An ongoing dialogue on HIV/AIDS, infectious diseases,
February 2nd, 2020
A Coronavirus ID Link-o-Rama, Because I’m Not Watching the Super Bowl
With so much of the ID-related news out there dominated by the novel coronavirus (2019-nCoV, hard to type) outbreak, it seems appropriate to collect some of the more interesting or useful findings in this busy past week.
Think of it as an ID Link-o-Rama — Special Novel Coronavirus Edition.
As with last week’s post, an important caveat — the outbreak continues to evolve rapidly, and data quickly become out of date. All are encouraged to check in with the excellent guidance and information on the CDC, WHO, and IDSA sites (among others), all of which are updated regularly.
On to the links:
- The mean incubation period of novel coronavirus disease after contact with an active case is around 5 days. The 95% confidence interval around that estimate is 4.1 to 7.0 days. Importantly, the onset of symptoms 2 weeks or more after exposure appears very unlikely. These data should dispel circulating rumors that this virus has a much longer incubation period than other coronaviruses — in fact, it appears quite similar (Figure 3).
- This case cluster demonstrates coronavirus can spread before the onset of symptoms. However, as in most infectious diseases, symptomatic cases are probably more contagious — usually because people with symptoms have a higher viral burden. While the findings in this report are of concern, the true contribution of asymptomatic spread of the virus in the present outbreak remains unknown. [Update: The “asymptomatic” person may have had symptoms after all. Additional details summarized here.]
- The New York Times has posted a widely cited figure comparing mortality and contagiousness of coronavirus with other infectious diseases. Current estimates are 3% mortality and transmission number (R0) between 1.5 and 3.5. It’s an impressive graphic (modeled on this one) that puts the infection into perspective. Importantly, note the log scale of the vertical axis in the Times figure, which prompted this revision:
This is one of those “please don’t judge me for making this horror” graphs that I’ve just thrown together with possibly the least reliable underlying data (hence extensive caveats in caption). All available on github, please scrutinise and send improvements pic.twitter.com/vtU3bUFDzH
— Isaac Florence (@IsaacATFlorence) January 31, 2020
- Here’s a clear explanation why the estimated mortality will likely change — for the better — as we gain greater understanding of the disease. Severe cases tend to dominate reports early in an outbreak; only later, when diagnostic tests and surveillance improves, will we understand how many mild (and even asymptomatic) cases occur. Remember when West Nile virus first appeared in North America? It was initially terrifying — yet we now know that 80% of people who acquire this infection do so without any symptoms whatsoever, and fewer than 1% develop encephalitis.
- Wonderful perspective from Dr. Elizabeth Rosenthal offering her advice on how to avoid coronavirus. Wash your hands frequently. Yep, that’s it — plus a few other things that fall squarely into the “common sense” category. The piece includes interesting anecdotes from when she covered SARS in 2002-3 as a journalist, living in China with her family.
- This online calculator estimates the effectiveness of screening travelers to detect people who have 2019-nCoV. You can move the sliders around on parameters such as incubation period, proportion who have fever, and R0 (transmissibility), among others. Not surprisingly, those most likely to be detected have both fever and a reported epidemiologic risk.
- Some patients with coronavirus disease have already received antiviral therapy with drugs demonstrating in vitro activity against the virus. In this report, a woman received lopinavir/ritonavir (along with oseltamivir). In another case, doctors received permission for compassionate use of the experimental drug remdesivir. Both patients improved — but obviously in these anecdotal cases, we don’t know if they would have improved anyway. A Chinese clinical trials registry cites at least one planned study. My virologist colleague Dr Jonathan Li summarized some of the background data in this thread.
- How did this novel coronavirus first spread to humans? This is critical information — not only for this outbreak, but also for prevention of future zoonotic infections. Excellent summary of ongoing work in this area.
- A pre-print reported that the novel coronavirus had insertions that bore an “uncanny” resemblance to HIV gp120 and Gag. This finding (later withdrawn) triggered a momentary spike in conspiracy theories that would be excellent evidence for the benefits of scientific peer review — which happened in this case anyway, only not in the usual way. For a good takedown, read this analysis.
- Many have tried to put the coronavirus outbreak in perspective by citing this year’s flu season. Here’s the brilliant opening from the linked piece:
The rapidly spreading virus has closed schools in Knoxville, Tenn., cut blood donations to dangerous levels in Cleveland and prompted limits on hospital visitors in Wilson, N.C. More ominously, it has infected as many as 26 million people in the United States in just four months, killing up to 25,000 so far.
In other words, a difficult but not extraordinary flu season in the United States …
So yes — get your flu shot! Listen to Dr. Stephenson!
