Fiocruz Genomics Network research constitutes mechanisms behind the rapid spread of lineages derived from the New Coronavirus Gamma Variant
After the second wave of SARS-CoV-2 infection in Brazil, marked by the emergence and wide dissemination of the Gamma variant (P.1), one of the concerns of the scientific community was with possible results of the evolutionary process continuity of this VOC. More specifically, the emergence possibility of new mechanisms that would make Gamma-derived samples more transmissible, infective, or more effective at evading the action of neutralizing antibodies reinforced the importance of continued surveillance of Gamma and derived variants.
The present paper, the result of the process of independent editing and review of data previously presented in preprint form, is derived from the analysis of the genomes of 1188 SARS-CoV-2 samples, the majority (99.7%) belongs to the Gamma VOC. There has been a significant increase in the prevalence of the so-called “Gamma+” samples – that is, those that accumulate additional mutations compared to samples initially classified as Gamma, as a result of the evolutionary process with the fixation of these new mutations. One of these Gamma variations, the so-called Gamma+N679K, accounts for 76.9% of the samples analyzed for June-July 2021. The work also discusses the biological importance of some of the mutations found, such as deletions in the protein S domain called NTD (which hinder neutralization by antibodies produced by the organism in response to an infection or vaccination) and changes in the structure of another region of protein S, the S1/S2 junction, which have the potential – still being studied by the researchers – to lead to greater infectivity due to a greater affinity with the molecular mechanism that allows the virus to fuse its envelope to the cell membrane and initiate the cell invasion (furin).
These Gamma-derived samples, designated P.1.3, P.1.4, P.1.5, P.1.6, P.1.7, and P.1.8, although they are in a process of expansion that may make them more prevalent within the lineage than the original Gamma, and despite having an apparent greater transmissibility, do not appear to be more effective in their ability to escape the action of antibodies – i.e., cause reinfection and/or infect previously vaccinated persons. The paper from the Fiocruz Genomics Network also brings a reminder that as SARS-CoV-2 spreads in the population, the risk of selecting new variants with greater infectivity is likely to increase.
Naveca, F. G., Nascimento, V., Souza, V., Corado, A. L., Nascimento, F., Silva, G., Mejía, M., Brandão, M. J., Costa, A., Duarte, D., Pessoa, K., Jesus, M., Gonçalves, L., Fernandes, C., Mattos, T., Abdalla, L., Santos, J. H., Martins, A., Chui, F. M., Val, F. F., Melo, G. C., Xavier, M. S., Sampaio, V. S., Mourão, M. P., Lacerda, M. V., Batista, E. L. R., Magalhães, A. L. A., Dábilla, N., Pereira, L. C. G., Vinhal, F., Miyajima, F., Dias, F. B. S., Santos, E. R., Coêlho, D., Ferraz, M., Lins, R., Wallau, G. L., Delatorre, E., Gräf, T., Siqueira, M. M., Resende, P. C., & Bello, G. (2022). Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Virology.
International study with participation of members of the Fiocruz Genomics Network unveils part of the mechanisms involved in the Omicron Variant’s ability to cause reinfection and infect vaccinated people
The Omicron Variant of Concern (B.1.1.529) brought about a major worldwide expansion of SARS-CoV-2 infections, even in countries where immunization against the virus was already advanced. To understand how the mutations collection in Omicron Glycoprotein S leads to immune response scape, an international research effort that included scientists from the Fiocruz Genomics Network analyzed protein structures as well as neutralization of the ability to cause infection by exposing Omicron samples to different antibody-containing preparations such as: 1) serum from patients infected with other samples of the virus; 2) so-called “monoclonal antibodies” selected in the laboratory; and 3) serum from vaccinated people.
The present paper, result of this collaboration to study multiple factors involved in the immune response escape presented by Omicron, has shown that the new variant is almost 17 times more resistant to neutralization by antibodies generated in response to a first-wave pandemic lineage. The study also shows that a three-dose vaccine regimen greatly increases the response to the virus, including neutralization of the Omicron variant, which was not sufficient with only two doses of the immunizer. The paper further shows that the portions structure of Omicron’s Glycoprotein S are involved in “compensating” antibody action by a stronger binding to ACE2, a molecule that acts as a viral receptor on human cells.
Dejnirattisai, W., Huo, J., Zhou, D., Zahradník, J., Supasa, P., Liu, C., Naveca, F. G., Nascimento, V., Nascimento, F., Costa, C. F., Resende, P. C., Pauvolid-Correa, A., Siqueira, M. M., … & Screaton, G. R. (2022). SARS-CoV-2 Omicron-B. 1.1. 529 leads to widespread escape from neutralizing antibody responses. Cell.
Innovative bioinformatics tool created by researchers at the Aggeu Magalhães Institute linked to the Fiocruz Genomics Network allows to centralize several viral genome analyses in a single software
With the pandemic of the novel coronavirus and the emergence of variants with different characteristics, the international scientific community was faced with a challenge: how to study the virus, its spread and evolution on a global scale? A series of tools for analyzing different data related to the pandemic is being developed to allow scientists around the world to study the virus causing COVID-19. Among the major challenges, the analysis of viral genome sequencing data obtained from patient samples is essential in detecting new variants and understanding mutations relevant to public health.
Multiple tools have already been developed for analyzing gene sequences for automating the sorting process in lineages and for detecting mutations. Still, there is no tool that centralizes quality analysis, genome assembly and lineages classification, mutation description, and intra-host analysis of variants (to detect when a person is infected with two or more variants at once). Thus, research groups have to work in a decentralized way with different tools to obtain and analyze the sequences. This way of working based on scattered tools is time consuming and requires research groups to invest in training to use various services. Furthermore, in cases where the same patient is infected with two or more variants, the separation and genomes assembly is not possible using these tools.
The present paper, published in the international journal Viruses, presents a tool developed by researchers at the Fiocruz Genomics Network, to centralize in a single features and complex analyses package such as those described above, in an economical way in terms of time spent, allowing the issuance of reports and data tables based on the sequencing results. This tool, called ViralFlow, automates several important processes for genomic surveillance and provides a platform for researchers to study multiple aspects of SARS-CoV-2 samples in a centralized and prompt manner.
Dezordi, F. Z., de Lima Campos, T., Jeronimo, P. M. C., Aksenen, C. F., Almeida, S. P., & Wallau, G. L. (2021). ViralFlow: an automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variants detection. medRxiv.
Paper by researchers from the Fiocruz Genomics Network is published in one of the world’s largest scientific journals, and reconstructs the dynamics of variants in the state of Amazonas and the emergence of the Gamma Variant
Among the 27 Brazilian Federative Units, the state of Amazonas was one of the most affected by the present pandemic of the novel coronavirus, with the occurrence of a second wave at the end of 2020 in which a large number of severe cases led to a health system collapse. The paper, published in one of the world’s most relevant scientific journals, Nature journal, is the result of the complete genome analysis of 250 SARS-CoV-2 samples collected in Amazonas between March 2020 and January 2021, and describes the succession dynamics of dominant lineages in the state. The paper had previously been published as a preprint, and has now gone through editing and peer review, which gives more certainty to its conclusions.
