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Discussion - Estimating the CFR for 2019-nCoV

I have posted this here because the 18% number is stunning. Maybe some of you who are good at math/statistics can look at their report and make a comment.


10 February 2020 - Imperial College London‌



Report 4: Severity of 2019-novel coronavirus (nCoV)

(Download Report 4)


Ilaria Dorigatti[SUP]+[/SUP], Lucy Okell[SUP]+[/SUP], Anne Cori, Natsuko Imai , Marc Baguelin, Sangeeta Bhatia, Adhiratha Boonyasiri, Zulma Cucunub?, Gina Cuomo-Dannenburg, Rich FitzJohn, Han Fu, Katy Gaythorpe , Arran Hamlet, Wes Hinsley, Nan Hong , Min Kwun, Daniel Laydon, Gemma Nedjati-Gilani, Steven Riley, Sabine van Elsland, Erik Volz, Haowei Wang, Raymond Wang, Caroline Walters , Xiaoyue Xi, Christl Donnelly, Azra Ghani, Neil Ferguson[SUP]*[/SUP]. With support from other volunteers from the MRC Centre.[SUP]1[/SUP]

WHO Collaborating Centre for Infectious Disease Modelling
MRC Centre for Global Infectious Disease Analysis
J-IDEA
Imperial College London

[SUP]*[/SUP]Correspondence: neil.ferguson@imperial.ac.uk [SUP]1[/SUP] See full list at end of document. [SUP]+[/SUP]These two authors contributed equally.

Summary Report 4

We present case fatality ratio (CFR) estimates for three strata of 2019-nCoV infections. For cases detected in Hubei, we estimate the CFR to be 18% (95% credible interval: 11%-81%).

For cases detected in travellers outside mainland China, we obtain central estimates of the CFR in the range 1.2-5.6% depending on the statistical methods, with substantial uncertainty around these central values.

Using estimates of underlying infection prevalence in Wuhan at the end of January derived from testing of passengers on repatriation flights to Japan and Germany, we adjusted the estimates of CFR from either the early epidemic in Hubei Province, or from cases reported outside mainland China, to obtain estimates of the overall CFR in all infections (asymptomatic or symptomatic) of approximately 1% (95% confidence interval 0.5%-4%). It is important to note that the differences in these estimates does not reflect underlying differences in disease severity between countries. CFRs seen in individual countries will vary depending on the sensitivity of different surveillance systems to detect cases of differing levels of severity and the clinical care offered to severely ill cases. All CFR estimates should be viewed cautiously at the current time as the sensitivity of surveillance of both deaths and cases in mainland China is unclear. Furthermore, all estimates rely on limited data on the typical time intervals from symptom onset to death or recovery which influences the CFR estimates.

Appendix data sources
Data on early deaths from mainland China: hubei_early_deaths_2020_07_02.csv
Data on cases in international travellers: international_cases_2020_08_02.csv


https://www.imperial.ac.uk/mrc-globa...n-coronavirus/
 
I have posted this here because the 18% number is stunning. Maybe some of you who are good at math/statistics can look at their report and make a comment.


Ok - so here is what I get out of it - They feel that Hubei is detecting and reporting only the most severe cases. For example, they estimate 24,000 to 33,000 infection onsets on Jan 31, a day when only 2,099 cases from all of China were reported. Thus the cfr is artificially high. They feel that the rest of China and other countries are detecting a greater number of milder cases, but still missing some. They have used math to normalize the reporting from the various regions and conclude an overall corrected cfr of 0.8-0.9%. That seems like a reasonable number to me and is probably in the right ballpark.
 
this assumes a time-lag of 22.2 days from "confirmed" to "death"
and it assumes that all cases are confirmed ; CFR=deaths/(confirmed cases)

My data starts Jan.25, before that there were 572 confirmed cases in Wuhan,
157 in Hubei ex Wuhan, 558 in China ex Hubei.
Currently there are ~70 daily deaths in Wuhan, 18 in Hubei ex Wuhan, 7 in China ex Hubei.
If those cases pre-Jan.25 were all attributed to Jan.18 , then with the 22-day-lag
I get CFR=12.2 in Wuhan, CFR=11.5 in Hubei ex Wuhan, 1.3% in China ex Hubei.
Obviously many cases were unconfirmed, especially in Wuhan. There were those 5M people
leaving the city at that time.It is likely that severe cases had a greater probability
of being confirmed.
You would expect deaths climbing sharply after 10-20 days already - even if 22 were the average.
I do not see this. Deaths in Hubei ex Wuhan (where I'd assume not much underreporting)
were 2,6,12,12,12,13,15,16,16,18,5,14,18,18

