Notes on Covid: New Variants in Brazil and South Africa, Herd Immunity Fails in Manaus, Success in Vietnam
By Lambert Strether of Corrente
We’re hoisting this really informative comment by alert reader Biologist from Links yesterday. (I cleaned up the formatting a little). Biologist characterizes all his notes as “gloomy,” but I think there’s nothing wrong with a little realism after looking at the data; how else will we get through this? Whether or not the note on Vietnam is gloomy — they did, after all, hold deaths to 35 (thirty-five) in a nation of 100 million — depends on whether you think the State in this country can ultimately be as functional as Vietnam’s.
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A few gloomy Covid notes, I think I posted one yesterday but it got lost in the ether.
New variants: The Brazilian and South-African ones are even more worrying than the UK one, as they seem to partly escape immunity. Like the UK one, these two variants contain the N501Y mutation in the Spike protein which probably contributes to its higher rates of transmission.
However, they also contain a new mutation E484K in Spike, which in a recent lab study was shown to strongly reduce neutralization by antibodies from plasma of donors that had recovered from Covid. With the caveats that sample size was small and there was a lot of variation between individuals, this is bad news. Why? Because it might mean that natural and vaccine-derived immunity against this variant could be lower or less long-lasting compared to the other virus variants. While this is still in the realm of (informed) speculation, it would mean that a) reinfection could be more likely or quicker, and b) vaccines might be less efficient or long-lasting.
Here is the non-peer-reviewed paper, and the author explaining:
Key results validate in neutralization assays. Mutations at E484 greatly reduce neutralization (>10 fold) by sera from some individuals (examples below). Unfortunately, the South African lineage has E484K, as do some other isolates from elsewhere. (6/n) pic.twitter.com/C3b7Xe8hH7
— Bloom Lab (@jbloom_lab) January 5, 2021
Not sure if it was the same study, but this mutation was identified in someone who was reinfected after 5 months:
1/📌Concerning case of reinfection: healthy 45 year old was reinfected with the genetically distinct SARS-CoV-2 variant that harbors the E484K mutation – this is the variant that was recently reported to escape neutralizing antibodies 1/6🧵 pic.twitter.com/h83eqc0sO8
— Dr. Ali Nouri (@AliNouriPhD) January 7, 2021
Note that the same mutations arising and rapidly spreading independently in several locations strongly suggests they have a selective advantage. The variants arose and spread in countries where the epidemic has been very severe (UK, Brazil, South Africa, new ones in USA), and there are indications that they arose in chronically infected immunocompromised patients that were treated with plasma. The reduced immune capacity of these patients kept the virus population alive, while the plasma provided strong selection to escape immunity. Basically, with the uncontrolled spread of this virus we’re providing it with lots and lots and lots of incubators to evolve. I am speculating here, but I wonder whether having a sizable population that’s been given just one vaccine dose might also increase selection pressure for escape variants.
Herd immunity is even harder to achieve than previously thought. Manaus was devastated in the first wave, in a mostly uncontrolled epidemic, but despite a whopping 76% of the population having been infected and mass death, herd immunity was not achieved:
“Buss et al. used data on the occurrence of SARS-CoV-2–specific antibodies (seroprevalence) in blood donors, adjusted for waning antibody responses over time, to calculate an estimated attack rate for COVID-19 of 66% in June, rising to 76% in October, in Manaus. (…) This attack rate resulted in a factor of 4.5 excess mortality in 2020 relative to previous years. The infection fatality rate was estimated to be between 0.17% and 0.28%, consistent with the population being predominantly young and at reduced risk of death from COVID-19. (…) Despite such a high proportion of the population being infected, transmission in Manaus has continued, even in the presence of nonpharmaceutical interventions (NPIs), with the effective reproduction rate R near 1.”
I strongly encourage you to read the very accessible write-up by Prof. Devi Sridhar and Dr. Deepti Gurdasani quoted above. The original technical article is here.
A lesson from Vietnam in how to do contact tracing and quarantining. From the CDC:
When 27 staff members in the catering company [of BMH hospital] tested positive for SARS-CoV-2, the entire BMH staff (7,664 persons) was put under quarantine. Contact tracing in the community resulted in an additional 52,239 persons being quarantined. After 3 weeks, the hospital outbreak was contained; no further spread occurred in the hospital.
📌1/CDC Report on Vietnam’s🇻🇳Incredible Tracing/Quarantine Program: after outbreak in major Hanoi Hospital, entire 7,664-persons staff quarantined. Contact tracing in the community resulted in an additional 52,239 people being quarantined. After 3 weeks, outbreak was contained🧵 pic.twitter.com/wzFiwAmmzE
— Dr. Ali Nouri (@AliNouriPhD) December 14, 2020
More on Vietnam from Global Asia:
Another effective containment strategy has been shutting down the border. A week after the first cases were confirmed, on Feb. 1, Vietnam declared a public health emergency and halted all flights to and from China. The flight ban gradually expanded to other virus-hit countries. By late March, the country had suspended all international flights. Since then, only Vietnamese nationals and some foreign experts and businessmen have been allowed in with strict conditions, including mandatory testing and a 14-day quarantine.
And quarantine actually means quarantine, none of that UK voluntary stuff that no-one adheres to:
All arrivals have to spend their quarantine at army-run camps or hospital facilities that are free of charge. Food expenses for foreign nationals are reportedly about double that of locals — the government is aware of diet differences and has made efforts to accommodate them by adding sausages and milk, thus increasing the cost.
Note that Vietnam – a poor country close to China with a population of almost 100 million – has had a total number of 35 (thirty-five) Covid deaths.