The publication presents data that support the hypotheses that the lineage responsible for most cases in the first moment of the pandemic (between March and May 2020) was B.1.195, that it was bypassed by B.1.1.28, which became the dominant lineage in the state between May and December 2020, and that in December the emergence of a B.1.1.28 variant, called P.1, with greater transmissibility, was responsible for the new rise in the number of cases and deaths. Thus, the local dynamics of new viral genetics emergence was an important driving force for the way in which the pandemic advanced over the state of Amazonas, directly influenced by the population circulation and its relation with the virus spread, which culminated with the substitution of B.1.1.28 by it descendent, the variant of concern P.1, in a process believed to have lasted less than two months.
Naveca FG, Nascimento V, de Souza VC, Corado AL, Nascimento F, Silva G, Costa Á, Duarte D, Pessoa K, Mejía M, Brandão MJ, Jesus M, Gonçalves L, da Costa CF, Sampaio V, Barros D, Silva M, Mattos T, Pontes G, Abdalla L, Santos JH, Arantes I, Dezordi FZ, Siqueira MM, Wallau GL, Resende PC, Delatorre E, Gräf T, Bello G. COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Researchers at Fiocruz Genomics Network create sequencing protocol that allows the identification of some key changes in the SARS-CoV-2 genome with lower costs
In light of the current pandemic facing humanity, the use of next-generation genome sequencing techniques has been one of the main strategies for the epidemiological surveillance of the novel coronavirus. Next-generation sequencing has allowed the rapid identification of new virus variants and the clustering of samples into lineages defined by common characteristics and shared genetic origin. Additionally, this type of sequencing provides the analysis of mutations found to understand their consequences for the evolutionary race that determines numerous aspects of the pandemic. In contrast to the possibilities offered by next-generation sequencing, the high cost of the equipment and ingredients required to perform it, and the need for properly trained technical personnel, make it unfeasible for more remote regions and countries with fewer possibilities for investment in research to maintain the long-term use of this technique. Especially when there is a need for imported ingredients such as reagents and kits, the risk of blackout periods in epidemiological surveillance is high, which highlights the importance of developing lower cost and easier to implement alternatives. Alternative techniques with these characteristics guarantee greater possibilities of sustaining a continuous monitoring of the samples circulating in a given locality, which is vital for the development of coping strategies.
The present publication – the result of peer review of a paper previously published as a preprint – presents an alternative based on Sanger sequencing of a single PCR fragment (725 base pairs), capable of detecting the main mutations in the Spike glycoprotein (S protein) and classifying samples as belonging to the main variants circulating in Brazil. The technique was tested on twelve positive samples, with results that provide reassurance that using Sanger sequencing to investigate this PCR fragment can prevent a monitoring “blackout.” Although the use of the technique entails an information loss when compared to sequencing the complete genome of the samples, having reliable and inexpensive ways to monitor the variants brings an important robustness to epidemiological monitoring in Brazil and other countries with similar socioeconomic challenges.
Bezerra, M. F., Machado, L. C., De Carvalho, V. D. C. V., Docena, C., Brandão-Filho, S. P., Ayres, C. F. J., … & Wallau, G. L. A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern
New Coronavirus Variants of Concern have mutations that decrease antibody effectiveness, allowing reinfection
The new variants rapid spread of the novel SARS-CoV-2 coronavirus, as exemplified by the high prevalence of the P.1 variant even within the first two months after its emergence, along with reinfection reports caused by these variants, raises for science the question of what the mechanisms behind this scenario might be. Of special interest to this research is the study of mutations in the genome of the variants – in particular, in the Spike glycoprotein gene (S protein), which promotes entry into human cells through interaction with Angiotensin Converting Enzyme 2 (hACE2), a molecule that acts as the virus receptor. The ability to bind to hACE2 may become greater or less according to changes in the structure of the S protein, which vary between lineages of SARS-CoV-2 and each of its variants. These changes in the protein S structure may also result in a decreased ability of antibodies generated in response to an infection – or possibly even after vaccination – to bind to protein S and neutralize the virus’ ability to cause infection.
The present publication investigates these two possible effects of protein S mutations detected in variants such as P.1, variants of the B.1.351 and B.1.1.7 lineages: that of a “stronger” interaction with the hACE2 receptor or that of a “weaker” interaction with anti-protein-S antibodies. The publication is the result of the complete editing process, with review by independent researchers, of the preprint initially published by network researchers in March 2021. The paper describes a series of experiments performed with computational modeling of the molecules involved (hACE2, antibodies, and the different “versions” of protein S, referring to each of the variants studied).
Based on the computational simulation of the interaction between the molecules, it was possible to verify that altering the protein S structure had no significant effects on the interaction with the hACE2 receptor. On the other hand, by simulating the interaction of antibodies generated in response to early SARS-CoV-2 lineages with the S protein of the new variants, it was possible to see that there is a decrease in binding between the molecules, a finding that points to a potential immune response “escape”. According to this hypothesis, the new variants would be more effective in evading the neutralization provided by antibodies, and this would be a more relevant mechanism to explain their rapid spread in the population. It is important to highlight, based on some affinity measurements between variations of the S protein and the hACE2 receptor, other research groups have previously suggested that increased transmissibility would be related to a higher affinity between the viral protein and the human receptor, in contrast to the results of the present study. However, these studies have not explored the interaction of the different S proteins with the neutralizing antibodies. The paper also points to the new variant named P.3 as a potential Variant of Concern (VOC), given that most of the antibodies analyzed in the study were unable to efficiently bind to the S protein of this lineage in the simulations performed.
Ferraz MVF, Moreira EG, Coêlho DF, Wallau GL, Lins RD. Immune Evasion of SARS-CoV-2 Variants of Concern is Driven by Low Affinity to Neutralizing Antibodies
International research cooperation focuses on unraveling how the novel coronavirus behaves on the border between Brazil and Uruguay
Despite having managed to control the spread of the novel coronavirus – being one of the few countries in the Americas to successfully contain the pandemic – its proximity to Brazil presents a risk to Uruguay. The high mobility between borders, together with Brazil’s situation as one of the worst countries in the world in number of cases and fatalities, are factors that can lead to multiple introductions of the virus to Uruguay, and to the arrival of more contagious variants in the country.
The present paper, the result of independent review and editing of a previously published preprint, reports the results of epidemiological surveillance in inland Uruguayan cities in the border region with Brazil and the reconstruction of the events of SARS-CoV-2 spread in the Brazil-Uruguay direction. Using genomes from 54 samples of the novel coronavirus collected in Uruguayan cities and 68 Brazilian samples from Rio Grande do Sul, research groups from 15 institutions from both countries were able to reconstruct a panorama characterized by multiple introductions of Brazilian lineages of B.1.1.28 and B.1.1.33 in border Uruguayan cities. The strains introduced into the country probably came from the Brazilian state of RS, and began circulating locally in these cities in less than three months (between early May, when the first events probably occurred, and mid-July). It was also possible to find that the strains that caused outbreaks in Uruguay had between 4 and 11 genetic changes when compared to the Brazilian ancestral strains B.1.1.28 and B.1.1.33, which supports the idea that the genome of the novel coronavirus seems to accumulate mutations very quickly in its rapid spread throughout South America.
