Welcome to 2020 in which we already have reports of our first cluster of viral-pneumonia-of-unknown-cause cases, generating worldwide media and evoking memories of the sudden acute respiratory syndrome (SARS) coronavirus outbreak of 2002.

These things take time

Early days in an outbreak means we know pretty much nothing (Jon Snow). And that’s always how it goes, otherwise, the reports would be “here’s an outbreak which we’ve already confirmed by a pathogen we’ve already characterised among patients who are now recovering, causing a disease we know well that is now no longer at risk of being transmitted”. I mean, how many clicks would that get?

It takes time to do a lot of things. Like…

• reviewing cases to define disease and catalogue signs and symptoms,
  • if an unusual/novel syndrome, name it, define it, create guidelines to sensitively and specifically identify new instances of it
• looking at tests done so far
• conducting new lab tests by specialised labs (shipment of samples can take time)
• tracking contacts of cases
• watching for new cases to develop
• looking for shared exposures
• being sure human-to-human transmission isn’t occurring/hasn’t already occurred
• confirming any positive pathogen lab tests (sometimes off-site by a second specialist lab)
• possibly culturing the virus in cell lines, tissues, organs or organoids – this can easily take a week or more if everything is ready-to-go
• conducting genetic sequencing (subgenomic or whole genome) work and ensuring that is correct
• perhaps identifying an all-new pathogen.
  • design new, pathogen-specific tests
  • screen all samples and contacts and perhaps the local area

When exactly the public might get told about the outcome of some or all of that list depends on the reporting entities, politics, privacy, nature of the pathogen, global importance and so on.

What do we know so far?

I first heard about this outbreak thanks to Giuseppe Michieli. I checked with Crawford Kilian who had written about blogs already in place from Mike Coston who had, in turn, picked up on this from the avid disease trackers at FluTrackers.com. These are the core of flublogia; public horizon scanners par excellence.

Check out the latest on this subject at Mike’s blog, Avian Flu Diary and Crawford’s blog, H5N1. The initial thread from Flutrackers.com is here.

When did things seem to start?

We don’t really know that yet. It seems that hospitals in Wuhan, Hubei Province, China had been seeing cases of atypical pneumonia during December although for how long and whether these extended before December remain unknown. They were eventually diagnosed as viral pneumonia. Yes, viruses, not just bacteria, can cause pneumonia. This was noticed by the Wuhan Municipal Health Commission. The initial reports noted SARS – some social media talking heads implying the same SARS-CoV that caused more than 8,000 cases and 774 deaths in at least 27 countries, from 2002 to 2004,[7,8,9] but there was no official scientific support for that presumption at the time, nor for days afterwards.

Calm heads

Thankfully experienced virus hunters, including Professor Leo Poon of Hong Kong University [2] and Professor Yuen Kwok-yung [3] made clear public comments clarifying that as yet, we don’t have any data to work with so it’s just too soon to say the SARS-CoV is back. Or that any coronavirus is involved at all.

Vague hint, but is it reliable?

In one article, there was a tiny comment from an anonymous Wuhan Medical College researcher.[6]. They described some lab sequencing data that likely excluded SARS-CoV bt pout into play a possibly novel coronavirus. This has not been said officially, so just take it for space-filler for now (h/t Giuseppe).

Where are we at now?

And now we have a new update.[4,5]

The total number of patients with an unexplained viral pneumonia diagnosis has risen from 27 to 44 (+17) in three days, of which 11 – up from 4 – are critically ill. Is this just the result of time allowing capture of more of the initial cases or has there been a transmission from early cases over the past few days?

The rise in the number of cases is not good news in itself, but a rise without making it clear there has been a rise nor whether that rise (and the comment about households) means human-to-human transmission is occurring almost worse.

The latest articles, like all those before them, have gone to great pains to reassure their readers that there is no evidence of human-to-human (h2h) transmission. However, absence of evidence is not evidence of absence. I won’t be surprised when I read this has changed with new data. But this line is based on the evidence those on the ground have to share at the moment. That’s how good science works.

What was not detected

This is an important piece of information to have come from the update. We now know that at least a few of the many viruses that could cause pneumonia were not identified.

common respiratory diseases such as influenza, bird flu, and adenovirus infection have been ruled out

http://wjw.wuhan.gov.cn/front/web/showDetail/2020010309017

Take away the bias when hunting a virus

That leaves many other viruses though. This is where unbiased high-throughput sequencing (“next-generation” or “whole-genome” sequencing) could come into use.

These technologies can find viruses in samples that will be missed by looking for a few viruses with relatively specific molecular and biological tests or insensitive cell culture.

They just need enough sample left to use and enough virus in the sample and the right sample to be collected and to be kept in a good cold chain.

This sequencing technology and the expertise to use it, to enrich viral templates from complex human samples and to interpret the mountain of data the method erupts, have advanced sufficiently that they should really be the first stop public health discovery tool, rather than the research afterthought/publication enhancer, for investigations such as this. Here’s hoping that’s what’s happening.

Patience

For now, we have to wait for official information but rest assured that a lot of work is being done in labs right now to find and confirm the identity of the viral cause of this outbreak. No-one wants a repeat of the 2002-2004 SARS multi-country outbreak. But this is not then. We’ll know more when solid evidence is able to be reported. And then many of us in labs around the world will eagerly await virus sequence data so that we may prepare new tets and compare our existing tests to ensure we are ready for a worst-case scenario. Just in case.

References

1. Mainland reports suspected Sars outbreak
   https://news.rthk.hk/rthk/en/component/k2/1500301-20191231.htm?spTabChangeable=0 .
2. Too early to say Sars is back: HKU expert
   https://news.rthk.hk/rthk/en/component/k2/1500318-20191231.htm?spTabChangeable=0
3. Hong Kong takes emergency measures as mystery ‘pneumonia’ infects dozens in China’s Wuhan city
   https://www.scmp.com/news/china/politics/article/3044050/mystery-illness-hits-chinas-wuhan-city-nearly-30-hospitalised
4. Wuhan Municipal Health and Health Commission’s report on unexplained viral pneumonia, Published: 2020-01-03
   http://wjw.wuhan.gov.cn/front/web/showDetail/2020010309017
5. The number of pneumonia infections in Wuhan, China has increased to 44
   https://www.voachinese.com/a/wuhan-pneumonia-update-20200103/5230555.html
6. up to date! Wuhan pneumonia epidemic-related market closed, animal viscera scattered on street corners
   https://k.sina.com.cn/article_1315590387_4e6a50f301900p0k6.html?from=news&subch=onews
7. Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003
   https://www.who.int/csr/sars/country/2003_07_11/en/
8. Laboratory confirmation of a SARS case in southern China – update 2
   https://www.who.int/csr/don/2004_01_05/en/
9. CDC SARS Response Timeline
   https://www.cdc.gov/about/history/sars/timeline.htm