Supine
Newt Member
Your tone is snotty and I've worked in the industry for twenty years... But hey if your leet Google skills allow you to know more then great.
Coronavirus - worldwide breaking news, discussion, stats, updates and more
- Thread starter weltweit
- Start date
Your tone is snotty and I've worked in the industry for twenty years... But hey if your leet Google skills allow you to know more then great.
Cid
Proper break this time
I think they have actually... The 'click and collect' option is there, but if you select a store it says not available. At least near me.
Callie
Pivoting
You work in molecular amplification assay production?
I'd be interested to know if/how international/national health centres (PHE/CDC/I dunno what other countries vwould be called!) share their hastily designed primers etc and how these perform on different platforms.
Any new PCR assay for novel viruses is going to be 'research use only' until it's suitability and effectiveness can be assured. It really kind of goes against the grain of medical laboratory testing to use an assay which is unapproved but in these situations you absolutely have to.
As much as I understand it health centres will have different extraction and amplification equipment place to place (maybe several models/versions available), you can develop as hoc novel assays for novel targets (ooh new Coronavirus) but in my mind you can then have many different assays on different equipment around the world where the assays have slightly different performance characteristics. Maybe?
I wonder if that info is shared? How much access do commercial ventures have to the sequencing data for nCoV-2019 ?
We've never done any molecular work in my lab as we're pretty small and more bacteria focussed but initially in these scenarios all testing is performed by the PHE. You could in theory test locally too if you had a suitable assay but PHE would still want a sample for epidemiological purposes.
Supine
Newt Member
elbows
Well-Known Member
Shame your long experience didnt translate into any detail I could learn from. What was inaccurate about what I said?
Callie
Pivoting
l33t googling skills ?
elbows
Well-Known Member
It may not seem like it when I am in full flow, but I am always ready and willing to be taken down a peg or two, and there was nothing worse for me than threads where I was the only one left gibbering on about detail, without anyone to spot my mistakes and correct them. Because I know I will make mistakes, and a lot of what I have learnt is from those with the knowledge generously sharing it and discussing it very publicly for the benefit of all.
So its detail that can put me in my place, and I am sorry that I trod on your toes but I just didnt get that detail from you.
So its detail that can put me in my place, and I am sorry that I trod on your toes but I just didnt get that detail from you.
Does the link work for you?
elbows
Well-Known Member
Yeah the 'research only, not for clinical diagnosis' stuff has somewhat gone out the window for now!
This area interests me too and I'm sorry if I've ben rude about it, but I thrive on detail and I have to be able to try to separate commercial press release boasts from actual progress, whether that progress be some innovation or just an increase in capacity. I would like to learn more, and test my assumptions, thats all.
There seems to be a lot of completely open sharing of sequencing data for this coronavirus. eg on GISAID. This is one area I've seen lots of experts being happy about, including the timeliness of the data being made available, and new sequences being added all the time.
There may be additional clues in the 17th January WHO Laboratory testing for 2019-nCoV interin guidance, eg:
So I suppose its the availability of validated PCR tests that I'm most interested in (and the above doc is a few weeks old now). I note the language that sort of tip-toes gently on the theme that in the meantime the non-validated tests will still be used on the front lines, but you need reference labs to do the final proper official confirmation.
Callie
Pivoting
no me neither.
elbows
Well-Known Member
I found this paper on early work done on detection of 2019-nCoV by RT-PCR quite interesting too.
www.eurosurveillance.org
By the way some Roche equipment was used for RNA extraction from clinical samples (their MagNA Pure 96 system)
Eurosurveillance | Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR
Background The ongoing outbreak of the recently emerged novel coronavirus (2019-nCoV) poses a challenge for public health laboratories as virus isolates are unavailable while there is growing evidence that the outbreak is more widespread than initially thought, and international spread through...
By the way some Roche equipment was used for RNA extraction from clinical samples (their MagNA Pure 96 system)
Callie
Pivoting
I think the scientific community understand the need to share data for the good of all. If this virus does end up circulating in the general population yer commercial companies can flog their assay to all and sundry but not sure how keen people will be to take on local testing initially. I think your standard local hospital labs may not always have the expertise or resource to take on assays where the onus of validation is on them whereas the centralised public health centres will have that expertise and more and they will have been through this before (SARS, MERS, swine flu). Hopefully there have been lessons learnt and procedures refined when it comes to managing novel pathogen outbreaks.