In addition to being the first study with genomics data focused on this region, the study also highlights that outbreaks caused in this inland region stemmed from virus introductions from Brazil, in contrast to outbreaks in metropolitan regions in 2020 that were associated with virus introductions from Europe.
Mir, D., Rego, N., Resende, P. C., Tort, F., Fernández-Calero, T., Noya, V., Brandes, M., Possi, T., Arleo, M., Reyes, M., Victoria, M., Lizasoain, A. Castells, M., Maya, L., Salvo, M., Gregianini, T. S., Rosa, M. T. M., Martins, L. G., Alonso, C., Vega, Y., Salazar, C., Ferrés, I., Smircich, P., Silveira, J. S., Fort, R. S., Mathó, C., Arantes, I., Appolinario, L., Mendonça, A. C., Benítez-Galeano, M. J., Simoes, C., Graña, M., Motta, F., Siqueira, M. M., Bello, G., Colina, R. & Spangenberg, L.. Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan–Brazilian Border
How does the Novel Coronavirus circulate among our pets?
The novel SARS-CoV-2 coronavirus, causing the pandemic currently facing humanity on a global scale, has adapted to the human organism and has become capable of causing the disease and being transmitted from person to person, but its primary origin is in Asian bat populations. Additionally, it is believed that another intermediate mammalian species was involved, with first an adaptation from the bat to this other mammal, from which the virus accumulated new mutations and “jumped” to the human species (also called the spillover infection). Thus, investigating the ability of SARS-CoV-2 to cause infection and circulate among other animal species, especially those that live in closer proximity to humans, such as domestic dogs and cats, becomes an important research question: not only can one from this surveillance monitor risk factors and prevent a possible additional “jump” to these other species, but also understand the role of domestic animals in the epidemic spread.
The present paper, published in the open access journal PLOS One, investigated the presence of symptoms, viral RNA and antibodies against SARS-CoV-2 in 29 dogs and 10 cats living with patients with a COVID-19 history in the city of Rio de Janeiro. Among these, 9 dogs (31%) and 4 cats (40%) from 10 of the 21 households analyzed in the study presented infection symptoms or were seropositive for SARS-CoV-2. Samples were collected from the animals every two weeks, and aspects of their health status were evaluated to allow an estimate of the time span between the first confirmed case of COVID-19 in the human patients and the first positive test in the pets. The animals tested positive between 11 and 51 days, on average, after the first symptoms in patient zero of each household. Collecting more than one sample also allowed the identification of three cases of dogs that tested positive twice (with intervals of 14, 30, and 31 days between the first and second positive tests), as well as the detection of antibodies in one dog (3.4% of cases) and two cats (20%). Among thirteen animals infected or seropositive for SARS-CoV-2, six developed moderate symptoms of the disease, but their conditions were reversible.
In addition to demonstrate that pets can contract SARS-CoV-2, the study identified among possible risk factors that castrated animals are more likely to be infected by their owners, as well as those who sleep in the same bed as humans. This allows for the important recommendation that people who test positive for the novel coronavirus avoid excessive proximity to their pets.
Calvet, G. A., Pereira, S. A., Ogrzewalska, M., Pauvolid-Corrêa, A., Resende, P. C., Tassinari, W. D. S., … & Menezes, R. C. Investigation of SARS-CoV-2 infection in dogs and cats of humans diagnosed with COVID-19 in Rio de Janeiro, Brazil
Variants of the COVID-19 virus circulating in Brazil are able to cause infections in people who already have antibodies for the disease
The first case of reinfection by the novel coronavirus formally recognized by the Ministry of Health was on December 9th, 2020. This paper is the result of the peer review and editing process of the text originally posted on the expert-oriented virology research discussion forum, Virological.Org. The paper describes a series of information and research findings derived from this reinfection, and draws conclusions regarding the significance of this event for surveillance and combating the pandemic in Brazil.
The case affected a 37-year-old health professional, who was seeing patients in Paraíba, although she lived in Rio Grande do Norte. The patient had two clinical episodes compatible with SARS-CoV-2 infection separated by 116 days (onset of symptoms of the first infection: June 17th; second infection: October 11th) and, after sequencing and comparison between samples from these two events, reinfection was found, since the first infection was caused by a virus compatible with the B.1.1.33 lineage and the second infection was caused by a virus compatible with the B.1.1.28 lineage. This second agent of infectious agent also had an amino acid substitution in the S E484K protein, associated with antibodies escape ability generated in response to infection and SARS-CoV-2 vaccination. In addition to demonstrating the circulation of variants capable of causing reinfection in Brazil, the publication also shows the circulation of the B.1.1.28(E484K) lineage outside the state of Rio de Janeiro, where it is believed – based on reconstructions – that the lineage initially originated.
Resende PC, Bezerra JF, Vasconcelos RHT, Arantes I, Appolinario L, Mendonça AC, et al. Severe acute respiratory syndrome coronavirus 2 P.2 lineage associated with reinfection case, Brazil, June–October 2020
N9: A new variant of SARS-CoV-2 identified for the first time between 2020 and early 2021, in samples from ten Brazilian states
The SARS-CoV-2 pandemic in Brazil was dominated by two main lineages throughout 2020 and early 2021. Among these lineages, B.1.1.28 has already given rise to two important variants carrying mutations in the Spike glycoprotein (S protein), such as the E484K amino acid substitution in the receptor-binding domain (RBD), implicated as a major factor in the neutralization escape by antibodies against the virus. These lineages are the variant of interest P.2 and the variant of concern (VOC) Gamma. Gamma, which probably emerged in December 2020, has spread rapidly throughout the state of Amazonas and reached other regions of the country, and has additional mutations that presumably give the variant an increased ability to cause reinfection, and higher viral loads in patients.
This paper is the result of the independent review and editing process of the publication originally posted on the virology research discussion forum Virological.Org, which described the first Brazilian variant positive for the E484K mutation derived from lineage B.1.1.33, the other dominant lineage in Brazil. VOI N.9 probably emerged in August 2020, and its discovery from samples from ten states (São Paulo, Santa Catarina, Amazonas, Pará, Bahia, Maranhão, Paraíba, Pernambuco, Piauí and Sergipe) collected between November 2020 and February 2021 confirms its rapid spread throughout the national territory, reflecting a hardship in ensuring social isolation and distance, and containing the people flow between different Brazilian regions. Despite this rapid spread, N.9 appears to have a low prevalence, corresponding to approximately 3% of samples on a national scale. In addition to carrying the E484K mutation in protein S, N.9 also has four other non-synonymous mutations that define the lineage.
