COVID (SARS-CoV-2) - Preliminary thoughts. JJackson personal opinion.

[gsgs]

wikipedia has a good summary about the measures :https://en.wikipedia.org/wiki/2019%E...Mainland_China
more detailed in the WHO-China-Mission report , with a nice summary from @kaka , I wrote about it here:

https://thisbluemarble.com/showthread.php?t=79399

Note also their sophisticated case tracking with AI,apps, lots of teams.
As I understood in most parts of China there were almost no measures, except prolonged holiday. In come cities outside
Hubei i.e. Zhejiang they allowed only 1 person per household to shop every 2 days

[JJackson]

There is one more point and it probably should have been the first. Speed!
The main enemy on a battle field is a lack of information and China has put together a command center that is using 5G coms to each contact trace team so they can ask for expertise and feed data into the system as it is being collected. Ditto for labs, hospitals and researcher.
The Ebola outbreak taught us that bringing help into an area experiencing exponential growth too slowly is hopeless. If you have a doubling time of 10 days and need a 1000 beds you actually need 8000 if it is going to take you a month to get them built, staffed and fully operational. China seems to have absorbed this and applied it, they converted a stadium into a 1000 bed hospital fully staffed (all of whom had had PPE training) complete with CT scanners etc. in 24hrs.
They have sent in an additional 40,000 medical staff but what I loved was that anyone entering in these teams had to come with all the equipment and PPE they would need and be full trained in their use and know what they were going to do. They would be kept as a team and given a unit to run. All other logistics (food, accommodation, transportation) are handled by non medical teams.

[Thornton]

Curiosity the lesson learnt from China regarding containment I would summarise as 1] If you are not clear what is going on but there is evidence of transmission in a geographic area shut things down massively until you do understand. 2] Support anyone caught in the shut down with information, practical and psychological help. 3] Get your population to understand it is everyone's responsibility to do what they can to help. 4] One size does not fit all and local authorities need flexibility to tailor measures to local circumstances but within, and understanding, the bigger plan. 5] Be flexible if things are not working change them. (the clinical guidance has been changed 6 times already). 6] If you are in a low impact area send your medical staff and all their equipment and PPE to the hot spots, do not stock pile it in anticipation of a wave in your area.
.

Clear lessons. I will cite in other settings.

[JJackson]

Curiosity the lesson learnt from China regarding containment I would summarise as 1] If you are not clear what is going on but there is evidence of transmission in a geographic area shut things down massively until you do understand. 2] Support anyone caught in the shut down with information, practical and psychological help. 3] Get your population to understand it is everyone's responsibility to do what they can to help. 4] One size does not fit all and local authorities need flexibility to tailor measures to local circumstances but within, and understanding, the bigger plan. 5] Be flexible if things are not working change them. (the clinical guidance has been changed 6 times already). 6] If you are in a low impact area send your medical staff and all their equipment and PPE to the hot spots, do not stock pile it in anticipation of a wave in your area.

China is beginning a phased return to work in selected areas but it will be high priority products (PPE & drug chemical precursors etc) and in areas with little or no transmission, which is now most of China. This will increase transmission but, if done slowly while monitoring the effects, it should not overload the system, if they begin to loose control they will re-apply them.
The Chinese culture is very different to the US where the curtailing of freedom of movement or anything else viewed as infringement of civil liberties or the ability to earn money are likely to meet resistance. Additionally State and local authorities value their independence from central government and may set their own rules leading to very different spread in different areas (as happened in 1918). Healthcare provision is a commercial operation with many independent companies who are likely to be less amenable to sending their staff or PPE to areas that need them.
These are observation of an outsider so I don't really understand what may be workable in a US context but I do worry about some of the US reports giving the impression that China is a lower income country without our advanced health system and that the US would handle it better. Time will tell but I agree with the UN's head of COVID response (Mike Ryan) if I catch this I would want to be treated in China.
Yes China has the numbers, but that cuts both ways, big population means more potential patients as well as more people to help them. I don't think scale matters much and any country or area can use its unaffected population to support its clusters as long as they do not let growth overwhelm capacity, through adequate containment, and the unaffected are willing to go into the epicentre.
I have not been following the containment measures outside China in any detail so can not comment, beyond saying that it is too early to judge their efficacy anyway which is why I have not taken the time to look at these actions.