Pretty sure PHE also look at commercial assays to assist local labs to make informed choices re selection when possible
Pretty sure PHE also look at commercial assays to assist local labs to make informed choices re selection when possible
elbows
Well-Known Member
Also from the press release department, I found this article that is probably based on a press release from BGI/MGI Tech to be a bit more clearcut, probably because one of its main themes was getting emergency use approval from China's National Medical Products Association, and they are a bit clearer about the context of 'in a few hours time'.
www.360dx.com
How many different manufacturers work in this are anyway?
BGI Sequencer, Coronavirus Molecular Assays Granted Emergency Use Approval in China
The DNBSEQ-T7 ultra-high-throughput sequencer, metagenomic sequencing kit for coronaviruses, and 2019-nCoV RT-qPCR kit have received authorization from China's NMPA.
www.360dx.com
How many different manufacturers work in this are anyway?
elbows
Well-Known Member
Plus you get to prove that your detection system works (to some extent at least).
I wasnt overjoyed when the UK had no positive results, because various models suggested there should be some. So in one sense I am more reassured now that we've had a couple!
cupid_stunt
Chief seagull hater & farmerbarleymow's nemesis.
Just updated*, confirmed cases now 11,955, of which 11, 818 are in China, 137 in 23 other countries. Death toll now 259, all in China.
There was a professor on the TV news saying it's fairly safe to say, now we around two months into the outbreak, that the fatality rate is around 2%, compared to 10% with SARS, 37% with MERS, and 1% with flu. He went on to explain the majority of deaths have been in people with existing medical conditions, as with flu, and although sensible precautions should be taken, based on what we know so far, there's no need to panic.
* Geographical distribution of 2019-nCov cases globally
There was a professor on the TV news saying it's fairly safe to say, now we around two months into the outbreak, that the fatality rate is around 2%, compared to 10% with SARS, 37% with MERS, and 1% with flu. He went on to explain the majority of deaths have been in people with existing medical conditions, as with flu, and although sensible precautions should be taken, based on what we know so far, there's no need to panic.
* Geographical distribution of 2019-nCov cases globally
elbows
Well-Known Member
Whether its safe to say 2% depends on what people think that number means.
I was droning on about this yesterday. This article is very helpful in explaining:
Clarity, Please, on the Coronavirus Statistics
Taking all this detail into account, there is no way I would claim that the mortality rate is 2%, if it leads people to think that means that 2% of the people who catch this coronavirus will die. Mostly because there are people who show up in the confirmed infected stats who are currently still alive but wont survive, and because of the god knows how many milder cases there are that dont show up in the stats at all and can potentially make a huge difference to the overall mortality rate.
elbows
Well-Known Member
Here is a tiny bit more detail for you:
Coronavirus: UK patient is University of York student
The university says the risk of the infection being passed on to other people on campus is "low".
www.bbc.co.uk
Also in regards the question of how long coronavirus can survive on surfaces, that article mentions somethng about this, sourced from Public Health England:
Sounds reasonable to me. I've previously mentioned timespans such as 'several days' and even 5 days maximum when the subject came up, but I was deliberately using a study that I assumed to be biased in the direction of making the problem seem as bad as possible. I'd rather deal in absolute worst-cases than the more moderate, realistic numbers, its good to have some wiggle room!
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elbows
Well-Known Member
By the way, if anyone bumps into hysterical articles going on about unnatural genetic sequences in the 2019-nCoV that resemble HIV, dont panic or buy into sinister theories. Due to the urgency of the situation a lot of papers are being shared in a 'pre-press' state, without any of the peer review stages having yet happened. And I believe there was one such research paper made available a couple of days ago that made claims about a bunch of short sequences in the 2019-nCoV, and how these sequences were somehow unepected, and could also be found in HIV-1. Well, this paper was then savaged by the experts I saw who read it and then commented online. Apparently those sequences can be found all over the place, and there are quite large estimates for how frequently we'd expect to find them occurring all over the place in the natural world by chance. The critics used data tools to find those same sequences in all sorts of other places unrelated to HIV, and I believe they even found them in a bat coronavirus. This rather punctured the bold claims made in the research paper. I dont have any links for this today, but if the bogus story gets sustained legs I'm sure I'll have reason to comment on it again and will provide more detail then.