Resende PC, Gräf T, Paixão ACD, Appolinario L, Lopes RS, Mendonça ACdF, da Rocha ASB, Motta FC, Neto LGL, Khouri R, de Oliveira CI, Santos-Muccillo P, Bezerra JF, Teixeira DLF, Riediger I, Debur MdC, Ribeiro-Rodrigues R, Leite AB, do Santos CA, Gregianini TS, Fernandes SB, Bernardes AFL, Cavalcanti AC, Miyajima F, Sachhi C, Mattos T, da Costa CF, Delatorre E, Wallau GL, Naveca FG, Bello G, Siqueira MM. A Potential SARS-CoV-2 Variant of Interest (VOI) Harboring Mutation E484K in the Spike Protein Was Identified within Lineage B.1.1.33 Circulating in Brazil.
Study by researchers at the Fiocruz Genomics Network reconstructs the evolutionary history of Lineage B.1.1.33, which spread rapidly in Brazil in 2020
The new SARS-CoV-2 coronavirus initially arrived in Brazil in February 2020. Weeks later, from the mutation of a central lineage, the B.1.1.33 strain emerged in the country. Its spread has made it one of the leading and most widespread among Brazilian patients until at least February 2021. This publication describes, from the analysis of 190 complete genomes derived from clinical samples, the evolutionary history and the spread patterns of this strain. The paper also discusses the impact of sanitary measures to control the spread of the disease in curbing the advance of the lineage, discussing how the adoption of poorly restrictive measures in some regions of the country, as well as the low adherence of the population to the measures in place, resulted in wide spread of B.1.1.33. In Rio de Janeiro state, the strain reached a prevalence of 80% of cases, becoming the main driving force of community-acquired infection in the region. This publication is an expansion of the work initially presented in the form of a posting on the virology expert forum Virological.Org, which is also described on our website.
Resende, P. C., Delatorre, E., Gräf, T., Mir, D., Motta, F. C., Appolinario, L. R., da Paixão, A., Mendonça, A., Ogrzewalska, M., Caetano, B., Wallau, G. L., Docena, C., Dos Santos, M. C., de Almeida Ferreira, J., Sousa Junior, E. C., da Silva, S. P., Fernandes, S. B., Vianna, L. A., Souza, L., Ferro, J., … Siqueira, M. M. Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil.
Modeling the early steps of COVID-19: researchers at the Fiocruz Genomics Network reconstruct the possible initial route by which the virus crossed continents
The pandemic of the new SARS-CoV-2 coronavirus had an initial phase characterized by the rapid spread of the virus across several territories, but pinpointing the time of arrival of the virus in different countries is a difficult task. In this publication, Genomics Network researchers propose a model based on the number of deaths reported in the early pandemic states in 2020 to estimate the most likely dates of arrival of the virus in each territory. The result of the estimates points to a scenario in which, still between the middle of January and the middle of February, the virus had already reached all the countries analyzed in the study, which used data from countries in the Americas and Western Europe.
Delatorre, E., Mir, D., Gräf, T., & Bello, G. Tracking the onset date of the community spread of SARS-CoV-2 in Western Countries.
First large-scale genomic surveillance study in the state of Pernambuco reveals different pandemic dynamics in the region compared to what is observed in other states in Brazil
Although it is one of the world epicenters of the novel coronavirus pandemic, Brazil’s territorial breadth and structural differences mean that genomic epidemiology surveillance is not homogeneous across states and regions of the country. By the time this paper was published in December 2020, few genomes had been sequenced in the state of Pernambuco, the sixth most affected Federative Unit in Brazil, a knowledge gap about the behavior of the pandemic that researchers at the Fiocruz Genomics Network set out to cover.
Based on the sequencing and analysis of 101 genomes of SARS-CoV-2 isolated from symptomatic patients in the state, it was possible to identify that, in Pernambuco, the behavior of the pandemic differed from that observed in Southeastern states such as Rio de Janeiro and São Paulo, in which the presence of a dominant lineage per region was verified, responsible for most cases – a phenomenon also reported by a Genomics Network study published as a preprint in February 2021 for the state of Amazonas. In Pernambuco, several lineages of the B.1.1 clade have been found, suggesting the entry of the virus into the state in several isolated events. The detection of lineages both in the capital city of Recife and in the inland cities of the state further suggest that community transmission between municipalities played a relevant role in the virus spread dynamics in the state.
Paiva MHS, Guedes DRD, Docena C, Bezerra MF, Dezordi FZ, Machado LC, Krokovsky L, Helvecio E, da Silva AF, Vasconcelos LRS, Rezende AM, da Silva SJR, Sales KGdS, de Sá BSLF, da Cruz DL, Cavalcanti CE, Neto AdM, da Silva CTA, Mendes RPG, da Silva MAL, Gräf T, Resende PC, Bello G, Barros MdS, do Nascimento WRC, Arcoverde RML, Bezerra LCA, Brandão-Filho SP, Ayres CFJ, Wallau GL. Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil.
Study by researchers from the Fiocruz Genomics Network reveals genome origins and details of a sample of the novel coronavirus coming from Spain to the Amazon
The arrival of the novel coronavirus pandemic in Brazil took place in the first months of 2020, with the first case being reported in February in the city of São Paulo. New cases have been detected in different regions of the country, in Federative Units such as Bahia, Brasilia, and Rio Grande do Sul, with the detection of the disease in the North region being reported on March 13th, from a traveler returning from England. The present study reports the genome sequencing of the second case detected in the state of Amazonas, a 56-year-old asymptomatic man returning from Madrid, Spain.
In addition to presenting what is probably the first complete SARS-CoV-2 genome from the Northern Region of Brazil, the study also describes the protocol developed to enable sequencing, as well as results from the genome analysis in comparison to other sequences previously deposited in the GISAID database. This analysis allowed the sample classification in the A.2 lineage, the identification of 9 mutations in the genome compared to the original genome of SARS-CoV-2 detected in Wuhan (China), and the phylogeographic analysis, which points to the probable origin of the sample as European.
Nascimento, V. A. D., Corado, A. D. L. G., Nascimento, F. O. D., Costa, Á. K. A. D., Duarte, D. C. G., Luz, S. L. B., … & Naveca, F. G. (2020). Genomic and phylogenetic characterisation of an imported case of SARS-CoV-2 in Amazonas State, Brazil. Memorias do Instituto Oswaldo Cruz, 115.
What can water and sewer systems tell about epidemics? Study in partnership with the Fiocruz Genomics Network maps SARS-CoV-2 genomes in sewage samples from Niteroi, RJ
Monitoring disease-causing agents in public wastewater systems, such as domestic sewage and industrial waste, can be a valuable tool in epidemiological monitoring. The practice, known as “wastewater-based epidemiology” has been used as an additional source of information regarding the spread of diseases such as COVID-19, especially in localities in which there are logistical and financial difficulties for direct mass testing of the population. From a public health perspective, monitoring wastewater can provide quick answers to inform epidemic control measures. This paper reports the methods and results of applying wastewater-based epidemiology to samples collected from sanitary sewer manholes and sewage treatment plants in the city of Niteroi/RJ, totaling 223 samples collected over 20 weeks.