#Influenza and #coronavirus are the same problem. It’s not a competition over which virus is the scariest. They are circulating at the same time which complicates diagnosis and treatment and add together to stress our health care systems. Flu #vaccine helps *both* outbreaks.
— Katy Stephenson (@k_stephensonMD) February 1, 2020
As for the title of this post …
Nope.https://t.co/ElJH4KIpvp via @sciam
— Paul Sax (@PaulSaxMD) February 2, 2020
12 Responses to “A Coronavirus ID Link-o-Rama, Because I’m Not Watching the Super Bowl”
Paul E. Sax, MD
Contributing Editor
NEJM Journal Watch
Infectious Diseases
Biography | Disclosures | Summaries
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Thank you for this.
I am wondering what else has to go. Hockey and rugby certainly. This is not a race thing sorry. Hockey is a white sport and rugby too. You cannot get anywhere by banning this or that.
we have to offer and LIONIZE better sports. I live on running and jogging and cross country skiiing. soccer needs work–no headers. Volleyball should have male and female and co-ed leagues. Is baseball beaten? Is Swimming too boring? Skaters need helmets but the ABATE fiasco shows the culture must change and not merely from top down.
You are in a hurry, understandably. But nature and human nature are miserably slow. Keep trying but don’t put your efforts on Prohibition. it makes danger more attractive.
Hi Paul! Hey, please note that the report in NEJM of the cluster of cases from Germany alleged to have occurred during the index patient’s period of asymptomatic infection has been thrown into question because the investigators never actually interviewed the index case: https://www.sciencemag.org/news/2020/02/paper-non-symptomatic-patient-transmitting-coronavirus-wrong. Although the data for transmission form Patient #1 to Patients #3 and #4 seems compelling for asymptomatic spread, the sloppy work of these investigators raises general concerns about the overall accuracy of the report, sadly. BTW I can’t find the letter from Robert-Koch Institut on the NEJM website yet but hope they will link it to the report itself post haste since the webpage with the original report is approaching 300,00 page views.
Thanks for this comment, John. I’ve updated the post with the bracketed material so people are aware.
My gut feeling is that there will be ***some*** pre-symptomatic spread, as there is with many viral infections, but the likelihood is lower due to the reasons I mentioned.
Paul
I agree!
This is so, so helpful. Many thanks for posting it.
Dr Sax, thank you for hard data putting the novel Corona virus outbreak in perspective. Perhaps an article in the traditional International lay press as well to allay the hysterical reports evident so far?
Your views on doubts being put forward that it could actually have been designed to be a tool for bioterrorism
Hi everybody.
As a pathologist, I have a question regarding the possible animal source of the new coronavirus.
I think there is an usual emphasis on genetics these days, rather than microbiology or epidemiology. Pangolins are the newest culprit said to spread coronavirus to humans.
Can genetic analysis identify what animal species the coronavirus jumped from into humans?
I am Biochemist specializing in translating research into Pathways, Diagnoses and Treatments.This approach is common with Human Gene Variants/SNP’s and there are databases to search on.My search shows this new Coronavirus is in the RNAS-L Pathway like HepC,HIV-1-all RNA viruses, and including Asian Flu, Epstein Barr,and Herpes vIruses.I do not feel it came from animals recently as HIV-1 cane from green Monkey,Millions of years ago.So these “newer” viruses do not always trigger the immune system RNASE-L Pathway as it is TLR triggered by Interferon-usually Interferon 1,or Alpha.I feel best treatment is an antiviral Protease Inhibitor along with Interferon or an Interferon activator to activate RNASE-L and induce Auyophagy virus killing by Macrophages,which is more natural and better than Antigens used by Vaccines.So,my biggest fear is Vaccine will take too long to test and make,and,it may not work.So,least risk and fasted,most certain approach is ARV Therapy+Interferon.A small number of patients were treated this way in 2003 with SARS and again with this new virus,and I understand the results were favorable.I would treat patients with minor.early symptoms with Interferon,and more serious patients with appropriate antiviral drug which prevents viral entry into cell to form RNA a sit is a retrovirus and next boost immune with Interferon.Time is of the essence so this is Plan B,except I would go down parallel path with 2 approaches to get maximum success. Interferon will lower TNF Alpha and IL-6, improving cell signaling.High dose Green Tea in a Gelcap with Olive Oil and some Chinese Herbs+Caffeine will slow down viral entry and enter the brain, minimizing Encephalitis,so this is really needed.Ask Jarrow,they know.Both ERK 1/2 and GP 129 will be inhibited.
Very good summary brings some sanity and perspective to this whole situation, thank you.
Unbelievable.
Nine years ago, movie about the coronavirus epidemic came out.
Name: Cantagion (2011) – Link bellow: