Friday, January 29, 2021

Preprint: Pervasive Transmission of E484K & Evidence of SARS-CoV-2 Co-infection in Rio Grande do Sul, Brazil


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#15,757

Over the past few weeks most of our South American COVID attentions have been focused on the variant driven epidemic in Amazonas state in Northwest Brazil, but Brazil is an immensely large, populous (211 million people), and geographically diverse country. 

What happens with the COVID virus in Amazonas can differ greatly from what goes on in Rio De Janeiro nearly 3,000 km to the south and east. 

A little over 3 weeks ago we looked at early reports of a COVID variant in Argentina bearing the E484K mutation which had first been detected in Rio De Janeiro, Brazil. Relatively little is currently known about the spread of these - and likely other - COVID variants in Brazil. 

E484K - which has been detected in both the South American and South African variants - has been linked to reduced antibody recognition, which is feared might increase reinfection risks and potentially lower the effectiveness of current vaccines.

All of which brings us to a new preprint that examines the COVID variants circulating in the Southern Brazilian state of Rio Grande do Sul, and finds growing viral diversity along with evidence of at least two different coinfections with B.1.1.28 (E484K) and two other lineages (B.1.1.248 and B.1.91). 

The B.1.1.28 lineage has undergone considerable changes in the past few months, resulting in several new branches, including the P.1 variant. These researchers have also identified a new variant - dubbed VUI-NP13L - which is currently under investigation.

The picture we get is of a virus undergoing significant evolution and continued diversification, and while not all of these variants will end up being `biologically fit enough' to compete on the world stage, several have already demonstrated robust transmissibility and the possibility of antigenic escape. 

The first confirmation of co-infections with different lineages of COVID adds yet another layer of complexity - and uncertainty - about the ways that SARS-CoV-2 could evolve going forward. 

A Reuters report overnight quotes lead researcher Fernando Spilki as saying “These co-infections can generate combinations and generate new variants even more quickly than has been happening" and  “It would be another evolutionary pathway for the virus". 

I've only included the Abstract and a small excerpt from the discussion, so follow the link to read the paper in its entirety. 

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Ronaldo da Silva Francisco Jr, L. Felipe Benites, Alessandra P Lamarca, Luiz G P de Almeida, Alana Witt Hansen, Juliana Schons Gularte,  Meriane Demoliner,  Alexandra L Gerber,  Ana Paula de C Guimarães,  Ana Karolina Eisen Antunes,  Fagner Henrique Heldt,  Larissa Mallmann,  Bruna Hermann,  Ana Luiza Ziulkoski, Vyctoria Goes,  Karoline Schallenberger,  Micheli Fillipi,  Francini Pereira,  Matheus Nunes Weber,  Paula Rodrigues de Almeida,  Juliane Deise Fleck, Ana Tereza R Vasconcelos, Fernando Rosado Spilki
Abstract

Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. 

In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. 

We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. 

In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.

Highlights
  • The novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil;
  • The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul;
  • B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.
(SNIP)

(Excerpt)

The present work demonstrates a pervasive spread of B.1.1.28 (E484K), the possibility of occurrences of co-infection events and emergence of a novel SARS-CoV-2 lineage (VUI-NP13L) across the state of Rio Grande do Sul. The impact of the mutation E484K is still not fully understood; however, its strong association with escaping neutralizing antibodies highlights the necessity for development studies to better establish mechanisms of viral infection. Our results not only increase the number of sequences from the state, but also shed light on an important seeding event between distant Brazilian regions.

  

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