The analysis of the samples allowed not only the presence of viral RNA to be detected, but also quantitative data on the number of copies of the virus present in the samples. Analysis of samples from treatment plants provided better answers regarding the evolution of virus contagion curves, while pipe samples were more useful for the implementation and monitoring of local public health interventions. The study also allowed the identification of the lineage to which the SARS-CoV-2 samples found belonged (B.1.1.33) and the construction of weekly risk monitoring maps, highlighting how useful this approach is for fighting the current pandemic on different fronts.
Prado T, Fumian TM, Mannarino CF, Resende PC, Motta FC, Eppinghaus ALF, et al. Wastewater-based epidemiology as a useful tool to track SARS-CoV-2 and support public health policies at municipal level in Brazil. Water Res. 2021;191:116810.
International study with participation of researchers from the Fiocruz Genomics Network unveils relationship between some mutations of the Novel Coronavirus and the ability to evade antibodies
One of the main concerns of the scientific community brought about by the new SARS-CoV-2 variants is the possibility that some of the mutations present in the variants of concern (VOCs) B.1.1.7, B.1.351 and P.1 give these lineages the ability to evade antibodies generated in response to infection or vaccination. This publication, the result of international research cooperation, evaluated the impacts of three amino acid changes in the spike glycoprotein (S protein) from mutations characteristic of the P.1 and B.1.351 variants on antibody neutralization of the novel coronavirus. These three changes (positions 417, 484, and 501) in the S protein structure affect the portion of the protein that binds to ACE2, a protein present on the human cells surface, and only one of them (N501Y) is present in another VOC, B.1.1.7.
Investigating the impact of these structural alterations of the protein on the neutralization of the virus infective capacity by antibodies brings important answers to the relevance of the mutations in the so-called “immune escape”, since the binding between this portion of the S-protein and the cellular receptor ACE2 is the first step in the infection process. The study concluded that the changes in the VOC P.1 S protein appear to increase the protein’s ability to bind to the ACE2 receptor, and conversely, that they reduce the neutralizing ability of antibodies generated in response to SARS-CoV-2 samples without the mutations. Compared to a sample isolated at the beginning of the pandemic, variants P.1 and B.1.351 had an approximately 3-fold decrease in neutralization by serum from patients convalescing or vaccinated against SARS-CoV-2 with immunizers from Pfizer-BioNTech and Oxford-AstraZeneca. Based on these findings, it can be considered that the risk of immune escape is real, although the changes in the circulating protein S at the time do not completely prevent neutralization of the infection by antibodies. It should also be noted that some vaccines, such as Oxford-AstraZeneca, induce a strong cellular response and this mechanism would also play an important role in the protective response. Still, the possibility that future mutations in these genes will cause further escape from vaccine-stimulated immunity mechanisms is a risk that should not be ignored, and measures to decrease virus circulation are needed to reduce the chances of the emergence and spread of such changes.
Dejnirattisai, W., Zhou, D., Supasa, P., Liu, C., Mentzer, A. J., Ginn, H. M., … & Screaton, G. R. Antibody evasion by the P. 1 strain of SARS-CoV-2.
Lugon P, Fuller T, Damasceno L, Calvet G, Resende PC, Matos AR, Machado Fumian T, Malta FC, Salgado AD, Fernandes FCM, Abreu de Carvalho LM, Guaraldo L, Bastos L, Cruz OG, Whitworth J, Smith C, Nielsen-Saines K, Siqueira M, Carvalho MS, Brasil P. SARS-CoV-2 Infection Dynamics in Children and Household Contacts in a Slum in Rio de Janeiro.
Espíndola, O. M., Siqueira, M., Soares, C. N., Lima, M., Leite, A., Araujo, A., Brandão, C. O., & Silva, M. (2020). Patients with COVID-19 and neurological manifestations show undetectable SARS-CoV-2 RNA levels in the cerebrospinal fluid.
Espíndola OM, Brandão CO, Gomes YCP, Siqueira M, Soares CN, Lima MASD, Leite ACCB, Torezani G, Araujo AQC, Silva MTT. Cerebrospinal fluid findings in neurological diseases associated with COVID-19 and insights into mechanisms of disease development.
de Macedo, P. M., Freitas, D., Varon, A. G., Lamas, C., Ferreira, L., Freitas, A. D., Ferreira, M. T., Nunes, E. P., Siqueira, M. M., Veloso, V. G., & do Valle, A. (2020). COVID-19 and acute juvenile paracoccidioidomycosis coinfection.
Fintelman-Rodrigues N, Sacramento CQ, Ribeiro Lima C, Souza da Silva F, Ferreira AC, Mattos M, de Freitas CS, Cardoso Soares V, da Silva Gomes Dias S, Temerozo JR, Miranda MD, Matos AR, Bozza FA, Carels N, Alves CR, Siqueira MM, Bozza PT, Souza TML. Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production
Dias, H. G., Resck, M. E. B., Caldas, G. C., Resck, A. F., Da Silva, N. V., Dos Santos, A. M. V., Sousa, T. C., Ogrzewalska, M. H., Siqueira, M. M., Pauvolid-Corrêa, A. & Dos Santos, F. B. (2021). Neutralizing antibodies for SARS-CoV-2 in stray animals from Rio de Janeiro, Brazil.
Andrus, J. K., Evans-Gilbert, T., Santos, J. I., Guzman, M. G., Rosenthal, P. J., Toscano, C., Valenzuela, M. T., Siqueira, M., Etienne, C., & Breman, J. G. (2020). Perspectives on Battling COVID-19 in Countries of Latin America and the Caribbean.
Barbosa GR, Moreira LVL, Justo AFO, Perosa AH, de Souza Luna LK, Chaves APC, Bueno MS, Conte DD, Carvalho JMA, Prates J, Dantas PS, Faico-Filho KS, Camargo C, Resende PC, Siqueira MM, Bellei N. Rapid spread and high impact of the variant of concern P.1 in the largest city of Brazil.
Barreto-Vieira DF, da Silva MAN, Garcia CC, Miranda MD, Matos ADR, Caetano BC, Resende PC, Motta FC, Siqueira MM, Girard-Dias W, Archanjo BS, Barth OM. Morphology and morphogenesis of SARS-CoV-2 in Vero-E6 cells.
Dos Santos CA, Bezerra GVB, de Azevedo Marinho ARRA, Sena LOC, Alves JC, de Souza MSF, de Oliveira Góes MA, Teixeira DCP, Silva PCR, de Siqueira MAMT, Martins-Filho PR. First Report of SARS-CoV-2 B.1.1.251 lineage in Brazil.
Silva, M., Lima, M. A., Torezani, G., Soares, C. N., Dantas, C., Brandão, C. O., Espíndola, O., Siqueira, M. M., & Araujo, A. Q. (2020). Isolated intracranial hypertension associated with COVID-19.
Dias SSG, Soares VC, Ferreira AC, Sacramento CQ, Fintelman-Rodrigues N, Temerozo JR, Teixeira L, Nunes da Silva MA, Barreto E, Mattos M, de Freitas CS, Azevedo-Quintanilha IG, Manso PPA, Miranda MD, Siqueira MM, Hottz ED, Pão CRR, Bou-Habib DC, Barreto-Vieira DF, Bozza FA, Souza TML, Bozza PT. Lipid droplets fuel SARS-CoV-2 replication and production of inflammatory mediators.
