Wuhan virus: 2019-nCoV came from bats, still spreading in China, may not be locked down in the USA

Since we published our initial overview of the Wuhan Coronavirus epidemic, there have been a number of new developments, many of them concerning.

Key developments:

  • We’ve learned that the virus originated in bats, has transmitted from human to human in Vietnam, and that the CDC is evaluating dozens of potential cases in the United States.
  • In China the case numbers are escalating into the thousands as travel restrictions in Hubei are expanded to Beijing, the country’s capital.
  • Meanwhile, scientists around the world are locked in a fierce debate over the virus’s epidemiological parameters, with little consensus yet to emerge on key points.

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On Friday January 24, the WHO confirmed the first known human-to-human transmission of the Wuhan coronavirus outside China. The Vietnamese patient had not been to Wuhan, but contracted the virus in Vietnam from a close family member who had been to Wuhan. This is still not an indication of transmission between unrelated people in public spaces.

In the United States, as of this writing there are still only two confirmed cases of 2019-nCoV. The CDC confirmed Friday night it had been evaluating 63 potential cases in 22 states, and that 11 of these had already proven negative. There has been no news since then about the state of the other 52 potential cases, and there is still no evidence of human-to-human transmission inside the United States.

More cases are expected and limited outbreaks are considered possible.

In Hubei province itself, the situation continues to escalate about as expected, with relatively little unexpected news. The number of cases has risen to over 2000, while over 14,000 people are in quarantine awaiting test results, up from 8,000 yesterday.

The rising death toll now includes one of the medical personnel known to have contracted the disease from early patients, while reports indicate a higher number of infected medical personnel than previously known.

Social media reports from inside Wuhan suggest widespread difficulty with the shelter-in-place protocol due to supply shortages and some cases of untreated illness. The government has arranged six thousand free taxis but is still banning private road traffic. China has also sent 1,230 additional medics, including 450 military doctors, to Wuhan, and has announced it is building a second coronavirus-specific emergency hospital, expected to bring 1300 beds online in two weeks.

Outside Wuhan, the lockdown has expanded to cover at least 16 cities with 46 million inhabitants, making the locked-down population larger than the U.S. state of California.

It is still unclear how many cases of coronavirus are expected in Hubei outside Wuhan.

Amid the widening lockdown, the United States government announced it will charter private jets to carry all US citizens out of Wuhan.

In China outside Hubei, the situation continues to worsen, as human-human transmission has been confirmed in several cities, and major Chinese cities like Beijing, Shanghai, and Guangzhou host dozens of confirmed cases each.

The Chinese government has announced a halt to all intercity bus and train traffic in and out of Beijing, but it’s unclear if this is intended to halt transmission from Beijing, to prevent infected people from flocking to Tier One cities, or for some other reason.

Chairman Xi has announced via state television that China faces “a grave situation” with the widening epidemic. However, amid all of this, we still do not have confirmation of whether human to human transmission has gone widespread in areas outside Hubei, and may not have such confirmation for weeks.

A new genetic study confirmed the origin of the 2019-nCoV strain: bats. Sequence alignment of the Wuhan strain’s genome to all known animal coronaviruses has revealed a 96% alignment with an endemic bat coronavirus. Although bats are sometimes sold as food in China, current scholarly thinking is aligning on the notion of an intermediary, although it is not clear which one.

This study has largely displaced an earlier codon distribution analysis suggesting an origin in venomous snakes.

The scientific work to nail down the epidemic’s key epidemiological parameters continues in earnest, with stiff debate and no real consensus as of yet. Initial reports suggested possible values of Ro, the basic reproductive number, as low as 1.4 or as high as 4. In the time since then, a number of research groups have announced differing Ro figures.

The WHO released an estimate last week suggesting a value between 1.4 and 2.5, but has not yet released methods or source data. Computational epidemiologists at the University of Bern in Germany on January 23 announced a wide ranging estimate of 1.4 to 3.8, while a team of epidemiologists at Harvard Medical school using a different simulation method announced a range of 2.0 to 3.3.

The Jon Read group at Lancaster University in England gained massive attention for a simulation study suggesting that a high-range value of 3.6 to 4.0 was most likely. The analysis suggested that over 20,000 cases of the Wuhan coronavirus were already latent in Hubei and that the epidemic could expand to a quarter of a million cases by the time then-current protective measures began to show in case numbers in early February.

However, Dr. Read Friday announced on Twitter that his lab’s latest analysis based on new data had bracketed the Ro value in a narrow range of 2.4-2.6 and would release a new paper imminently.

Other scholars called this claim into question, particularly the narrow range of values.

Quantitative estimates of other key epidemiological parameters like latent periods and case fatality rates have been even less forthcoming.