And we clearly have no exponential increase in confirmed cases as they assume
--------------------------------------------
I'm unsure, that all doesn't make so much sense to me.
The CFR might be changing. The CFR might be different in Wuhan.
The 22-day-lag might be too long.
(CFR=deaths per all infections).
------------------------------------------------------
and then we have "severe cases" . These counts were up quite a lot since Feb.03,
but now they somehow have redefined "severe":
daily reported new severe cases in Hunan Jan.26-Feb.09 : 109,400,189,89,106,200,268,139,442,377,564,918,1193,52,258
daily reported new severe cases in China ex Hunan , Jan.26-Feb.09 :
28,115,74,42,51,68,47,47,50,54,96,44,87,135,38 (212)
 
That does seem a more plausible explanation, if only because it is questionable whether the Chinese themselves would have accurate records, given the chaotic situation in Wuhan that is visible on the videos.
So the sad truth is that we have no real idea of the actual numbers, just that it is desperately bad in Wuhan. My heart goes out to them, they are fighting for us as well.

Two papers just published, one from Hubei & one from Beijing, again have death rates consistent with those on flutracker - 4% in hospital acquired cases in Hubei; 0% in Beijing. The Hubei cases had some evidence of faecal/oral infection; if disease is more severe if infected by this route, that would explain much.
 
ɪᴀɴ ᴍ ᴍᴀᴄᴋᴀʏ, ᴘʜᴅ @MackayIM
"the declining trend of Rt after the beginning of January was most likely due to delayed reporting rather than reduced transmissibility"

Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China
Background: The ongoing outbreak of the 2019 novel coronavirus (2019-nCoV) in China has led to the declaration of Public Health Emergency of International Concern by the World Health Organization....
medrxiv.org

3:50 PM ? Feb 12, 2020?TweetDeck

------------------------------------------------------------------------

Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China

Yang Yang, Qingbin Lu, Mingjin Liu, Yixing Wang, Anran Zhang, Neda Jalali, Natalie Dean, Ira Longini, M. Elizabeth Halloran, Bo Xu, Xiaoai Zhang, Liping Wang, Wei Liu, Liqun Fang
doi: https://doi.org/10.1101/2020.02.10.20021675
...
The overall CFR was estimated be 3.06% (95% CI 2.02-4.59%), but male patients, ≥60 years old, baseline diagnosis of severe pneumonia and delay in diagnosis were associated with substantially elevated CFR. The R0 was estimated to be 3.77 (95% CI 3.51-4.05), ranging 2.23-4.82 in sensitivity analyses varying the incubation and infectious periods. Conclusions: Compared with SARS-CoV, 2019-nCoV had comparable transmissibility and lower CFR. Our findings based on individual-level surveillance data emphasize the importance of early detection of elderly patients, particularly males, before symptoms progress to severe pneumonia.
...
https://www.medrxiv.org/content/10.1....10.20021675v1
 
For discussion - I have not found a corroborating first hand report yet.

https://www.taiwannews.com.tw/en/news/3871594

(Photo of screenshot at above link)

TAIPEI (Taiwan News) — As many experts question the veracity of China's statistics for the Wuhan coronavirus outbreak, Tencent over the weekend seems to have inadvertently released what is potentially the actual number of infections and deaths, which were astronomically higher than official figures.

On late Saturday evening (Feb. 1), Tencent, on its webpage titled "Epidemic Situation Tracker", showed confirmed cases of novel coronavirus (2019nCoV) in China as standing at 154,023, 10 times the official figure at the time. It listed the number of suspected cases as 79,808, four times the official figure.
...snip

https://www.theguardian.com/world/20...-and-new-cases

Victor Shih, a specialist in Chinese politics at the school of global policy and strategy at University of California San Diego, said the switch in methodology was “disturbing”. “The adjustment of the data today proved without doubt that they have had two sets of numbers for confirmed infected all along,” he said.

Does this easy adjusting to new reporting criteria lend credence to the Taiwan News report?
 
No - the increase in numbers was relatively small, and compensated for an unusual relative lack of cases for a few days before the "correction" was added. More worrying is a discussion around what the denominator should be. If you take deaths as of this week, then it makes no sense to take confirmed cases from this week, as you have only just identified them and they have not had a chance to die; the correct denominator should be the confirmed cases something like 2 weeks ago (because on average those that die or recover do so something like 2 weeks after identification. This makes the CFR to be something like 20%. Similarly if you obtain a denominator by adding confirmed deaths and confirmed recoveries, you get a similar value. However if you take only the numbers outside mainland China, you get a CFR of a little under 4%.
 
