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Discussion - Estimating the CFR for 2019-nCoV

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  • #91
    Very interesting article on the figures coming from Deputy Director-General of Medical Administration Bureau of National Health and Family Planning Commission of the PRC, Jiao Yahui
    https://www.taiwannews.com.tw/en/news/3873016

    "...due to the lack of medical resources, the mortality rate in Wuhan has reached 4.9 percent. Meanwhile, the death rate for China as a whole is said to have remained at a steady 2.1 percent.

    However, Jiao quickly contradicted her own statement about the mortality rate when she said the number of confirmed cases of novel coronavirus (2019-nCoV) in Wuhan has exceeded 20,000 and there had been 425 deaths, with 414 of the dead concentrated in Hubei Province, accounting for 97 percent of the total, reported the Broadcasting Corporation of China. She then pointed out this is a mortality rate of 2.1 percent, inadvertently revealing the number of deaths must have been significantly underestimated.

    Again, contradicting the numbers and the official government dictated 2.1 percent mortality rate, she said the death rate in Hubei Province is 3.1 percent. She then added that Wuhan had the highest mortality rate in the province at 4.9 percent, and claimed the rate of death in the rest of the province had dropped by 0.16 percent.
    ".....

    "As early as January, netizens started to notice that government death tolls have routinely maintained an exact percentile for days on end. Many noticed that in the early days of reporting, the government put the death rate at 3.1 percent.

    Jan. 22: 17 deaths / 542 infections = 3.1 percent
    Jan. 23: 26 deaths / 830 infections = 3.1 percent
    Jan. 24: 41 deaths / 1,287 infections = 3.1 percent

    By the end of the month, the government apparently decided to set the new official mortality rate at 2.1 percent. As can be seen in the image below, the mortality rate was kept at a precise 2.1 percent, regardless of the numbers from Jan. 30 to Feb.

    If this is the Government "spin" I can only conclude that 2.1 is the "optimistic" figure that is generated to ensure - "She claimed there are many cases in other provinces, but the mortality rate is quite low. She said the government is still confident the vast majority of these cases are minor, so there is no need to panic"

    I have checked some of the figures quoted - am having trouble finding our actual numbers - someone probably has these easily to hand - but the two I have from a comparison graph - do tally with the 3.1%. Jan 22 (17 deaths per 542 confirmed) Jan 23 (26 deaths per 830).
    The steady 2.1% quoted is suspicious even in the fact that the word "steady" is used.

    The interview quoted was probably this one conducted in mandarin and quoted here;

    https://www.cnbc.com/2020/02/04/coronavirus-latest-updates-china-hubei.html
    "7:20 pm: Fatality rate ‘should gradually decline’ - Chinese health officials


    “I’m confident that it won’t require that long of a time period before the effects [of our efforts] will be evident, and Wuhan’s case-fatality rate should gradually decline,” Jiao Yahui, deputy director of the medical affairs and hospital administration of the National Health Commission, said Tuesday at a daily press conference in Mandarin, according to a CNBC translation.

    Jiao pointed out that 74% of coronavirus deaths, or 313, are in the city of Wuhan, where there is a case-fatality rate of 4.9%. That’s primarily due to lack of hospital beds in the early days of the virus’ spread, she said. At that time, she said there were only three designated hospitals with 110 beds for the critically ill... "...snip


    I have not found a full translated script and will continue to search... The interview was conducted February 3rd - so is almost old news now...
    “The only security we have is our ability to adapt."

    Comment


    • #92
      I have checked some of the figures quoted - am having trouble finding our actual numbers - someone probably has these easily to hand - but the two I have from a comparison graph - do tally with the 3.1%. Jan 22 (17 deaths per 542 confirmed) Jan 23 (26 deaths per 830).
      The steady 2.1% quoted is suspicious even in the fact that the word "steady" is used.
      Based on the daily data published by Johns Hopkins University, the table below lists the daily ratio of deaths to confirmed case and daily recovered cases to confirmed cases in Hubei Province . There does appear to be a slight decrease in deaths each day relative to the number of newly infected cases. What should be disturbing is that so few cases are being recorded as recovered even though this outbreak began it exponential increases in cases in mid January.

      Click image for larger version

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      Attached Files
      http://novel-infectious-diseases.blogspot.com/

      Comment


      • #93
        Originally posted by Laidback Al View Post

        Based on the daily data published by Johns Hopkins University, the table below lists the daily ratio of deaths to confirmed case and daily recovered cases to confirmed cases in Hubei Province . There does appear to be a slight decrease in deaths each day relative to the number of newly infected cases. What should be disturbing is that so few cases are being recorded as recovered even though this outbreak began it exponential increases in cases in mid January.

        The outbreak in China reached 2,744 confirmed cases on Jan 26. We reached 2,772 resolved cases yesterday. A gap of 12 days. We should see a significant increase in hospital releases over the next few days.
        Twitter: @RonanKelly13
        The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

        Comment


      • #94
        https://www.scmp.com/news/china/soci...eaths-and-2841
        Shanghai warns of aerosol infection


        Shanghai’s health commission added aerosol transmission the list of ways of contracting the coronavirus.

        But the National Health Commission and the World Health Organisation have yet to take similar action.

        In its latest treatment plan for the virus, the NHC said aerosol transmission had yet to be confirmed.
        “The only security we have is our ability to adapt."

        Comment


        • #95
          Official rate "The fatality rate is not high, about 2.1%." is being dispersed to Pacific Islands. China has a lot of investment to protect https://flutrackers.com/forum/forum/...-shen-zhiliang

          Comment


          • #96
            1.7 : https://github.com/calthaus/ncov-cfr

            I'm interested in expert panflu damage estimates
            my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

            Comment


            • #97

              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+, Lucy Okell+, Anne Cori, Natsuko Imai , Marc Baguelin, Sangeeta Bhatia, Adhiratha Boonyasiri, Zulma Cucunubá, 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*. With support from other volunteers from the MRC Centre.1

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

              *Correspondence: neil.ferguson@imperial.ac.uk 1 See full list at end of document. +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/

              Comment


              • #98
                Originally posted by sharon sanders View Post
                [I]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.
                Twitter: @RonanKelly13
                The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

                Comment


                • #99
                  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 : 109,400,189,89,106,200,268,139,442,377,564,918,119 3,52,258
                  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)
                  I'm interested in expert panflu damage estimates
                  my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

                  Comment


                  • Originally posted by etudiant View Post

                    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.

                    Comment


                    • 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
                      "Safety and security don't just happen, they are the result of collective consensus and public investment. We owe our children, the most vulnerable citizens in our society, a life free of violence and fear."
                      -Nelson Mandela

                      Comment


                      • Originally posted by kiwibird View Post
                        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?
                        “The only security we have is our ability to adapt."

                        Comment


                        • 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%.

                          Comment


                          • kiwibird
                            kiwibird commented
                            Editing a comment
                            Thank you Alan.

                        • Originally posted by AlanBaxter View Post
                          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.

                          Comment


                          • 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/10.1....12.20022434v1
                            Twitter: @RonanKelly13
                            The views expressed are mine alone and do not represent the views of my employer or any other person or organization.

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