Congratulations to Fuhan Yang @Fuhan_Yang who successfully defended her PhD yesterday in @PSUBiology @ciddpsu. Fuhan's defense was on the seasonality of respiratory disease in the tropics (hint: not annual), periodic signals in these data, and the influence of stochasticity. 1/ Fuhan moved from neurosci to computational epidemiology in Jan 2020 and was hoping for a slow gradual intro to her new field. Which is not what happened. She was immediately thrown into COVID analytics & had to learn lit review, data assembly, & basic epi stats all on the fly. 2/

Hi #epitwitter #malaria twitter, in drug treatment, we accept that combination therapy is a good way to prevent drug-resistance emergence. And that #tripletherapy is likely to be more preventative than #doubletherapy. 1/ For #falciparum malaria, we may soon have the option of deploying triple artemisinin combinations therapies (TACTs) as a replacement for currently recommended artemisinin combination therapies (ACTs) that contain 2 drugs, thru the DeTACT clinical trial 2/

tropicalmedicine.ox.ac.uk/news/patient-r…

Hi #epitwitter, sorry to pile on with bad news, but we're not as immune as we think, and it's not just #Omicron's immune escape. In southern New England, it turns out that ~27% of vaccines were given to previously infected individuals. Pre-print below. 1/ medrxiv.org/content/10.110… Estimates are that 34% of vaccines in Rhode Island, 28% in Massachusetts, and 25% in Connecticut were administered to seropositives. This is consistent Moghadas et al's ballpark estimate that half of previously infected individuals were vaccinated. 2/ acpjournals.org/doi/full/10.73…

Hi #epitwitter SARSCoV2 attack rate in MA thru Feb 28 is estimated at 24.6% (95% CI: 22.4%-26.3%). It's difficult to pin this down closer than 3 to 4 percentage points, as there are still several model fits that work well. Underreporting is still at about 3 for Massachusetts. 1/ The Jan 31 estimates had a higher underreporting rate (2.9 to 3.3), & Dec 31 estimate was even higher, closer to 4. Estimates in summer & fall were in the 3.0 to 3.4 range. Estimating the underreporting is difficult when conditions are changing quickly. 2/

https://twitter.com/maciekboni/status/1361759994052546560

#epitwitter, on the anniversary of @CBSEveningNews @mlipsitch letting >5M Americans know that a million people could die a couple comments on what we need to fix before next winter - comments here: bit.ly/3be0YEH original CBS here cbsnews.com/news/coronavir… 1/ tl;dr (1) there's still no good behavioral model capturing the long-term population trends from urgency to complacency and back. This probably drove waves+ebbs in spring, summer, & late winter more than we expected. But no one has measured it. Plz RT/reply if this is out there 2/

Hi @NYMag not a good idea to have no scientific co-authors, no science journalists, and probably no scientific fact checking on a piece like this. This belongs under screenplay drafts not investigations. Plz leave science reporting to science writers 1/
nymag.com/intelligencer/… The author cherry-picks scientific opinions that cautiously state what *may* have happened but for which there is no evidence. Scientists do this all the time. We honestly state when we cannot rule a hypothesis out, even if there is zero evidence supporting that hypothesis. 2/

Hi #epitwitter our state-level analysis is up on medRxiv. We look at 11 data streams (cases, hospitalizations, ICU, vent numbers, deaths etc) available from DOHs in RI, MA, PA. Data assembly not automatable, unfortunately (help welcome) medrxiv.org/content/10.110… Key points below 1/ 1. **Vulnerable populations are not always able to isolate effectively during a lockdown**. Very clear signals, visually in the data and in our inference, that contact rates for >80 individuals were the highest (among age groups) during the lockdown. 2/

Thanks @Virusnerdette and @hrogier. Yes, Vietnam has had a number of experiences in this area, and #epitwitter readers should remember that H5N1 outbreaks in poultry are regular occurrences, so the public health system is set up for this type of response. 1/

https://twitter.com/Virusnerdette/status/1244669996602720257

In 2009, when a new subtype/variant of influenza was announced to be infecting humans (Friday April 24 2009) Rogier and I were at a happy hour at O'Brien's in HCMC (early evening in HCMC, daytime/morning in Geneva/NY). The public health response got moving right away ... 2/

Dear #COVID19 twitter, a short respite from the bad news on the epi side, to share neutral results from the genomics side. Coronaviruses are highly recombinant; this means identifying evol origins is challenging, as different parts of the genome can have different origins. 1/ We used 3 approaches to identify non-recombining regions of the genome. Here is an example w the peaks in this graph showing the degree of support for a recombo breakpoint at that nucleotide position (x-axis). The A'BC region is one of our candidate non-recombining regions. 2/

Since 2003, #H5N1 avian flu outbreaks have regularly occurred in small-scale farming systems, mostly in Southeast Asia, resulting in >800 human infections with #avianinfluenza and >400 deaths. These outbreaks occur on small chicken farms or in small duck flocks. 1/

How much risk do smallholder poultry farmers face in SE Asia? What environmental conditions and farm management strategies leave them most exposed to #avianinfluenza outbreaks? When faced with an outbreak risk, do farmers optimize to minimize health risk or maximize profit? 2/

Python the language and python the reptile, together at last in this veterinary epidemiology publication on the demographics of smallholder domestic poultry farms in #SEAsia. There is substantial overlap of flocks, species, and ages: they are not run as all-in-all-out-systems. 1/ For those interested in #mathematicalmodeling of #avianinfluenza, including circulation of #H5N1 in poultry flocks, diagram below gives you the birth, death, purchase, sale parameters you need. Paper is here: 2/ rdcu.be/bG8xx