Xavier J, Giovanetti M, Adelino T, Fonseca V, Barbosa da Costa AV, Ribeiro AA, Felicio KN, Duarte CG, Ferreira Silva MV, Salgado Á, Lima MT, de Jesus R, Fabri A, Soares Zoboli CF, Souza Santos TG, Iani F, Ciccozzi M, Bispo de Filippis AM, Teixeira de Siqueira MAM, de Abreu AL, de Azevedo V, Ramalho DB, Campelo de Albuquerque CF, de Oliveira T, Holmes EC, Lourenço J, Junior Alcantara LC, Assunção Oliveira MA. The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
Aguiar-Oliveira M. L., Campos A, R. Matos A, Rigotto C, Sotero-Martins A, Teixeira PFP, Siqueira MM. Wastewater-Based Epidemiology (WBE) and Viral Detection in Polluted Surface Water: A Valuable Tool for COVID-19 Surveillance—A Brief Review
Rangel, E. F., Afonso, M. M. D. S., Sotero-Martins, A., Campos, A., Coelho, W. N., Gama, E. L., Flores, G. L., Siqueira, M. M. & Aguiar-Oliveira, M. D. L. (2021). Can Climate and Environmental Factors Putatively Increase SARS-Cov2 Transmission Risks?
Matos, A., Motta, F. C., Caetano, B. C., Ogrzewalska, M., Garcia, C. C., Lopes, J., Miranda, M., Livorati, M., Abreu, A., Brown, D., & Siqueira, M. M. (2020). Identification of SARS-CoV-2 and additional respiratory pathogens cases under the investigation of COVID-19 initial phase in a Brazilian reference laboratory.
Prado T, Fumian TM, Mannarino CF, Maranhão AG, Siqueira MM, Miagostovich MP. Preliminary results of SARS-CoV-2 detection in sewerage system in Niterói municipality, Rio de Janeiro, Brazil.
Melgaço, J.G.; Azamor, T.; Silva, A.M.V.; Linhares, J.H.R.; dos Santos, T.P.; Mendes, Y.S.; de Lima, S.M.B.; Fernandes, C.B.; da Silva, J.; de Souza, A.F.; Tubarão, L.N.; Brito e Cunha, D.; Pereira, T.B.S.; Menezes, C.E.L.; Miranda, M.D.; Matos, A.R.; Caetano, B.C.; Martins, J.S.C.C.; Calvo, T.L.; Rodrigues, N.F.; Sacramento, C.Q.; Siqueira, M.M.; Moraes, M.O.; Missailidis, S.; Neves, P.C.C.; Ano Bom, A.P.D. Two-Step In Vitro Model to Evaluate the Cellular Immune Response to SARS-CoV-2.
Liu C, Ginn HM, Dejnirattisai W, Supasa P, Wang B, Tuekprakhon A, Nutalai R, Zhou D, Mentzer AJ, Zhao Y, Duyvesteyn HME, López-Camacho C, Slon-Campos J, Walter TS, Skelly D, Johnson SA, Ritter TG, Mason C, Costa Clemens SA, Gomes Naveca F, Nascimento V, Nascimento F, Fernandes da Costa C, Resende PC, Pauvolid-Correa A, Siqueira MM, Dold C, Temperton N, Dong T, Pollard AJ, Knight JC, Crook D, Lambe T, Clutterbuck E, Bibi S, Flaxman A, Bittaye M, Belij-Rammerstorfer S, Gilbert SC, Malik T, Carroll MW, Klenerman P, Barnes E, Dunachie SJ, Baillie V, Serafin N, Ditse Z, Da Silva K, Paterson NG, Williams MA, Hall DR, Madhi S, Nunes MC, Goulder P, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum.
Preliminary scientific paper (preprint) provides important insights into the ability of Variants of Concern to infect people with antibodies
One phenomenon that caught the attention of scientists studying the novel coronavirus pandemic in Brazil was the rapid spread of the variant of concern (VOC) Gamma between late 2020 and early 2021, even in regions of the country with high rates of previous infection. This fact led to the research question of how much of the virus spread was due to reinfections – that is, the ability of some SARS-CoV-2 variants to evade antibodies generated in response to previous infections or vaccination.
In this preprint (a scientific work still in a preliminary stage, without independent review of methods and results), researchers from the Fiocruz Genomics Network studied in depth 25 cases of reinfection confirmed by RT-PCR – that is, with the identification of a virus genetic profile in the first event of infection and a second profile different from the first in the second event. Prior to reinfection by VOC Gamma, the patients had been infected with distinct viral lineages between March and December 2020, between three and twelve months prior to reinfection. Serum analysis of these patients revealed that more than half showed antibodies capable of neutralizing the novel coronavirus, including VOC Gamma itself, after reinfection, although this immune response is only partial – that is, the patients had the full cycle of infection, being able to transmit the disease to other potential hosts.
The paper concludes that reinfection by variants of concern plays an important role in the transmission of COVID-19, as the ability to partially evade the immune response of individuals already exposed to the virus means a greater potential for the pathogen to continue circulating in the population.
Naveca, F. G., Nascimento, V. A., Nascimento, F., Ogrzewalska, M., Pauvolid-Correa, A., Araujo, M. F., Arantes, I., Batista, E. L. R., Magalhães, A. L. A., Vinhal, F., Mattos, T. P., Riediger, I., Debur, M. C., Grinsztejn, B., Veloso, V. G., Brasil, P., Rodrigues, R. R., Rovaris, D. B., Fernandes, S. B., Fernandes, C., Santos, J. H. A., Abdalla, L. G., Costa-Filho, R., Silva, M., Souza, V., Costa, A. A., Mejía, M., Brandão, M. J., Gonçalves, L. F., Silva, G. A., Jesus, M. S., Pessoa, K., Corado, A. L. G., Duarte, D. C. G., Machado, A. B., Zukeram, K. A., Valente, N., Lopes, R. S., Pereira, E. C., Appolinario, L. R., Rocha, A. S., Tort, L. F. L., Sekizuka, T., Itokawa, K., Hashino, M., Kuroda, M., Wallau, G. L., Delatorre, E., Gräf, T., Siqueira, M. M., Bello, G. & Resende, P. C. (2021). A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil. medRxiv. (2021). A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil.
