Attitude]

“However they can use the Reverse Transcriptase enzyme to convert the RNA strand to DNA.”

To clarify “they” refers to the scientists.

[SunkenCiv]

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[gandalftb]

Here is a link to a daily report being done on the worlwide spread of the disease:
................
https://bnonews.com/index.php/2020/01/the-latest-coronavirus-cases/
.................
There are the beginning rumors that this was a lab created disease. Not likely, as 6 of the first 7 patients were vendors at the Wuhan seafood market . They sell bats there for food.
................
This virus shares 80% of the SARS virus, its closest relative. It has a 96% match with a known virus in fruit bats. Snakes are not the origin.
................
This virus is much weaker than SARS but has some unusual traits. It is an RNA rather than a DNA virus like smallpox. That means that it mutates very quickly. Current patients are showing a 4th generation mutation from the original patients amonth ago.
..............
That makes vaccines very difficult to be effective.
..............
The new virus also has a very high binding energy to human tissue, about 4 times higher than SARS. That means that infection is far more likely when exposed. In fact, there are about 40% new patients every day, that is extraordinary.
...............
As usual, vulnerable people are more likely to die. Most people will be able to quickly fight off the virus.

[AdmSmith]

13JAN2010:

Phylogenetic tree showing the relationship of Wuhan-Hu-1 (circled in red) to selected coronaviruses.

https://ncbiinsights.ncbi.nlm.nih.gov/2020/01/13/novel-coronavirus/

[AdmSmith]

Note that China has two large, sophisticated biological weapons research facilities within 20 miles of the city of Wuhan.

1979-nCoV is not a suitable bio-weapon.

[nuconvert]

Thanks

[janetjanet998]

just reported that it DID NOT start at that seafood market and the first case may ave been dec 1

[AdmSmith]

Estimated country-specific influenza-associated respiratory excess mortality rates (EMR).

The estimated mean annual influenza-associated respiratory EMR ranged from 0.1 to 6.4 per 100 000 individuals for people younger than 65 years, 2.9 to 44.0 per 100 000 individuals for people aged between 65 and 74 years, and 17.9 to 223.5 per 100 000 for people older than 75 years. We estimated that 291 243- 645 832 seasonal influenza-associated respiratory deaths (4.0 - 8.8 per 100 000 individuals) occur annually. The highest mortality rates were estimated in sub-Saharan Africa (2.8 - 16.5 per 100 000 individuals), southeast Asia (3.5 - 9.2 per 100 000 individuals), and among people aged 75 years or older (51.3 - 99.4 per 100 000 individuals). For 92 countries, we estimated that among children younger than 5 years, 9243 -105 690 influenza-associated respiratory deaths occur annually.

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(17)33293-2/fulltext

according to data so far the mortality is 3 %, SARS had less than 1% in patients below age 24 years to more than 50% in patients aged 65 and older.
https://emedicine.medscape.com/article/237755-overview

[SunkenCiv]

That pork and rice imported from the US doesn't look so bad now, does it, hmm, commies?