COVID rates are:
- declining in India, US, most of Europe
- stable & high in Latin America
- rising in sub-Saharan Africa & UK
Why such "random" waves of disease?
It's easy to blame variants, but this doesn't explain variability.
Segregated networks can explain five phenomena.
First, an orientation to this figure.
- Dot: person
- Dark line: very close contact (e.g., household)
- Light line: occasional contact
- Dotted circle: mini-network (e.g., same employer/school)
- Blue = uninfected, red = infected, orange = secondary infection, green = immune.
1. Small epidemics can occur without triggering a nationwide epidemic.
Say the person in the red square gets infected (via the line to the left). This will cause a micro-epidemic among their 2 close contacts, but might not spread.
2. By contrast, if other people/groups are infected, major epidemics are likely to occur.
If either of the people in the red squares below get infected, then half the population will almost certainly get the disease.
But even major outbreaks may not infect the whole population.
3. Epidemics can occur in waves at seemingly random times.
Say the person in the lower left is infected at one time, then the person in the upper right is infected later. This can trigger two independent waves b/c people on the left have few links w/ people on the right.
4. Outbreaks can still occur in populations where the majority of people are immune.
In the diagram below, ~70% of the population is immune (e.g., vaccinated or previously infected). Yet if the person in the lower right is infected, an outbreak will very likely occur.
5. New waves can occur without new variants.
Assume the person in the lower left gets infected first, then the person in the lower right at a later time. The 1st wave will be slower, making the virus look less transmissible. But the only difference is the density of the network.
In summary, segregated networks can explain:
- small initial outbreaks
- the pandemic eventually reaching most places
- multiple epidemic waves at "random" times
- waves despite broad immunity (e.g., UK)
- waves of different size/speed
...without needing to invoke new variants.
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Are you a prospective PhD/fellow/postdoc looking for the right mentor?
A thread on how to approach the process.
Long story short, two steps: 1) Define your "must-have" priorities. 2) Find evidence (reputation & track record) that a potential mentor will help you achieve those.
Step 1. Define your "must-have" priorities.
There are many things you can accomplish in a 2-4 year program. No mentor will be excellent in helping mentees achieve all of these. List out your "must-haves": things that you will be disappointed if you don't have/accomplish.
13 things a mentor can provide (non-exhaustive):
- Role model
- High-impact publications
- Work-life balance
- Technical skills
- Networking/introductions
- Support for future job
- Personality fit
- Freedom to choose projects
- Strong team
- Time
- Name recognition
- Funding
One term I worry that we (as a public health community) have mis-messaged during the pandemic:
"herd immunity threshold"
A non-technical thread on why this is not "% of the population that needs to be vaccinated for us to return to life as normal while eradicating COVID-19"...
Disclaimer to the experts: This is for a non-expert audience.
Let's start with the virus that's currently circulating, and estimate roughly that - with no vaccine, no immunity, and "life as normal" - this person would infect ~5 other people before recovering (or dying).
Next, let's take a situation similar to the USA. Out of these 5 possible people infected, 2 might be vaccinated; 1 out of the remaining 3 might be someone who's already have had COVID; and 1 of the remaining 2 might be prevented by current behaviors (masks, distancing, etc).
The B117 variant is now the dominant strain of SARS-CoV-2 in the UK, Ireland, Israel, Denmark. Likely also Portugal, Belgium, France, Italy, Norway.
Yet for the most part, these are not the countries where COVID-10 cases are rising (see below). What gives?
One explanation is that B117's transmission is being offset by restrictions, population immunity, etc. And that those countries w high B117 (UK, Ireland, Portugal) have locked down most. There is likely some truth to this - but not too much correlation w stringency index (below).
But it's also worth considering B117 and non-B117 COVID as separate epidemics. For example, look at Danish data below - it's tempting to think of B117 (red) as "replacing" non-B117 (grey). But that's not what's actually happening...
In the past week, COVID cases have fallen in the majority of countries across the globe (see below for weekly change). But not all countries are locked down.
A thread on what might be - and what probably isn't - happening.
1. Lockdowns/restrictions have almost certainly had a major effect in countries that instituted them. Look at the peaked curves in the UK and South Africa - natural processes are generally smoother. But it's notable that current declines are even sharper than w the 1st lockdowns.
2. If this were just due to seasonality, one might expect similar behavior as with flu. But historically, flu rates in the US generally do not start to fall until March (see non-red lines below). Seasons likely contributed to the Oct rise, but likely not the Jan decline.
Many are interpreting data from Denmark as strong evidence of increased transmissibility of B117.
With the caveat that I believe this prevailing hypothesis to be credible, if not likely...
A thread on how Danish data can be explained w/o invoking increase in transmissibility.
First, Denmark should be applauded for their rigorous genomic surveillance. Other countries should follow their example!
The data, in brief, show an increase in the percentage of sequenced cases that are B117, from 0.2% in early December to (prelim) 12% in mid-Jan.
This was, however, occurring in the context of a dramatic fall in cases throughout the country, likely reflecting the effects of a country-wide lockdown.