The Covid pandemic has reached the point where we can begin to step back and consider the life cycle of the pandemic. We have learnt that Covid is a nasty, highly infectious airborne virus that preys mostly on the old and infirm, and enough people have required hospitalization that has nearly overwhelmed the health care system.
Covid first appeared in Wuhan China in the fall of 2019, and proceeded through a series of waves. The initial wave in spring 2020 was centered on the North East and was cut off by a nation wide shut down. An attempt to reopen in many states in summer 2020, forced a re-closure. The next partial reopening in the winter 2020, coincided with the start of vaccinations, which seemed to control the pandemic so that in the second half of 2021 there was progressive relaxation of shut down. By the spring of 2022, the delta and omicron variants have caused additional waves of infection.
The virulence of a virus is generally characterized by the "Reproduction Number" or number of people infected by each infectious individual under "normal' levels of social interactions, and while the susceptible population has no resistance to infection. Covid had a initial Reproduction number of 5-7, much higher than the flu with a Reproduction number of 1.5-2. As vaccination and the infection progresses through the population, some resistance to infection develops which varies as the virus mutates.
The exponential rise and fall in daily cases are driven by 3 factors; the number of people infected by each infectious individual, the fraction of the population that is infectious and the fraction of the population that is susceptible to infection.
Managing the life cycle of the pandemic has required 3 phases of control:
1) Initial infections were controlled by social distancing. During this period doctors made progress as to how best to manage outcomes.
2) Once vaccinations became available, this reduced the susceptible population leading to control of the infection. The shut down could be relaxed and many of the unvaccinated picked up some protection due to prior infection.
3) Finally, variants cause new waves primarily in the unvaccinated, "self" controlled as each variant runs out of un-protected targets.
The impact of any future variants will depend on the protection provided by vaccination or prior infection.
The critical resource in managing the infection is hospital capacity. We have around 3000 hospital beds per million, with a 65% average occupancy that can rise to 100% in flu season. In the case of the original Covid virus, the Hospital Admissions seem to be roughly the same as daily case count, so the critical daily case count was around 1000 per day per million.
The most surprising element of the Covid story has been the rise of the anti-vaccination movement and political advantage at the expense of their supporters.
The characteristics of the virus are the parameters that describe the pandemic. I have developed an extended model of the infection that accounts for the impact of social distancing, vaccinations, and variants.
The infection propagates by exponential growth, so it can be best understood through plots of the log of the infected population and where the growth rate can be measured as the slope of linear sections of the data.
Covid is a coronavirus that causes respiratory infection that spreads primarily by aerosol transmission. It is highly infectious such that when it first appeared, one infected person infected at least 5 other during the 10 days that they were infectious. For comparison this is 3x MORE infectious than flu. Unconstrained, Covid would have run through the entire US within months, causing catastrophic collapse of the health care system.
The model illustrates the importance of the un-protected fraction of the population in determining the progress of the pandemic. The degree of protection varies with vaccination, prior infection and the variant doing the infecting.
The model shows that is also clear that infections are controlled by human behavior such as social distancing.
The resulting hospitalizations and deaths are controlled by the demographics of the infected population and the skills of the health care system.
The progression of the infection in the US has formed a series of "waves". The first wave primarily hit the North East (NY et al.), the second wave hit the large southern states (FL, TX, AZ, CA). The current third wave is focused on the North Central region (ND, SD, WI, ID) but most of the country is seeing increased infection, so the virus is becoming more uniformly spread across the country.
