Read on Twitter
Manaus has now surpassed the very tragic 26/04 burial record of 167 with 198 burials in the past 24H (13/01) for a total of 1486 burials in January with 50% higher ICU occupancy than in April. Hard to see how Manaus avoids crossing 5k pandemic-related excess DPM. https://twitter.com/marioadolfo/status/1349498117058658313
Recall: worst case scenario modelling for excess deaths from the Imperial report back in March was ~8200 excess DPM for much older US and UK population.
As @OYCar aptly points out, the likely reasons for the second wave in Manaus are all very bad options with significant implications. There is evidence that some or a combination of these possible factors are playing a role in the resurgence in Manaus https://twitter.com/OYCar/status/1349559465318641665
1. Its possible seroprevalence estimates from wave 1 in Manaus are way off and much lower than suggested. Several others pointed out at the time the various limitations of the available seroprevelence estimates from Manaus. https://twitter.com/WesPegden/status/1308135840195981312
A much lower seroprevalence from wave 1 could explain some parts of the new surge although it should be noted that back calculations from reported and excess mortality at the time all suggested minimum seroprevalence of 40-50% in Manaus https://twitter.com/CovidSerology/status/1308462795537612800
However this raises some questions. a. How low was seroprevalence after wave 1? 40%? 25%? A 25% AR from wave 1 would imply a 0.72% IFR (based on excess COVID + SARI unknown) in a city where just ~5% of the population is over 65. b. what caused the epidemic to wane in wave 1?
2. Is it possible IFR is higher than reported in the literature? There is modelling and observational evidence to suggest CFR and IFR will differ greatly depending on healthcare capacity and availability. https://science.sciencemag.org/content/369/6502/413
e.g individuals requiring high-flow O2 receiving insufficient lower flow O2 will increase CFR. Also a significant portions of deaths in wave 1 in Manaus happened at home where proper medical attention was lacking.
There is also observational data from Israel suggesting increased CFR during periods of high patient load. This would bias CFR significantly and cause overestimates from back calculation of population infected from mortality data
Furthermore, they have been dozens of news reports on large spikes in mortality from ICUs all across the world where some sort of malfunction affects O2 delivery to patients needing them https://twitter.com/CovidSerology/status/1346864840728449024
These lines of evidence above could provide clues as to why back calculations all suggested very high attack rates from reported and excess mortality which may vary significantly from actual population attack rates.
3. Modelling and re-analysis of case data from earlier in the pandemic suggest "natural" R of SARS-COV-2 under pre-pandemic conditions is ~3-3.5. Could this explain the surge in Manaus if we assume a 40-50% seroprevalence from wave 1? https://www.nature.com/articles/s41586-020-2554-8
After a huge dip at the peak of its epidemic, mobility in Manaus have been trending upwards for a while now. Moreover, as seen in other parts of the world (e.g Mumbai, Barranquilla etc), high seroprevalence in wave 1 (>50%) does not preclude the emergence of a second wave
4. Increased transmissibility (high R = higher herd immunity threshold) and/or some form of immune escape from new variant in Manaus could explain the new surge https://twitter.com/AdamJKucharski/status/1349070778415898631
There is some evidence from the epidemic in South Africa particularly the Western Cape to suggest that both increased transmissibility and some form of immune escape are likely results from the B.1.151 variant circulating there https://twitter.com/cap1024/status/1348959997334614017
This has been postulated as some of the driving factor for the huge second wave there after (non-random) seroprevalence and back calculations from excess suggested very high attack rates (>40%). Note: excess deaths has nearly doubled in the WC and no downtrend (yet)
Could a similar scenario as in the western Cape be playing out with the recently discovered variant in Manaus? We should have more data soon but overall whatever is the driving factor for the recent surge in Manaus does not bode well for pandemic trajectory in other LMIC areas
Source:
https://www.medrxiv.org/content/10.1101/2021.01.11.21249526v1
https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586 https://www.samrc.ac.za/reports/report-weekly-deaths-south-africa?bc=254
https://www.medrxiv.org/content/10.1101/2021.01.11.21249526v1
https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586 https://www.samrc.ac.za/reports/report-weekly-deaths-south-africa?bc=254
Addendum 1: A new study from PHE found 83% protection against reinfection in those with SARS-COV-2 antibodies and around ~30% of reinfections were symptomatic with potential for onward transmission from reinfected individuals. https://www.gov.uk/government/news/past-covid-19-infection-provides-some-immunity-but-people-may-still-carry-and-transmit-virus
If 40-50% sero+ve after Wave 1 is presumed for Manaus and a similar reinfection risk as in the PHE study is assumed then it is likely that only about a third of the population remained immune from infection at the start of the second wave in Manaus. https://twitter.com/JustForReading9/status/1349672657168588801