[curiosity]

JJackson - If these countries were to work to contain, how would they do so and at what point?
In California would that be now? And what part? The Bay Area? The State? In Italy? Should the whole country be locked down? Or just the regions affected? I am asking sincerely because a realistic strategy eludes common people like me.

One thing China does have that most the other countries do not is human resources. Same disease, same attack rate, same amplification of illness ... but the number of people to help contain is NOT the same.

I have seen few updates on the type of quarantine measures still in place in China and other countries. Did Italy stop trains to Northern Sections? Japan closed schools, but have they shut down businesses and transportation?

[JJackson]

Things are moving rapidly now and the situation is very different. China has done a phenomenal job in containment but now S. Korea, Italy & Iran are all now reprising the experience of Wuhan at the outset. Again the numbers are causing a problem.
Firstly it is important to understand the size of China, which is better thought of as a continent than a country. The world has a population about 7.8 billion and 60% of them are Asians. China’s 1.4 billion is larger than any continent, accept its own, and greater than Europe and N. America combined. It is divided into 31 provinces the largest being Guangdong which, if it was a country, would replace the Philippines as the 13^th largest. Hubei is much smaller and is only slightly smaller than the combined size of Texas & California and about the same as the 4 countries that constitute the UK.

Now for some key dates. 31^st Dec China reports its first Pneumonia of unknown cause, it took them 3 days to find the original cluster of 44 cases and on 7^th Jan. they reported the causative agent, on the 11^th the epidemiological team found the fish market source and on the 12^th they released the first sequence. The first two cases outside China were reported on the 13^th and 14^th. So to recap China managed to pick up the first case, against a background of about 150 community acquired pneumonia cases a day in Wuhan, find the clusters source, identify it as COV, sequence it & report all of this to the world via the WHO in two weeks and before any cases had shown up outside China. Nothing like this has ever been done before and if you look back at the H1N1(2009) outbreak the US and Mexico were far slower at getting a handle on what was going on, and with a much better understood disease and massive flu surveillance network.

Now if we look at S. Korea, Italy & Iran they have populations of 50, 60 & 84 million respectively putting them in the same ball park, population wise, as Hubei. Iran is a special case as it is suffering from an economic war which will have hampered its ability to cope and now has a per capita GDP slightly lower than China where as S. Korea and Italy, GDP per cap, are twice as rich as China. So how well are they responding?

S. Korea reported its first case on Jan. 20^th today they reported 813 new cases bringing the total 3150 confirmed cases and 17 deaths (only China seems to be submitting suspected case numbers despite repeated requests from WHO for this important data). If we look at Henan, which is a neighbouring province to Hubei and has twice S Korea’s population, they currently have 20 deaths and 1272 confirmed cases with no deaths or confirmed case and one suspect case today. Outside of Hubei China’s 1.4 billion reported 23 confirmed cases, 120 suspect cases and 3 deaths. China is not the problem anymore. The graphs below show the epi curves for Wuhan and China (from the WHO China fact finding mission report).




There are two possible explanations either China is giving the rest of the world an object lesson in how to handle a zoonotic outbreak or it is somehow managing to hide a massive uncontrolled outbreak. The English language MSM (and sadly too many FT posters) seem to believe the later I and the WHO believe the former. If I am right I fear for the rest of us. As I pointed out in the first post in this thread neither the R0 nor CFR are fixed numbers for a disease and will reflect the containment and treatment measures taken. I also posted a guestimate for the R0 of 2 to 3 and CFR of 1% but these were based on data coming out of China which I now think has handled its problem far better than any other country is likely to do and expect much worse elsewhere. The CFR age distribution is very worrying with a 10%+ CFR for the over 80’s that’s 17 million (twice the population of New York) US seniors and both my parents.

[JJackson]

Preliminary Thoughts update.
It is 6 weeks since I wrote the first post and not a lot has changed. There are more cases and some more spread but we have not advanced a great deal in terms of our understanding of the disease. In 2009 I started a thread for new visitors in anticipation of the confusion the numbers, and case definitions, which were beginning to come out in the MSM, were going to cause. The first post in this thread aimed to do the same but was a little more technical as the target audience was more FT's regular posters.

