Submitted by No Soap Radio
On the first of December 2019 a man woke up a fever and a dry cough that wouldn’t go away. Seven days later he presented at a local hospital. The next day he was struggling to breathe. He had not visited the Huanan seafood market recently. Eight days later three more patients arrived at various hospitals across Wuhan with similar symptoms. Only one of these three had been recently exposed to the Huanan seafood market. By January 1st 59 patients presented at various hospitals across Wuhan complaining of a fever that more often than not was accompanied by a dry cough. Of that 59, the presence of what had just been given the interim name of 2019 Novel Coronavirus or 2019-nCoV (recently formally named SARS-CoV-2 or SARS-2 for short), was confirmed in 41 of them.
As of February 11th the International Committee on Taxonomy of Viruses settled on SARS-CoV-2 as the formal name for the virus itself, as the two pathogens are closely related. In an attempt to avoid aggravating China WHO announced it was calling the disease COVID-19. While different names for the pathogen and the disease they cause is very common, the timing of WHOs announcement certainly is suspect (11)
On December 31st Wuhan City’s health committee quietly issued an epidemiological alert while the Western world celebrated the new year. The next day, the Huanan seafood market was closed. Three more patients were confirmed as having SARS-2 up until the 3rd of January (44 total). That day Chinese national authorities formally notified the World Health Organization. As of the 16st of February there have been 67193 confirmed cases, and 1527 fatalities. In contrast in 2003 there were a total of 1718 SARS cases identified and 253 fatalities. While almost certainly neither of these are the true numbers, the picture they present is still by no means a good one.
Unfortunately a timely global response to the situation has most certainly been hampered by both the Chinese state’s attempts to save face and our efforts to not appear racist. For example, on January 11th the Wuhan City health committee made a public report, claiming that no new cases had been detected since January 3rd and that there was no evidence of human-to-human transmission (1). Using this early data Hong Kong University estimated an R0 of 0.3 (2)
R0 is the basic reproduction number and is a measure of how contagious an infectious disease is. It represents the average number of people an index case will spread the disease to and is pronounced R naught. An R0< 1 indicates that the contagion will peter out and an R0 > 1 indicates the infection will grow and spread through the population. This number changes over time as human behavior changes. That change can either be people making an individual choice, for example increasing personal hygiene, or it can come from outside forces, for example a government restricting travel inside of an infected area. For reference, SARS had an estimated R0 ranging from 2.2-2.7 in the early phase (before response) and 0.14-1 in the later phase (after response).
In the case of SARS-2, a R0 of 0.3 appeared to be very good news, indicating that with the closure of the seafood market, the worst of the infection was over. Clearly this is not the case. The same team who made the initial R0 estimation later revised their prediction up to 2.2 (3), which matches with other estimates (4). However; others disagree and put the R0 at 3.11 (5) and as high as 4.08 (6). (please note that (5) and (6) are pre-published and have not been peer reviewed yet)
Unfortunately, SARS-2 is no longer contained within Wuhan and conservative modeling estimates that at around 860 infections were imported into other major Chinese cities between December 31st and January 28th. This large of a seed population(infected people moving to unaffected areas)makes it a near certainty that the disease is self-sustaining outside of Wuhan. With a median incubation period of 3 days (12)and assuming no intervention other cities in China would lag around 1-2 weeks behind Wuhan (7).This means that in the next couple of weeks, if not for the drastic measures in cities outside of Wuhan we would of expected to see similar number of cases to Wuhan now in Chongqing, Beijing, Shanghai, Guangzhou and Shenzhen, with peak daily incidence in April/May. With a 25% reduction in transmissibility, modeling suggests that the peak would be pushed back to May/June (12) with a lower daily incidence but not necessarily a dissimilar number of total cases.
On an international scale we know much less. Fortunately, international air travel only makes up approximately 15% of air travel from Wuhan. As the total number of infected travelers are much lower the likelihood of a self sustaining infection outside of China is also much lower. That is not to say it can’t happen and indeed it likely has already in Japan, Singapore and possibly France. Exactly how bad an infection we don’t know yet and won’t know for the next few weeks. Of course, accurately predicting outcomes relies on models having good data and the risk could easily be much higher, especially if potentially contagious people are going out of their way to hide their status (8) or going out of their way to break quarantine (14). Whatever the case, if a city that operates flights to China is going to be seeded, it has likely already happened. It likely already happened in early January. That is not to say that there is no point in closing off travel to China or other outbreak areas as they occur, as stopping the inflow of new cases is always an important part of limiting the spread of a contagion.
