When it comes to emerging infectious diseases and outbreaks, so much can happen in a week. In the case of the coronavirus outbreak in China, I've gone from not being too alarmed, to thinking, oh, crap! But that still doesn't mean we should all panic.
The likelihood of a case of the coronavirus arriving here is high, especially as the number of cases in China increases. That was the assessment yesterday from New Zealand's director general of health, Dr Ashley Bloomfield, and director of public health, Dr Caroline McElnay, in a briefing to the media. As a result, public health protection officers and nurses are at Auckland and Christchurch airports to help people arriving from China who feel unwell.
But here's the important message: the chances of us seeing an outbreak like that happening in China is very low. That's because we don't have the same population density as China and are in a good position to be able to identify and isolate infected people and anyone they have had contact with to stop the infection spreading.
What a difference a week makes
On Sunday the January 19 I started getting calls from journalists asking about cases of a new virus in Wuhan City, China. At that time, the World Health Organisation was reporting that China had informed them of an outbreak of pneumonia caused by a novel coronavirus, related to the virus responsible for SARS.
The numbers being quoted were from January 12: 41 laboratory-confirmed cases, including two deaths. One case had also been reported in Japan and two in Thailand. They were in people who had travelled from Wuhan. There were no reports of healthcare workers becoming ill, so it looked like the virus wasn't spreading easily between people.
It was a case of watch and wait, and keeping fingers and toes crossed that person-to-person spread would be limited. If this was the case, and the original source had been removed, the outbreak would hopefully fizzle out quickly.
Fast forward a week and the outlook doesn't seem so rosy, for China at least. There are now reports of over 2,700 confirmed cases in China with 81 deaths. Cases have been reported in Australia, France, Hong Kong, Japan, Macau, Malaysia, Nepal, Singapore, South Korea, Taiwan, Thailand, USA, and Vietnam.
Over the week several papers have been published - both peer-reviewed and in preprint - trying to shed some light on the outbreak. We'll get to the #snakeflu paper shortly…
A serious infection
In the Lancet and New England Journal of Medicine, Chinese researchers have reported the isolation and identification of the new virus and how it relates to other coronaviruses, as well as the symptoms of the people first infected.
The papers paint a picture of a pretty serious infection. In the paper by Professor Chaolin Huang and colleagues, they report the cases of the 41 people in Wuhan City with coronavirus pneumonia who had been admitted to hospital by the January 2.
Most of the patients were men (30 of the 41) and fewer than half had an underlying disease like diabetes or cardiovascular disease (13). Almost all of them had started with a fever. Other symptoms included cough, fatigue, and a headache. One patient also had diarrhoea. Thirteen of the 41 needed admitting to the intensive care unit and six of them died.
Also published in the Lancet, Dr Jasper Fuk-Woo Chan and colleagues shed a little light on the transmissibility of the virus. The paper involves a family of six from Shenzhen, a coastal area of south China bordering Hong Kong. The family visited an infected family in Wuhan and then returned home, infected, and spread the virus to another family member. The Lancet has also produced an excellent graphic showing when each person started to show symptoms.
These cases clearly show the virus can transmit from person-to-person, with five of the six family members becoming ill. The incubation period from these cases seems to be 3-6 days. But these cases are likely to have involved people in close and repeated contact.
None of these papers has been able to answer several really important questions: how infectious are people before they show symptoms, how much contact is needed to get infected, and whether all infected people go on to have symptoms.
The answers to these questions will determine what will be needed to bring the outbreak under control. If it does turn out that lots of people are infectious before they show symptoms, then we are really going to need a vaccine to bring this outbreak under control.
For now, my advice for Kiwis remains the same. Don't panic! If you need to travel to the areas of China with high numbers of coronavirus cases, perhaps see if you can postpone your travel. Otherwise, avoid live animal markets and people with flu-like symptoms, wash your hands frequently, and try to avoid touching your face.
If you've recently arrived from China and had contact with people who have fallen ill, isolate yourself for the next week or so if you can, just in case. If you didn't have contact with anyone who is ill, watch out for any of the symptoms and if they appear, isolate yourself and contact your GP, and make sure you practice good sneezing and coughing hygiene - into your elbow, not your hands.
For everyone else, wash your hands frequently and try to avoid touching your face.
And finally, no, it's not likely to be snake flu …
A few days ago, a paper was published concluding that the "snake is the most probable wildlife animal reservoir responsible for the current outbreak". They based that conclusion on their finding that after bats, the new coronavirus shared a bias for codon usage that was close to that of two species of snake, the many-banded krait (Bungarus multicinctus) and the Chinese cobra (Naja atra).
Soon after the paper was released, scientists took to social media expressing doubts, raising the fact that it's pretty rare for the codon usage of a virus to closely match its reservoir host. Others criticised the way the authors prepared their codon usage tables.
Kristian Andersen made some better codon usage tables and then calculated the codon usage of the new virus as well as the coronaviruses that cause SARS and MERS to see how closely they matched to a range of different species including the known reservoir species for SARS-CoV and MERS-CoV as well as some unlikely species.
Long story short: the codon usage bias of the novel coronavirus does indeed closely match several different snake species, but the same is also true for both MERS-CoV and SARS-CoV that have camels and bats as known reservoir species. In fact, the MERS and SARS viruses were even better matches.
The viruses also closely matched several fungi. And as Kristian says "no, fungi are not likely to have started the outbreak in Wuhan".