Saturday, January 25, 2020

Coronavirus Case Count Exceeds 1300, 41 Deaths - Epidemic Projection

Credit CDC


The reality of running a one-man blog is that you have to sleep sometime, and over the past 7 hours - while I've been oblivious to the world - roughly 400 new nCoV2019 cases have been announced, and the death toll has risen to 41 (see FluTrackers  2019-nCov Confirmed Case List by Country w/Links to Sources).

At least 12  governments outside of Mainland China have now confirmed cases, and many more are testing suspect cases.  Again from the FT list (update at 9:15pm EST tonight).
  • Australia: 1 case link
  • China: 1287 cases & 41 deaths link
  • France: 3 cases link
  • Japan: Japanese citizen with travel history from Wuhan, Hubei province, resides in Kanagawa prefecture - 2 case link
  • Nepal: 1 case link
  • Singapore: 3 cases link
  • South Korea: Chinese citizen from Wuhan, Hubei province - 1 case link
  • Taiwan: Taiwan citizen returned from Wuhan - 1 case link
  • United States: 2 cases link
  • Vietnam: 2 cases link

These numbers are increasing so rapidly that by the time I can post them, they are already out of date. And the reality is, reported cases are generally assumed to represent only a fraction of the actual number of cases.

In past outbreaks of MERS-CoV, and avian influenza, we've seen estimates of anything from a 10 fold to more than a 100 fold difference between reported and actual cases.

While these estimates are based on mathematical models, and are based - particularly early in an outbreak of a new disease - on less than solid assumptions, they can be useful in gauging the estimated size, and growth potential of an epidemic.
We've one such estimate - published today on the MedRxiv Preprint Server (not peer-reviewed) - that paints a stark picture of the current epidemic, and extrapolates its growth over the next 10 days. 
Estimates like this should be taken with a sizable grain of salt, as conditions on the ground may change (for better or worse) in the days ahead.  But if this paper is even close to right, the number of cases is forecasted to rise rapidly.

Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions
View ORCID Profile Jonathan M Read, View ORCID Profile Jessica RE Bridgen, Derek AT Cummings, Antonia Ho, View ORCID Profile Chris P Jewell
This article is a preprint and has not been peer-reviewed [what does this mean?].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.

Preview PDF

In December 2019, a novel coronavirus (2019-nCoV) is thought to have emerged into the human population in Wuhan, China. The number of identified cases in Wuhan has increased rapidly since, and cases have been identified in other Chinese cities and other countries (as of 23 January 2020).
We fitted a transmission model to reported case information up to 21 January to estimate key epidemiological measures, and to predict the possible course of the epidemic, as the potential impact of travel restrictions into and from Wuhan. We estimate the basic reproduction number of the infection (R_0) to be 3.8 (95% confidence interval, 3.6-4.0), indicating that 72-75% of transmissions must be prevented by control measures for infections to stop increasing. We estimate that only 5.1% (95%CI, 4.8-5.5) of infections in Wuhan are identified, and by 21 January a total of 11,341 people (prediction interval, 9,217-14,245) had been infected in Wuhan since the start of the year.
Should the epidemic continue unabated in Wuhan, we predict the epidemic in Wuhan will be substantially larger by 4 February (191,529 infections; prediction interval, 132,751-273,649), infection will be established in other Chinese cities, and importations to other countries will be more frequent. Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.
Our findings are critically dependent on the assumptions underpinning our model, and the timing and reporting of confirmed cases, and there is considerable uncertainty associated with the outbreak at this early stage. With these caveats in mind, our work suggests that a basic reproductive number for this 2019-nCoV outbreak is higher compared to other emergent coronaviruses, suggesting that containment or control of this pathogen may be substantially more difficult.
Competing Interest Statement
The authors have declared no competing interest.        
          (Continue . . . )

There are several key assumptions in this report that may - or may not - prove correct. Including that their estimated R0 (reproductive number) of the virus is 3.8.   Essentially, the number of new cases in a susceptible population likely to arise from a single infection. 

In the simplest of terms, with an R0 below 1.0, a virus (as an outbreak) begins to sputter and dies out. Above 1.0, and an outbreak can have `legs’. 

This estimated R0 is more than 50% higher than the R0 presented (1.4-2.5 ) by the WHO IHR Emergency Committee 36 hours ago.  That doesn't make it wrong, but it is an aggressive number.

Secondly, that  `. . .  travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission'.  While I tend to believe that is true, it is far from a given.

Given less-than-detailed reporting coming from the epicenter, and the fact that over the past week we're seeing a doubling of the `official case count' (always a lagging indicator) roughly every 48 hours,  it is certainly possible that this projection may not be that far off.

Stay tuned.