What is SARS-CoV-2?
The genus betacoronavirus (family Coronaviridae) is characterised by a large, linear, single chain (monopartite) ssRNA(+) (single stranded positive sense RNA). You may also see it referred to as a Group IV virus. That just means ssRNA(+). Some betacoronavirus species are zoonoses, which means they can be transmitted between animals and people. SARS-CoV, MERS-CoV and SARS-CoV-2 are all examples of zoonotic viruses.
Each virion (virus particle) is encased in a spherical envelope, in which a series of large molecules (glycoprotein trimers)that stick out like spikes. These spikes give the virus its name as they appear like a solar corona under transmission electron microscopy.
RNA viruses tend to evolve more rapidly than DNA viruses but new strains do not emerge as rapidly as segmented genomes like those of the ssRNA(-) Orthomyxoviridae can via reassortment (influenza’s family).
So if things get real bad what can you do to keep you and your family safe?
Hygiene. it is really that simple. Most viruses cannot live for more than a few hours outside of a suitable environment, coronaviruses however have been observed to persist on inanimate surfaces for as long as nine days(13). For an example of how easy microbes can spread in a house in just 2 hours check this story from Japan by way of China (9). With this in mind the best thing you can do is follow the same advice doctors give you regarding the flu. Shield your sneezes and coughs (not with your hand!), stay away from others as much as possible, 3 to 6 feet is considered a close contact. Wash your hands regularly, using warm soapy water or the alcohol rub mentioned below. When washing hands use proper technique. Avoid touching your face as much as possible, if you really need to use a tissue as a disposable barrier between your fingers and your face. This last part is amongst the most important but also the most difficult.
The median incubation period of SARS-2 is 3 days, however; there has been at least one case ranging as far as 24 days before the onset of symptoms(12). Additionally many cases are asymptomatic (no symptoms but positive test result) and there is some indication that viral shedding can still occur in these patients (15). Similarly while there is no evidence of direct transfer via the fecal oral route yet, it has been seen in other coronaviruses. Given that one of the less common symptoms of SARS-2 is diarrhea and SARS-2 nucleic acid has been detected in stool samples (10), fecal oral transfer is a near certainty. The way you stop this spread be it by droplet, fecal-oral or contact, is again simple hygiene. Wash. Your. Hands. If you are in a country where you can purchase high strength rectified alcohol (Everclear in the US for example) dilute it to 70% and put it in a spray bottle, and use it to spray down your hands. It can also be used on small surfaces, just spray and let it sit for a minute before wiping down. For larger surfaces use 5% bleach (household bleach) diluted to 1:50 (or 0.1% sodium hypochlorite). This will kill most microbes in about a minute, including SARS-2. if you need to wash more delicate fabrics soak them in water at 57°C (135°F) or higher for at least 30 minutes, stirring occasionally before washing normally.
The last thing that requires attention is the issue of personal protective equipment (PPE) in this case gloves and masks. These would seem to be the go to answer to protecting you and your family. Unfortunately things are a little more complicated. Masks are extremely important in reducing the number of potential infection events when worn by the sick. However what protection the masks provide to wearers are often overwhelmed by the sense of invulnerability they give. Simply wearing a mask often places the wearer under the mistaken belief that they cannot be infected. Habits such as face touching which a person would consciously police if not protected often return in their now relaxed state. Gloves suffer the same issues but lack the advantage of masks in keeping infectious people isolated from the world. Gloves are also limited in the sense that because of the basic function of hands they must continually interact with the environment. This means even if a gloved person avoids infection they can still spread it to others through incorrect use. A good rule of thumb is when using gloves replace them when your location or activity changes. Walking to the shops in a theoretical pandemic would be fine but you would not want to pick up shopping (which you intend on bringing inside your home) nor would you want to wear them inside your car and you most certainly wouldn’t want to wear them into your home at all. To be clear, none of this is to say gloves and certainly not masks are useless, only that when not used properly they offer little to no protection and in the worse case can aid in the spread of a contagion. In the HSE world PPE is considered an absolute last line of defense and not to be relied upon. The same is true here.
In the second part of this article we will be looking at the claims of a relationship between SARS-2 and HIV-1, why HIV antiviral drugs (and not influenza antivirals) might work, and the relationship between SARS-2 and ACE2 receptors.
One last thing: Avoid the Chinese like the plague.