COVID-19: more intense virus circulation has driven peaks of cases and P.1 in Amazonas

In a paper published (5/25) on Nature Medicine, researchers of the Fiocruz Genomic Network and of partner institutions point to the cause of the increase in the number of COVID-19 cases in the state of Amazonas and of the successive replacements of lineages of Sars-CoV-2. The study shows that these factors have been boosted by a combination of reduced social distancing measures and the appearance of a new, more transmissible form of the virus, the P.1 variation, identified in mid-November 2020. This variant has caused an exponential increase in case numbers, thus establishing a second wave of the epidemic in the state.

“We have a history of respiratory viral diseases following a different calendar here in Amazonas: our peaks normally take place before other states. The new, more infectious variant appeared in a period of less social distancing. P.1 was the consequence of virus circulation and it later caused the collapse of the public health system in Amazonas”, explains Felipe Naveca, researcher and vice-director of Research and Innovation of the Leônidas & Maria Deane Institute (ILMD/Fiocruz Amazônia).

The state of Amazonas has been through two waves of disease increase, the first at the beginning and the second at the end of 2020. For the genomic epidemiology study published on Nature, 250 sequences of the complete genome of Sars-CoV-2 were generated, all of high quality, from individuals of 25 municipalities, between 16 March 2020 and 13 January 2021.

The result reveals that the first increase in COVID-19 cases (between March and May) was boosted mainly by the dissemination of the B.1.195 lineage, then replaced by B.1.1.28 between May and June 2020. The situation remained stable between June and November, with small variations. The second phase took place in mid-December 2020 with the emergence of the P.1 variant and the consequent explosion in the number of cases.

For Felipe Naveca, the fact that P.1 hit young people as often as it affected older people may be related to more exposure by the first, be it for work-related issues or due to less social distancing by choice. “They got exposed when they went back to work as much as they did for social reasons. It appears that this was terrible in a context of circulation of an even more infectious variant”, he comments.
According to the researchers, the variant of concern, P.1, contains 21 lineage-defining mutations, including ten in the spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, and T1027I). It was first announced on January 10 this year, after a study on four people who had returned to Japan after going through the state of Amazonas. The variant was therefore acknowledged as a lineage that emerged in the state capital, Manaus.

The work of these researchers also analyzed more than 1,232 samples positive for Sars-CoV-2 available from the Central Laboratory of the State of Amazonas (Lacen-AM) to estimate a timeline for the appearance of P.1, by means of real-time PCR essays. The result shows that none of the samples positive for Sars-CoV-2 genotyped via RT-PCR before 16 December was positive for an NSP6 deletion, a characteristic of VOCs, indicating a very low prevalence of P.1 between late November and mid-December in 2020 in Amazonas. The result of the analysis carried out between the second half of December 2020 and January 2021 was different.

“Social distancing was still the best possible intervention to reduce virus transmission and, as a consequence, the evolution of the virus, while vaccination was not evolving at a desirable speed”, warns Naveca.

The paper COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence is the result of studies by researchers of the regional units of Fiocruz at Amazonas, Pernambuco and Bahia, and of the Oswaldo Cruz Institute (IOC/Fiocruz), in Rio de Janeiro; of the Foundation of Surveillance in Health of Amazonas (FVS-AM), of the Central Laboratory of Public Health of Amazonas (Lacen-AM), of the National Institute of Amazon Research (Inpa), of Hospital Adventista in Manaus, of the University of the State of Amazonas (UEA), and of the Federal University of Espírito Santo (Ufes). The researchers are: Felipe Gomes Naveca, Valdinete Nascimento, Victor Costa de Souza, André de Lima Corado, Fernanda Nascimento, George Silva, Ágatha Costa, Débora Duarte, Karina Pessoa, Matilde Mejía, Maria Júlia Brandão, Michele Jesus, Luciana Gonçalves, Cristiano Fernandes da Costa, Vanderson Sampaio, Daniel Barros, Marineide Silva, Tirza Mattos, Gemilson Pontes, Ligia Abdalla, João Hugo Santos, Ighor Arantes, Filipe Zimmer Dezordi, Marilda Mendonça Siqueira, Gabriel Luz Wallau, Paola Cristina Resende, Edson Delatorre, Tiago Gräf and Gonzalo Bello.

Felipe Naveca highlights that “this work is the result of Brazilian science and is 100% made in Brazil”. The work was supported by the National Council for Scientific and Technological Development (CNPq); of Fiocruz, by means of the Inova Fiocruz Program; and by the Foundation of Support to Research of the State of Amazonas (Fapeam), through the PCTI-EmergeSaúde Program and the Health Surveillance Genomic Network (Regesam).