The numbers & case definitions are again causing problems for the same reasons. Test capacity is slowly closing the gap on the numbers the CCDC would like tested in the epicentre. In the UK, where there is ample capacity at present, to get 9 positive tests they tested 2500 people. Each person is likely to need multiple tests, early testing often fails as viral load does not reach the test's diagnostic sensitivity threshold, once confirmed, tests may be taken to check on viral load progression under different treatment regimes and the patient will need two clear test prior to release. Currently the false negatives are as high as 50% and the US CDC is still the only test facility in the US, as the reagents package they shipped turned out not to work adequately across the range of RT PCR labs slated for testing. Sally started an excellent thread covering in more detail where problems can/are occurring, there are many steps and small errors at any point all end up aggregating and reducing the test's reliability. As a new disease sample collection, reagents, procedures, primers and probes all need fine tuning which should increase sensitivity and reduce errors.

The combination of a shortage of tests and the reliability problem addressed above have caused a change in case definitions so CT scans that show marked similarity to typical confirmed cases are being accepted as confirmed. While PCR is normally deemed the gold standard for disease confirmation here there are still problems and scan data is probably as reliable. The increased test capacity is allowing for more contacts testing amongst mild cases which is finding asymptomatic infections. The data collected from this group should help to shed light on how much undetected spread is likely to be going on. Serological testing should give much better data but is normally not taken until a month post infection. The candidates for testing here should be the first cured cases, to get a baseline on antibody development and concentrations, followed by a wider examination of the regular visitors to the fish and game market.
For all the reasons outline in the first post calculation of epidemiological numbers like CFR and Ro are still dodgy. Based more on overall observation of the outbreak than on calculation I will stick my neck out and suggest a Ro of 2 to 3 and a CFR of 0.5 to 1 – as I say a guess. The apparent stagnation in the increase in numbers is, I think, real and a reflection of the massive and unprecedented actions taken by China to slow/stop spread. The question is ‘how long can they keep this level of containment up?’ The economic and social consequences are enormous. I still do not think it will be enough, while spread outside China may be contained for the moment, in China there is still too much spread between areas. International land boarders are going to be much more difficult to quarantine than ports and airports and, while the creeping spread on land may be much slower than by air, it is going to get into regions without the resources or central control China can bring to bear.
The sequence data continues to increase with plenty of random nucleotide mutations but few are resulting in AA changes and, where they have occurred, there is no obvious pattern that can be attributed to host adaption. I have provide links below to a site that is updated regularly with new GISAID sequences where hovering over nodes in the phylogenic tree show the base and AA changes, I have also link to Sally’s thread on the problems encountered in getting clean tests.

https://nextstrain.org/ncov?branchLabel=aa&m=num_date set the tree options to 'rectangular' and the 'branch labels' to AA.

https://flutrackers.com/forum/forum/-2019-ncov-new-coronavirus/828326-how-is-the-false-negative-of-new-coronary-pneumonia-caused

[gsgs]

yes, I had seen that. Linked to it in other posts ... but didn't read it .. only "flying" over it. Mostly text, you can't skip things.

[JJackson]

Having written the opening post I have now found a truly excellent overview thanks to the author linking it at virological.org . This guy does have credentials, bucket loads of them, having been on the cutting edge of SARS, MERS, Ebola and H1N1(2009). It is written specifically for a general audience, not his peers, but the hard science is there in abundance if you want it. The bad news - it is 80 pages long plus references, I am on page 33 and have already doubled my knowledge on the protein structures and functions. The good news is I have not read anything, yet, which causes me to change my thinking in the first post.
http://virological.org/uploads/short...Yw2rfJASAS.pdf

[Commonground]

Thank you JJackson for taking the time to write this up for us all.

[JJackson]

Thanks all. As promised - if a little late - I have made some updates.
Sharon - thanks for doing the formatting, I was getting tired and not thinking clearly, so opted to just dump the draft text and fix it later.
tetano - no academic qualifications. What I know is all based on reading at FluTrackers (albeit for a very long time) and links. It is good here all these nice people keep finding interesting things for me to read. Much of any credit should go to you as I am a primary recipient of your postings to the Scientific library most of what I know came from there and I am deeply in your dept.

[tetano]

Thank'you JJackson, very interesting. Are you a virologist or an epidemiologist?

[sharon sanders]

Thank you for that thoughtful work. I changed the title to reflect the temporary name for this disease so that the thread will google better.

[Emily]

Thank you, JJackson! I appreciate your time to give us some background. I know I still know little, but it is a lot more than I knew before.

[kiwibird]

JJackson thank you. I look forward to reading further thoughts and updates from you.