Yu_Gi_Oh
天天好心情
elbows I keep wondering how many people must have the virus with minimal enough symptoms to not seek treatment, and as someone not versed in science, I did wonder why they don't take a random sample of seemingly well people and test them to find out. Just because they're so overwhelmed with cases anyway and lack resources? In an ideal world, would this be a feasible practice?
elbows
Well-Known Member
Yeah, serologic tests where you are looking for antibodies that demonstrate that person has been infected in the past.
Its a well established technique because so many infectious diseases can have widespread aymptomatic or mild cases. For the scientific and medical communities to ever be able to see beyond 'the tip of the iceberg' (cases that will present themselves to healthcare systems) such things need to be done.
So mostly its a question of when, not if, and on what scale. I get the idea it often happens much later on, for practical and priority reasons and because its often done as part of general research efforts rather than initial stages of emergency infection control. But I also have a sense that its the sort of thing authorities would ideally want to dabble with quite early too, as even a little bit of data could help with assumptions, model tuning and early estimates. But practicalities might get in the way. I've got no real expectation as to when we will hear about this being done, or the results, with this current outbreak. China might already have started some efforts on this front, or maybe its still too early.
elbows
Well-Known Member
Oh I should have explained why serology tests are favoured for that stuff, rather than the other sort of test(s) that they are already using on the suspected cases that present themselves to hospital etc.
Timing - the serology tests are looking for signs of past infection, so you wont miss the people that were infected but arent anymore. (although some ultimate time limits may still apply)
Capacity - the other forms of test are a finite resource that is best directed to suspected cases rather than using some of that capacity to test people that seem healthy.
Maybe other reasons too, eg if mild cases also limit the effectiveness of the non-serology tests, those tests may not end up being very good at getting positive results from certain mild cases, and such cases might have a better chance of being detected by serology tests.
Timing - the serology tests are looking for signs of past infection, so you wont miss the people that were infected but arent anymore. (although some ultimate time limits may still apply)
Capacity - the other forms of test are a finite resource that is best directed to suspected cases rather than using some of that capacity to test people that seem healthy.
Maybe other reasons too, eg if mild cases also limit the effectiveness of the non-serology tests, those tests may not end up being very good at getting positive results from certain mild cases, and such cases might have a better chance of being detected by serology tests.
elbows
Well-Known Member
Cheers 
Now, this weekend off I promised myself, I better start that any minute now!
Perhaps I love this era of information too much. But its so much better than just having to take the word of arbitrary authorities, or a world where specialists are only scrutinised in limited formal ways, or where knowledge is hoarded by experts who dont have the time or inclination to share it, or where the detail and merits of points are considered secondary to the participants status and formal qualifications.
Now, this weekend off I promised myself, I better start that any minute now!
Perhaps I love this era of information too much. But its so much better than just having to take the word of arbitrary authorities, or a world where specialists are only scrutinised in limited formal ways, or where knowledge is hoarded by experts who dont have the time or inclination to share it, or where the detail and merits of points are considered secondary to the participants status and formal qualifications.
JimW
支那暗杀团
Saw something here that profiled the deaths, apparently no-one under 30 has died, 30-50 less than 0.2% of ill have died, the overwhelming bulk of fatalities the elderly and those with underlying conditions. So again, no need to panic but take care of the vulnerable.
China reports H5N1 bird flu outbreak in Hunan province
Outbreak of avian flu reported in Hunan province, leading to a chicken cull.
Could this year get any worse?
It isn't spreading to humans but hopefully it is contained. The swine flu last year led to the decimation of China's pig livestock and high pork prices, which have apparently gotten even worse due to the Coronavirus. If the price of chicken goes up due to an outbreak of bird flu as well, then it is really bad.
Outbreak of avian flu reported in Hunan province, leading to a chicken cull.
Could this year get any worse?
It isn't spreading to humans but hopefully it is contained. The swine flu last year led to the decimation of China's pig livestock and high pork prices, which have apparently gotten even worse due to the Coronavirus. If the price of chicken goes up due to an outbreak of bird flu as well, then it is really bad.
weltweit
Well-Known Member
I could have sworn I read somewhere that Hong Kong was going to close the border .. oh well
