Posted on 03/03/2020 8:29:53 AM PST by ProtectOurFreedom
The field of genomic epidemiology focuses on using the genetic sequences of pathogens to understand patterns of transmission and spread. Viruses mutate very quickly and accumulate changes during the process of transmission from one infected individual to another. The novel coronavirus SARS-CoV-2 which is responsible for the emerging COVID-19 pandemic mutates at an average of about two mutations per month. After someone is exposed they will generally incubate the virus for ~5 days before symptoms develop and transmission occurs. Other research has shown that the "serial interval" of SARS-CoV-2 is ~7 days. You can think of a transmission chain as looking something like:
where, on average, we have 7 days from one infection to the next. As the virus transmits, it will mutate at this rate of two mutations per month. This means, that on average every other step in the transmission chain will have a mutation and so would look something like:
The first case in the USA was called "USA/WA1/2020". This was from a traveller directly returning from Wuhan to Snohomish County on Jan 15, with a swab collected on Jan 19. This virus was rapidly sequenced by the US CDC Division of Viral Diseases and shared publicly on Jan 24 (huge props to the CDC for this):
Our best guess of a scenario looks something like:
(Excerpt) Read more at bedford.io ...
The homeless camps (probably thousands of them) all up and down the west coast will be huge Petrie dishes: Seattle, Tacoma, Olympia, Portland, Eugene, San Francisco, Sacramento, San Jose, Monterey/Santa Cruz, LA, San Diego. You can probably throw in Ashland, Medford, Roseburg, and Grant’s Pass, too.
Public health has been so lax for so long in all of those liberal shitholes (all in the name of “tolerance”) that they have dug their own graves. It’ll spread from those camps to the volunteers and public health people who work with the crazy druggies who will take it home with them to infect their families, schools, churches, busses, trains, and stores.
Will this be enough to FINALLY get the public health authorities to round up all that human detritus, hose them down with disinfectant, and then take flame-throwers to their “camps”?
I was walking in downtown Menlo Park, CA around sunset last night and there were four or five crap-filled shopping carts used by the loony bums on the main drag, Santa Cruz Avenue. I don’t ever recall bums hanging around downtown MP before. They’ve been in downtown next-door Palo Alto for a long time making the public parks unusable with their filth, needles, and disease.
There’s nothing like a liberal, tolerant town with a warm climate for attracting these pathologies.
I’ve actually had the same questions as you.
We bought a second home in North Idaho a couple years ago as a possible retirement place if we decide to sell our Bay Area house. I spent the last 2-1/2 months on remodel projects in Idaho (delightfully isolated) and flew back to San Jose yesterday. I’m wondering if I should return to N Idaho after visiting the Bay Area for two or three months. I’d hate to be a carrier.
All the snowbirds will be returning to North Idaho at the beginning of May anyway, so there will be lots of other potential carriers from Southern California heading north.
“There’s the culture of unscrupulous people selling used lab animals for meat, too. One guy went to jail for 12 years in Beijing for selling government property (used animals).
Plus, the Chinese have been criticized for a long time for lax security and safeguards at their BSL-4 facility.”
Yes. Those sort of things.
I’m thinking a number of people got high level exposure randomly due to environmental contamination.
The Chinese government sent out videos of people eating bats as a cover story because they know it’s a bat strain and it’s better to blame it on that than their lax bio security in otherwise competent facilities.
Just speculation on my part.
Brings to mind the seconds-long monkey autopsy scene from Andromeda Strain: 
https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus-wuhan-china/
from link:
Unlike other related coronaviruses, the 2019-nCoV virus has a unique sequence about 1,378 bp (nucleotide base pairs) long that is not found in related coronaviruses.
Looking at the phylogenetic tree recently published derived using all the full genome sequence, we see the 2019-nCoV virus does not have clear monophyletic support given the bootstrap value of 75 (Fig 1).