The first wave came to the US from China via Europe and arrived in New York in early 2020. Early on, the dangers of the virus were pretty clear, and the states issued social distancing guidance and then it took around a month for the infection rate to start to drop. Based on the infection levels, we can visualize a spreading pattern out from NY. Many distant states such as TX, shut down early and dodged the worst of the first wave. NY was particularly badly hit because this was a new virus, and the medics did not know how best to treat it so the hospitals were overwhelmed. The second wave seems to have been triggered by Memorial day enthusiasm across the southern states. The third wave has been centered on the North Central states, although by late October most states were seeing rising infections. This wave seems to get started coincident with the Sturgis bike rally and opening of schools. These states have NOT embraced masks or distancing. Ever since we responded to the first infection with a shutdown, followed by cycles of opening and closing, the infections rates have been controlled by behavior rather then the inherent properties of the virus. By end of Jan '21, most states are seeing cases dropping. By end of March '21, cases have started to rise in a number of states - its a race between vaccinations and reopening. In April, Michigan had a serious wave apparently driven by new variants. Nationally vaccinations seemed to be keeping up with increases in contacts. By early May, vaccinations rates had started to drop as resistance to vaccines took hold with the right wing. By mid June national cases were level, rising in a few low vaccination states such as Wyoming. The key is watching the new Delta variant that has caused a rapid increase in cases in the UK. In July and August, hospitals across the country were overwhelmed. By Sept, the Delta wave had started to ebb with cases dropping sharply, without any obvious change in social distancing. It was notable that hospitalization and fatality rates did not change even though the Delta variant dominated.
At the end of '21, a new wave was formed by the Omicron variant , which rose rapidly due to the lack of distancing, and that preyed mostly on the remaining un-vaccinated. It dropped as quickly as it rose when it ran out of susceptible (un-protected) population.
The hospitalizations and deaths are a reflection of number of cases, the demographics of the cases, and the progress being made by the health system. By the end of Dec., ICU capacity is getting perilously close to the available. In Q1 hospitalizations dropped as vaccinations started to have a real impact.
The graph shows hospital admissions and deaths have fallen relative to cases. The medics have major strides in managing the infection. In the early stages (Wave 1), hospitals in NY were maxed out and the case fatality rate was near 10%. Today it is less than 2%. For the over 70 community, it started at 30%, today it is down to 6%. The time lag between infection and death has also increased noticeably as treatments have improved
Lethality is measured by the deaths divided by cases or Case Fatality Rate (CFR). Similar to other resipiratory illnesses, Covid preys on the old and infirm.
In March '21, we had a better idea of how this will pan out over the rest of the year, thanks to a UK study on people who recovered and got out of hospital – 7 in 10 still have problems 5 months after. It’s a nasty bug!
At the end of April '21, CDC published an update to the demographic impact. The over 65's had a CFR of 4%, everyone else averages out at 0.1% which will have a critical effect on the end game of the outbreak.
The Omicron variant wave in Dec '21, had notably better outcomes with lower Case Hospitalization and 5x lower Case Fatality Rate.
Seasonal flu has a repeating annual signature with a transmission of 1.4 infections per person. Covid with 5 infections per person rises much more quickly. If a lockdown had not been instituted, the deaths would have been nearly 100,000 a day !!! The solid lines show the standard model projections without any changes in pre-Covid behavior.
How best to live with Covid has become a terrible political football. The science on masks use, and the activities to avoid is clear. Covid is spread primarily by aerosol exposure - so close contact, indoors with poor ventilation maximises risk. Social distancing, wearing masks, meeting outdoors all minimize risk. Super-spreading events are major drivers of infections. Only 10-15% of infected people show symptoms, so there are a lot people who think they are fine, who are actually spreading the infection
Here are some examples of useful resources.
A really interesting paper used cell phone data to correlate activities to infections in 6 major metro locations. This gives clear evidence as to risky activities.
There has been huge progress in finding drugs that help mange infections and in developing a vaccine. The infection starts in the lungs, but it seems to trigger an overreaction of the immune system that can cause catastrophic inflammation. Combinations of anti-virals and anti-inflammatories have made a huge impact on outcomes.
Here are summaries of a few key papers on Remdezivir, HCQ, Steroids.
Multiple vaccines are in circulation having passed Phase 3 trials involving around 30,000 volunteers in each for 4 months. All show significant antibody reaction, early efficacy data on 3 different vaccines is better than 90%.
By fall '21, the mRNA vaccines has established efficacy, the Delta variant seemed to require a booster vaccination. In Jan '22, the Case Fatality Rate data continues to show that age is the single biggest factor determining outcomes. Vaccination reduces CFR by 5-10x depending on age. Omicron variant has reduced CFRby another 5x in the younger groups.
At the same time there has been a strong backlash against vaccination. The backlash is from the anti-vaccers who distrust the medical establishment and the libertarians who distrust the government. It appears that taking political advantage at the expense of the health and safety of your supporters is OK to some.