Amazonas State, Brazil - Credit Wikip
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Amazonas state, in Northwestern Brazil, saw some of the highest COVID attack rates on the planet last spring, and by late 2020 seroprevalence studies conducted in Manaus, the capital and largest city in Amazonas, indicated 3/4ths of the population had already been infected with the virus and were presumably immune.
Which is why their recent and dramatic resurgence of the epidemic (see Brazil: Amazonas Transfers 235 COVID Cases To Other States Amid Critical Oxygen Shortage), coupled with the rise of a new COVID variant - dubbed P.1 (see Virological: Another E484K South American Variant To Ponder) has raised so much concern.
Two days ago, in The Lancet: Resurgence of COVID-19 in Manaus, Brazil, Despite High Seroprevalence, we looked at the possible causes, and potential ramifications, of this new wave of infections in Amazonas.
While it is possible that previous infection rates were overestimated, it appears more likely that some combination of these other factors are at work:
A) preexisting immunity has waned over time;
B) the new P.1 variant is evades prior immunity from earlier variants (see Brazil MOH Confirms Reinfection With COVID Variant P.1 In Amazonas);
C) the new P.1 variant is vastly more transmissible than earlier variants
Today we've a new report from FIOCRUZ (Fundação Oswaldo Cruz) that provides the latest genomic sequencing data from Amazonas state, which finds that the P.1 variant has rapidly overtaken all other variants in the region, jumping from 51% of all sequenced samples in December to 91% by the first half of January.
Fiocruz technical note addresses Sars-CoV-2 and new variant in AM
1/29/2021
Fiocruz Amazonia
Technical Note prepared by the Leônidas & Maria Deane Institute (ILMD / Fiocruz Amazônia) and the State of Amazonas Health Surveillance Foundation (FVS-AM), through the Central Public Health Laboratory of Amazonas (Lacen-AM), points out that in this In January, the new variant of Sars-CoV-2, P.1, was identified in 91% of the genomes sequenced in Amazonas, which makes it the most prevalent in the state today.
Since March 2020, with the emergence of the first cases of Covid-19 in Amazonas, the monitoring and genetic characterization of Sars-CoV-2 has been carried out by the Virology Laboratory at Fiocruz Amazônia, coordinated by researcher Felipe Naveca and team; in addition, the laboratory contributes to the State in carrying out a molecular diagnosis of the disease and in the development of Genomic Surveillance actions for Sars-CoV-2 circulating in Amazonas.
250 genomes have already been sequenced, 177 from Manaus and the other 73 from 24 municipalities in the interior (Anori, Autazes, Barreirinha, Caapiranga, Carauari, Careiro, Iranduba, Itacoatiara, Jutaí, Lábrea, Manacapuru, Manaquiri, Manicoré, Maués, Nova Olinda do Norte, Parintins, Presidente Figueiredo, Rio Preto da Eva, Santa Isabel do Rio Negro, Santo Antônio do Içá, São Gabriel da Cachoeira, Tabatinga, Tapauá and Urucará).
Eighteen Sars-CoV-2 strains were identified in Amazonas, B.1.1.28 (33.6%), B.1.195 (18.8%), B.1.1.33 (11.6) %) and, since December 2020, the emergence of the P.1 strain (new Brazilian variant), which jumped from 51% of the samples sequenced in December, to 91% of the samples sequenced by the first half of January 2021.
The technical note also notes the detection of two substitution events for the main circulating lines in Amazonas: B.1.195 to B.1.1.28 and then to P.1.
Studies in the field of virology carried out by Fiocruz Amazônia receive support from Fiocruz, the National Council for Scientific and Technological Development (CNPq) and the Amazonas State Research Support Foundation (Fapeam). FVS-AM and Lacen-AM are partners in all research on emerging viruses.
Access the full technical note .
See information on the epidemiological situation of Amazonas .
The 11-page PDF full technical note is published in Portuguese, and while many will find it useful to (translate) and read in its entirety, I've posted the translated conclusions below.
Conclusions and highlights of genomic surveillance of the new coronavirus in Amazonas, Fiocruz partnership - FVS-AM.
- Obtaining and disseminating the first SARS-CoV-2 genome in the northern region of Brazil in March 2020;
- Detection of two replacement events for the main circulating strains, B.1.195 to B.1.1.28 and then to P.1;
- Confirmation of the origin of the new variant (P.1) from line B.1.1.28 of Amazonas;
- Urgent need to confirm the outcome of cases infected by P.1;
- Confirmation of the second case of reinfection by SARS-CoV-2 in Brazil, the first by the new variant described in the world;
- Identification of the circulation of variant P.1 in 11 municipalities in Amazonas: Manaus, Rio Preto da Eva, Careiro, Anori, São Gabriel da Cachoeira, Iranduba, Rio Preto da Eva, Presidente Figueiredo, Tabatinga, Careiro, Manacapuru. This data reinforces that genomic surveillance actions must always involve samples from the interior of the state.
- Identification of a substantial increase in the frequency of the P.1 line (51% December samples, for 91% of the sequenced samples up to 1/13/2021). It should be noted that the P.1 line was found for the first time in sample from a patient collected on 12/04/2020.
Version 2. On 01/28/2021
- Strengthening of the Genomic Health Surveillance Network in the State of Amazonas, an initiative promoted by FAPEAM; x 250 complete high quality genomes generated by Amazonians since March 2020, favoring the strengthening of a local S, T & I chain place to face new challenges.