No - the increase in numbers was relatively small, and compensated for an unusual relative lack of cases for a few days before the "correction" was added. More worrying is a discussion around what the denominator should be. If you take deaths as of this week, then it makes no sense to take confirmed cases from this week, as you have only just identified them and they have not had a chance to die; the correct denominator should be the confirmed cases something like 2 weeks ago (because on average those that die or recover do so something like 2 weeks after identification. This makes the CFR to be something like 20%. Similarly if you obtain a denominator by adding confirmed deaths and confirmed recoveries, you get a similar value. However if you take only the numbers outside mainland China, you get a CFR of a little under 4%.

Re the correct denominator. Until serology testing can give us a better idea of the number of sub clinical infections the denominator could be badly out, any significant numbers of undiagnosed infections will up the R0 and reduce the CFR.
 
Early epidemiological assessment of the transmission potential and virulence of 2019 Novel Coronavirus in Wuhan City: China, 2019-2020
View ORCID ProfileKenji Mizumoto, Katsushi Kagaya, Gerardo Chowell
doi: https://doi.org/10.1101/2020.02.12.20022434
This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
AbstractInfo/HistoryMetrics Preview PDF
Abstract

Background: Since the first cluster of cases was identified in Wuhan City, China, in December, 2019, 2019-nCoV has rapidly spread across China as well as caused multiple introductions in 25 countries as of February, 2020. Despite the scarcity of publicly available data, scientists around the world have made strides in estimating the magnitude of the epidemic, the basic reproduction number, and transmission patterns. Recently more evidence suggests that a substantial fraction of the infected individuals with the novel coronavirus show little if any symptoms, which suggest the need to reassess the transmission potential of emerging disease. The present study aimed to estimates of the transmissibility and virulence of 2019-nCov in Wuhan City, China, by reconstructing the underlying transmission dynamics.

Methods: We employ statistical methods and publicly available epidemiological datasets to jointly derive estimates of transmissibility and severity associated with the novel coronavirus. For estimation, the daily series of laboratory-confirmed nCov cases and deaths in Wuhan City and epidemiological data of Japanese evacuees from Wuhan City on board government-chartered flights were used.

Results: We found that our posterior estimates of basic reproduction number (R) in Wuhan City, China in 2019-2020 is calculated to be as high as 7.05 (95%CrI: 6.11-8.18) and the enhanced public health intervention after January 23rd in 2020 has declined R to 3.24 (95%CrI: 3.16-3.32), with the total number of infections (i.e. cumulative infections) estimated at 983006 (95%CrI: 759475-1296258) in Wuhan City, raising the proportion of infected individuals to 9.8% (95%CrI: 7.6-13.0%). We also found that most recent crude infection fatality ratio (IFR) and time-delay adjusted IFR is estimated to be 0.07% (95% CrI: 0.05%-0.09%) and 0.23% (95%CrI: 0.17-0.30%), which is several orders of magnitude smaller than the crude CFR at 4.06% Conclusions: We have estimated key epidemiological parameters of the transmissibility and virulence of 2019-nCov in Wuhan, China, 2019-2020 using an ecological modelling approach. The power of our approach lies in the ability to infer epidemiological parameters with quantified uncertainty from partial observations collected by surveillance systems.

...
https://www.medrxiv.org/content/10.1101/2020.02.12.20022434v1
 
[h=1]2019-nCoV: preliminary estimates of the confirmed-case-fatality-ratio and infection-fatality-ratio, and initial pandemic risk assessment[/h] [h=4]Mike Famulare (Institute for Disease Modeling)[/h] [h=4]v2.0: substantive revision 19 February 2020. (v1.1 February 4; v1.0 January 31.)[/h] [h=1]Recap of substantive revision on 19 February 2020[/h]
On February 16, I (Mike Famulare) received an email from Neil Ferguson who kindly pointed out a technical error in the published estimate of the overall infection-fatality-ratio (IFR). Despite the attention paid to adjusting for delays in outcomes, I neglected to adjust the estimate of the case-ascertainment rate–the fraction of all infections reported as cases–for the delays from infection onset to symptom onset and case confirmation, and thus over-estimated the total number of infections denominator and under-estimated the IFR. With this additional adjustment and using the same methodology and data from the original version of this report, the corrected estimate of the infection-fatality-ratio (IFR) is 0.94 (0.37, 2.9) percent. While the uncertainty remains large, this estimate now excludes CDC’s reference estimate for the 1957 H2N2 pandemic flu (0.1 to 0.3 percent) and is only two-fold lower than and overlapping with CDC’s reference estimate of 2.04 percent for the 1918 H1N1 pandemic flu. This estimate from early data (globally representative of what was known at the time, but mostly from Wuhan) is also now compatible with the independent estimate published by the Imperial College group on February 10. While this correction does not change the assessment that COVID-19 exhibits severe pandemic potential in the absence of effective interventions, the shift in framing brought about by this three-fold revision from ‘possibly comparable to the 1957 flu but not 1918’ to ‘possibly comparable to 1918’ may meaningfully impact risk perception.

