University of São Paulo: Coronavirus variant identified in Manaus has more potential for transmission and reinfection

A new strain was present in 42% of infected patients tested in the city and was also detected in Japan, suggesting that the virus variant was taken by travelers from Amazonas – Image: Cadde Project
A new strain of coronavirus was identified in the city of Manaus, in Amazonas, in December. The variant, which has a set of genetic mutations with the potential to increase transmission and reinfection by the virus, was present in 42% of infected patients tested in the city. The new strain was also detected in Japan, suggesting that the variant of the virus was reportedly carried by travelers from the Amazon. The discovery is the result of a study by researchers from the Brazil-United Kingdom Center for Discovery, Diagnosis, Genomics and Epidemiology of Arbovirus (CADDE group), which includes the participation of the Institute of Tropical Medicine (IMT) and the Faculty of Medicine of USP (FMUSP).

The identification of the new variant is reported in the pre-print (previous version of a scientific article) “Genomic characterization of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings”, published on the Virological.Org website, published on January 12th. “The new strain, called P.1, was identified in 13 of the 31 positive samples for the RT-PCR test collected between December 15 and 23, 2020, that is, in 42% of the tested patients”, reports Ingra Morales Of course, a researcher at IMT and FMUSP, one of the authors of the article. “The variant, however, was absent in 26 genome surveillance samples publicly available and collected in Manaus between March to November 2020.”

What differentiates the variant from the known strain is a set of genetic mutations, explains the researcher. “Mutations of the virus are often identified and new variants appear regularly. We know that SARS-CoV-2 has an average of two to three mutations per month. So since the first case identified in Wuhan, China, at the end of 2019, the virus genome has been different after almost a year of this identification ”, he reports. “The new lineage, descended from lineage B.1.1.28, contains a unique composition of lineage-defining mutations, including several mutations of known biological importance, such as E484K, K417T and N501Y”.

Local broadcast
According to Ingra, the discovery of the variant indicates local transmission of the virus and recent increase in the frequency of the new strain. “Manaus was severely affected by the covid-19 pandemic, with an attack rate, that is, an estimated number of people infected by the SARS-CoV-2 virus in three quarters of the population in October 2020, as shown in a recently published study ” observes. “Despite this, there has been a rapid increase in cases where the previous attack rates have already been estimated. Therefore, it is essential to quickly investigate whether there is an increase in the rate of reinfection in previously exposed people. ”

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The new strain was detected and reported by researchers from Japan on two adults and two children who arrived in the Asian country, from Brazil, from the state of Amazonas. “From the phylogenetic study containing sequences and sampling data previous to the P.1 strain. in Manaus, our work corroborates the travel information of the cases recently detected in Japan “, points out the researcher,” suggesting that the direction of the trip was Manaus to Japan “.

According to the study, the new strain may increase the risk of increased transmissibility and reinfection by the coronavirus. “One of the genetic mutations present in the variant, E484K, occurs in the receptor-binding domain (RBD), a site that the virus uses to bind to the ACE2 receptor in human cells, and which has been associated with the escape of neutralizing antibodies”, he points out Ingra. “The recent emergence of variants with multiple mutations shared at the peak raises concerns about the convergent evolution towards a new virus phenotype, potentially associated with an increase in transmissibility or propensity for reinfection of individuals.”

The research was coordinated by the Brazil-United Kingdom Center for Discovery, Diagnosis, Genomics and Epidemiology of Arbovirus, which conducts studies involving discovery, genetics and virus transmission. Researchers from USP, Federal University of Minas Gerais (UFMG), Imperial College London, University of Oxford, University of Edinburgh, Edinburgh and University of Birmingham, in the United Kingdom participated in the work, in addition to the Hematology and Hemotherapy Foundation of Amazonas (HEMOAM) , DB Diagnósticos do Brasil (São Paulo) and CDL Laboratório Santos e Vidal Ltda (Manaus).