Fiocruz Genomics Network research constitutes mechanisms behind the rapid spread of lineages derived from the New Coronavirus Gamma Variant
(Permanently published under DOI: 10.1128/spectrum.02366-21)
After the second wave of SARS-CoV-2 infection in Brazil, marked by the emergence and wide dissemination of the Gamma variant (P.1), one of the concerns of the scientific community was with possible results of the evolutionary process continuity of this VOC. More specifically, the emergence possibility of new mechanisms that would make Gamma-derived samples more transmissible, infective, or more effective at evading the action of neutralizing antibodies reinforced the importance of continued surveillance of Gamma and derived variants. The present work, published in preprint form (i.e., without the process of independent review by other research groups) is derived from the analysis of the genomes of 1188 SARS-CoV-2 samples, most of which (99.7%) belong to the gamma VOC. There has been a significant increase in the prevalence of the so-called “Gamma+” samples – that is, those that accumulate additional mutations compared to samples initially classified as Gamma, as a result of the evolutionary process with the fixation of these new mutations. One of these Gamma variations, the so-called Gamma+N679K, accounts for 76.9% of the samples analyzed for June-July 2021. The work also discusses the biological importance of some of the mutations found, such as deletions in the protein S domain called NTD (which hinder neutralization by antibodies produced by the organism in response to an infection or vaccination) and changes in the structure of another region of protein S, the S1/S2 junction, which have the potential – still being studied by the researchers – to lead to greater infectivity due to a greater affinity with the molecular mechanism that allows the virus to fuse its envelope to the cell membrane and initiate the cell invasion (furin).
These Gamma-derived samples, designated P.1.3, P.1.4, P.1.5, and P.1.6, although they are in a process of expansion that may make them more prevalent within the lineage than the original Gamma, and despite having an apparent greater transmissibility, do not appear to be more effective in their ability to escape the action of antibodies – i.e., cause reinfection and/or infect previously vaccinated people. The paper from the Fiocruz Genomics Network also brings a reminder that as SARS-CoV-2 spreads in the population, the risk of selecting new variants with greater infectivity is likely to increase.
Naveca, F. G., Nascimento, V., Souza, V., Corado, A. L., Nascimento, F., Silva, G., Mejía, M., Brandão, M. J., Costa, A., Duarte, D., Pessoa, K., Jesus, M., Gonçalves, L., Fernandes, C., Mattos, T., Abdalla, L., Santos, J. H., Martins, A., Chui, F. M., Val, F. F., Melo, G. C., Xavier, M. S., Sampaio, V. S., Mourão, M. P., Lacerda, M. V., Batista, E. L. R., Magalhães, A. L. A., Dábilla, N., Pereira, L. C. G., Vinhal, F., Miyajima, F., Dias, F. B. S., Santos, E. R., Coêlho, D., Ferraz, M., Lins, R., Wallau, G. L., Delatorre, E., Gräf, T., Siqueira, M. M., Resende, P. C., & Bello, G. (2021). Spread of Gamma (P. 1) sub-lineages carrying Spike mutations close to the furin cleavage site and deletions in the N-terminal domain drives ongoing transmission of SARS-CoV-2 in Amazonas, Brazil.
Preprint: What are the consequences for virus evolution of co-infections of two different variants at the same time?
In periods such as the present SARS-CoV-2 pandemic, in which several lineages and variants of the same virus circulate simultaneously in a population, the co-infections occurrence is always a concern. Defined as events in which the same person or cell is infected by two or more viral samples of distinct genetic profiles, co-infections may represent a risk to public health if they make possible recombination events, that is, new viral genetic profiles derived from a “mixture” between the genetic lineages infecting the same patient.
The present work, developed by researchers from several Fiocruz units linked to the Genomics Network and published as a preprint (without independent review by other researchers), investigates the phenomenon of reinfections based on 2,263 samples of SARS-CoV-2, using computer analysis methods developed by Fiocruz itself. These methods allowed us to identify signs of high variability in the genome sequencing data, variability associated with the simultaneous sequencing of more than one viral genetic profile.
Dezordi, F. Z., Resende, P. C., Naveca, F. G., Nascimento, V. A., Souza, V. C., Paixão, A. C. D., Appolinario, L., Lopes, R. S., Mendonça, A. C. F., Rocha, A. S. B., Venas, T. M. M., Pereira, E. C., Salvato, R. S., Gregianini, T. S., Martins, L. G., Pereira, F. M., Rovaris, D. B., Fernandes, S. B., Ribeiro-Rodrigues, R., Costa, T. O., Sousa Jr., J. C., Miyajima, F., Delatorre, E., Gräf, T., Bello, G., Siqueira, M. M., Wallau, G. L. (2021). Unusual SARS-CoV-2 intra-host diversity reveals lineages superinfection
Preprint: New Coronavirus Variants of Concern have mutations that decrease antibody effectiveness, allowing reinfection
(Permanently published under DOI: 10.1039/D1CC01747K)
The new variants rapid spread of the novel SARS-CoV-2 coronavirus, as exemplified by the high prevalence of the P.1 variant even within the first two months after its emergence, along with reinfection reports caused by these variants, raises for science the question of what the mechanisms behind this scenario might be. Of special interest to this research is the study of mutations in the genome of the variants – in particular, in the Spike glycoprotein gene (S protein), which promotes entry into human cells through interaction with Angiotensin Converting Enzyme 2 (hACE2), a molecule that acts as the virus receptor. The ability to bind to hACE2 may become greater or less according to changes in the structure of the S protein, which vary between lineages of SARS-CoV-2 and each of its variants. These changes in the protein S structure may also result in a decreased ability of antibodies generated in response to an infection – or possibly even after vaccination – to bind to protein S and neutralize the virus’ ability to cause infection.
The present publication – now also available in its peer-reviewed version – investigates these two possible effects of the S protein mutations detected in variants such as P.1, B.1.351 and B.1.1.7 variants: a “stronger” interaction with the hACE2 receptor or a “weaker” interaction with anti-protein-S antibodies. In the ChemRxiv link still in preprint stage, prior to review by independent researchers, the paper describes a series of experiments performed with computational modeling of the molecules involved (hACE2, antibodies, and the various “versions” of protein S, referring to each of the variants studied).
Based on the computational simulation of the interaction between the molecules, it was possible to verify that altering the protein S structure had no significant effects on the interaction with the hACE2 receptor. On the other hand, by simulating the interaction of antibodies generated in response to early SARS-CoV-2 lineages with the S protein of the new variants, it was possible to see that there is a decrease in binding between the molecules, a finding that points to a potential immune response “escape”. According to this hypothesis, the new variants would be more effective in evading the neutralization provided by antibodies, and this would be a more relevant mechanism to explain their rapid spread in the population. Importantly, based on some affinity measurements between variations of the S protein and the hACE2 receptor, other research groups have previously suggested that increased transmissibility would be related to a higher affinity between the viral protein and the human receptor, in contrast to the results of the present study. However, these studies have not explored the interaction of the different S proteins with the neutralizing antibodies. The paper also points to the new variant named P.3 as a potential Variant of Concern (VOC), given that most of the antibodies analyzed in the study were unable to efficiently bind to the S protein of this lineage in the simulations performed.
Ferraz, M., Moreira, E., Coêlho, D. F., Wallau, G. & Lins, R. SARS-CoV-2 VOCs Immune Evasion from Previously Elicited Neutralizing Antibodies Is Mainly Driven by Lower Cross-Reactivity Due to Spike RBD Electrostatic Surface Changes.