The document below has been edited from previous versions to correct the technical issue described above. Unless noted, the results reflect the state of data and interpretation as of February 4 and are otherwise unchanged. Please see WHO Situation Report 29 for a summary of public modeling on this topic to date, and seek more recent sources for updates in response to new data–especially regarding the impacts of age and comorbities as recently published by China CDC (mirror).
...
https://institutefordiseasemodeling...ality_rates_and_pandemic_risk_assessment.html
 
I am not sure if this helps or hinders in estimating the number of severe cases to be expected. From Iran's Tabriz University
https://translate.googleusercontent...%D8%AA&usg=ALkJrhjwZKnzCCgim2CX80qw3L8mwWtEzw
"Coronavirus appears asymptomatic or mildly symptomatic in 5% to 4% of cases," he said. "These people do not need to go to the hospital and recover by resting at home and having good health care." Health centers are also ready to accept the remaining 5% with more severe symptoms or requiring hospitalization.
 
Since this new virus is a big risk mostly for older seniors and health compromised people, I'd like to know what the mortality rate for that population would be over the next year if the virus were taken out of the equation. Is it already close to 2%? That might put some perspective on the situation. Of course, the compression of mortality into a tighter time frame is still going to put a strain on the health care system.
 
Since this new virus is a big risk mostly for older seniors and health compromised people, I'd like to know what the mortality rate for that population would be over the next year if the virus were taken out of the equation. Is it already close to 2%? That might put some perspective on the situation. Of course, the compression of mortality into a tighter time frame is still going to put a strain on the health care system.

Recent epidemiological study of over 40,000 patients in China revealed a much higher CFR for persons over 70. gsgs posted a pdf version in one of the discussion forums.

In this study, adding all CFR rates from three categories - 60-69, 70-79, and 80+, then dividing by 3 to get an average - the CFR was 8.8%

The good news for younger than 60 is the CFR drops considerably. However, the emotional toll of losing parents and grandparents will be profound.

Additionally, one of the biggest concerns and game changers is the ability for any area to manage the severe and critical cases before being overwhelmed. Once the system is saturated, the CFR will increase significantly. China's system worked very well and they keep reinforcing resources and staff. I am not confident most countries can do the same.
 
Since this new virus is a big risk mostly for older seniors and health compromised people, I'd like to know what the mortality rate for that population would be over the next year if the virus were taken out of the equation. Is it already close to 2%? That might put some perspective on the situation. Of course, the compression of mortality into a tighter time frame is still going to put a strain on the health care system.

Also, in US, almost 3,000,000 people die from all causes annually. A CFR 2% with 30% attack rate would double or triple that number.
 
Unfortunately there are current figures showing Italian rates of infection and, sadly, many have passed away due to the Covid-19 Coronavirus.

From the Italian figures which appear to be incredibly thorough and accurate with vigorous testing of even asymptomatic people I have tried to document the sequence of events.

We understood that you would normally need two weeks to get to a severe state -- that would make 16th February to compare todays CFR to (29th February). On the 16th there weren't even 29 people in Italy identified as being positive for Covid-19, (29 is the current number of fatalities). There are reports of people developing symptoms around the beginning of the month however and this might explain the shortened timeframe.

We have to move to the 21st (pm) before we see 35 cases confirmed. Two people had died, earlier - by the 16th. This would give an initial 6% CFR.

On the 23rd am there were 132 Confirmed cases including 26 severe cases and 4 deaths. - 20%severe and 3% CFR.

27th February 650 Confirmed cases, 17 deaths. CFR 2.5%

29th February 1139 Confirmed Cases, 29 deaths 2.5% CFR. Also known that there are 48% need to be hospitalised and 10% of those need intensive care.

I am very aware that these are not statistics but reflect the sad reality of peoples lives. I really hope that people who are affected, both victims, their families and loved ones - and healthcare workers, will understand that I am really sorry for their loss and suffering. It is important that we take a step back and look at the pattern of illness involved with this new virus in order to know what the world that has so far remained relatively untouched has in store so we can better prepare.

Any help with correcting any misunderstood figures would be appreciated.
 
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