Close-up on Bootstrap value of 75 for available 2019-nCoV from Lu et al., 2020 The Lancet article [Full Text]
There is no doubt that there is a novel sequence in 2019-nCoV; we confirmed this via sequence alignment. Here’s the DOT plot:
The gap in the line shows a lack of sequence homology beween the most similar bat coronavirus and 2019-nCoV. The inserted sequence, which should not be there is here:
inserted-portionDownload
A database search by the first team to study and publish the whole genome sequence for the origins of the inserted sequence turned up no hits (Ji et al., 2020). They conducted a codon-bias analysis which led them to speculate that perhaps there had been a recombination event between a coronavirus in snakes with a coronavirus from bats (Ji et al., 2020). [Full Text]
This led to criticism on Wired(3) with quote dismissing the snake origin hypothesis as lacking evidence. There is, however, clear evidence that the novel sequence, which I will refer to henceforth as INS1378, is from a laboratory-induced recombination event. Specifically,
(1) The sequence similarity to other coronavirus sequences is lower to its most similar sequences in any coronavirus than the rest of the genome (IPAK finding)
(2) The high sequence similarity of INS1378 to a SARS spike protein (2; IPAK Confirmed).
(3) We also found significant sequence similarity of INS1378 to a pShuttle-SN vector that was in use in the 1980’s in China to create a more immunogenic coronavirus (IPAK finding, details below, Option 4).
...the hypothesis that 2019-nCoV is an experimental vaccine type must be seriously considered.Evidence for: Sequence homology between INS1378 to pShuttle Coronavirus vaccine; presence of a SARS-like Spike protein in bat coronavirus, otherwise most similar to bat coronaviruses; low bootstrap value.
Evidence against: Low sequence homology (but highly signifiant). NB these viruses are RNA viruses and they can evolve quickly, even under laboratory conditions.
Status: Most likely.
Test: Determine the nucleotide sequence all laboratory types of coronavirus being studied in China (a match will confirm). Find an isolate that matches 2019-nCoV in the wild and reproducibly independently isolate the virus from a wild animal (a match will falsify).
The available evidence most strongly supports that the 2019-NCoV virus is a vaccine strain of coronavirus either accidentally released from a laboratory accident, perhaps a laboratory researcher becoming infected with the virus while conducting animal experiments, or the Chinese were performing clinical studies of a Coronavirus vaccine in humans.
Dr. Dale Brown brought to my attention the studies that have reported serious immunopathology in animals – rats, ferrets, and monkeys – in which animals vaccinated against coronoviruses tended to have extremely high rates of respiratory failure upon subsequent exposure in the study when challenged with the wild-type coronavirus.
Yasui et al., (2012) reported severe pneumonia in mice who were vaccinated against SARS who were subsequently infected with SARS. Another study of a double-inactived SARS vaccine found increased eosinophilic proinflammatory responses in vaccinated mice, especially older mice, writing:
“Importantly, aged animals displayed increased eosinophilic immune pathology in the lungs and were not protected against significant virus replication.”In the worst-case scenario, if the vaccination strain is more highly contagious and lethal, 2019-nCoV could become the worst example of vaccine-derived contagious disease in human history. With an uncharacteristic aysmptomatic prodromal period of 5-7 days, individuals returning from China to other countries must be forthright and cooperative in their now-prescribed 2-week quarantine.
What exactly do these mutation do?
Make it deadlier, less deadly, easier to transmit, harder?
And what causes the mutation? What had the germ run into that caused it to have to change?
Yes...depending on which way it mutates. Graph below: “ Fig 2. A fitness landscape showing three genotypes on different places on the landscape (A, B, and C) and a schematic pie chart of the distribution of mutations available to each genotype. The genotype at A is not well adapted to the environment (far from a fitness peak) so has a larger fraction of mutations that would be beneficial. The genotype at B is more fit than A and is closer to a fitness peak, so it has a smaller fraction of beneficial mutations than that at A. The genotype at the fitness peak C does not have any way to become more fit on this landscape and thus has no beneficial mutations available to it. The allocations of mutations as beneficial, neutral, and deleterious is for representational purposes only (not based on actual data), and the proportion of neutral mutations was held constant for all three genotypes.”
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