Preprint: Fiocruz Genomics Network researchers create protocol for sequencing that allows identification of some key changes in the SARS-CoV-2 genome at lower costs
(Permanently published under DOI: 10.1016/j.meegid.2021.104910)
In light of the current pandemic facing humanity, the use of next-generation genome sequencing techniques has been one of the main strategies for the epidemiological surveillance of the novel coronavirus. Next-generation sequencing has allowed the rapid identification of new virus variants and the grouping of samples into lineages defined by common characteristics and shared genetic origin. It also provides the analysis of mutations found to understand their consequences for the evolutionary race that determines many aspects of the pandemic. In contrast to the possibilities offered by next-generation sequencing, the high cost of the equipment and ingredients required to perform it, and the need for properly trained technical personnel, make it unfeasible for more remote regions and countries with fewer possibilities for investment in research to maintain the long-term use of this technique. Especially when there is a need for imported ingredients such as reagents and kits, the risk of blackout periods in epidemiological surveillance is high, which highlights the importance of developing lower cost and easier to implement alternatives. Alternative techniques with these characteristics guarantee greater possibilities of sustaining a continuous monitoring of the samples circulating in a given locality, which is vital for the development of coping strategies.
The present publication – at this link in preprint status, but already published in the journal Infection, Genetics and Evolution after peer review – presents an alternative based on Sanger sequencing of a single PCR fragment (725 base pairs) capable of detecting the main mutations in the Spike glycoprotein (S protein) and classifying samples as belonging to the main variants circulating in Brazil. Although the use of the technique entails a loss of information when compared to sequencing the complete genome of the samples, having reliable and inexpensive ways to monitor the variants brings an important security to epidemiological monitoring in Brazil and other countries with similar socioeconomic challenges.
Bezerra, M. F., Machado, L. C., De Carvalho, V. D. C. V., Docena, C., Brandão-Filho, S. P., Ayres, C. F. J., … & Wallau, G. L. A Sanger-based approach for scaling up screening of SARS-CoV-2 variants of interest and concern.
Three cases of P.1 (Gamma) and what they can teach us about reinfection and the spread of COVID-19
In this report (preprint), three cases of reinfection caused by Variant of Concern (VOC) P.1, also known as the “Manaus strain”, are presented. All three patients were adult women, and had their first infection during the early wave of the pandemic in the first half of 2020. In all three cases, the lineage detected at the first molecular diagnosis was different from that found later, reinfection evidence. Two of the reinfection cases had mild symptom presentation, while the third was asymptomatic, although the amount of viral genetic material detected suggested high viral loads. The evidence presented here suggests that immunity after primary infection by lineages prior to circulation of those containing the E484K mutation does not prevent new infection by the P.1 variant, nor even from people reinfected with this variant spreading the virus, although it is possible that it protected these three patients from developing severe symptoms.
Naveca, F.G., Costa, C., Nascimento, V. et al. Three SARS-CoV-2 reinfection cases by the new Variant of Concern (VOC) P.1/501Y.V3
Preprint by researchers from the Fiocruz Genomics Network reconstructs the dynamics of variants in the state of Amazonas and the emergence of the Gamma Variant
(Permanently published under DOI: 10.1038/s41591-021-01378-7)
Among the 27 Brazilian Federative Units, the state of Amazonas was one of the most affected by the present pandemic of the novel coronavirus, with the occurrence of a second wave at the end of 2020 in which a large number of severe cases led to a health system collapse. This preprint, resulting from the analysis of the complete genome of 250 SARS-CoV-2 samples collected in Amazonas between March 2020 and January 2021, describes the dynamics of dominant lineage successions in the state. More recently, it has been published in Nature Medicine, after editing and review by independent researchers.
The publication presents data that support the hypotheses that the lineage responsible for most cases in the first moment of the pandemic (between March and May 2020) was B.1.195, that it was bypassed by B.1.1.28, which became the dominant lineage in the state between May and December 2020, and that in December the emergence of a B.1.1.28 variant, called P.1, with greater transmissibility, was responsible for the new rise in the number of cases and deaths. In this way, the local dynamics of new viral genetics emergence was an important driving force for the way in which the pandemic advanced over the state of Amazonas, directly influenced by the population circulation and its relation with the virus spread, which culminated with the substitution of B.1.1.28 by the variant of concern P.1 in a process believed to have lasted only two months.
Naveca, F.G., Nascimento, V., de Souza, V.C. et al. COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new variant of concern P.1.
Preprint: International research cooperation focuses on unraveling how the novel coronavirus behaves on the Brazil-Uruguay border
(Permanently published under DOI: 10.3389/fmicb.2021.653986)
Despite having managed to control the spread of the novel coronavirus – being one of the few countries in the Americas to successfully contain the pandemic – its proximity to Brazil presents a risk to Uruguay. The high mobility between borders, together with Brazil’s situation as one of the worst countries in the world in number of cases and fatalities, are factors that can lead to multiple introductions of the virus to Uruguay, and to the arrival of more contagious variants in the country.
The present preprint reports the results of epidemiological surveillance in inland Uruguayan cities in the border region with Brazil and the reconstruction of the events of SARS-CoV-2 spread in the Brazil-Uruguay direction. Using genomes from 54 samples of the novel coronavirus collected in Uruguayan cities and 68 Brazilian samples from Rio Grande do Sul, research groups from 15 institutions from both countries were able to reconstruct a panorama characterized by multiple introductions of Brazilian lineages of B.1.1.28 and B.1.1.33 in border Uruguayan cities. The strains introduced into the country probably came from the Brazilian state of RS, and began circulating locally in these cities in less than three months (between early May, when the first events probably occurred, and mid-July). It was also possible to find that the strains that caused outbreaks in Uruguay had between 4 and 11 genetic changes when compared to the Brazilian ancestral strains B.1.1.28 and B.1.1.33, which supports the idea that the genome of the novel coronavirus seems to accumulate mutations very quickly in its rapid spread throughout South America.
In addition to being the first study with genomics data focused on this region, the study also highlights that outbreaks caused in this inland region stemmed from virus introductions from Brazil, in contrast to outbreaks in metropolitan regions in 2020 that were associated with virus introductions from Europe.
Mir D, Rego N, Resende PC, Lopez-Tort F, Fernandez-Calero T, Noya V, et al. Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border. medRxiv. 2021;1–27.
Sotero-Martins, A., Coelho, W. N., Flores, G. L., Gama, E. L., Carvajal, E., Siqueira, M. A. M. T. D., & Aguiar-Oliveira, M. D. L. (2021). Demographic, socioeconomic and epidemiological aspects of COVID-19 in the Cunha Canal Sub-Basin Region, Rio de Janeiro
Preliminary scientific work by the Fiocruz Genomics Network discusses the prevalence of the Delta variant in Amazonas, where it has replaced other variants such as Gama and Mu
The beginning of the year 2021 saw the pandemic situation of COVID-19 worsening in Brazil. In particular, in the state of Amazonas, the pandemic advance had characteristic dominance of the Variant of Concern (VOC) Gamma, also known as P.1. More recently, as pointed out by research conducted by the Fiocruz Genomics Network (preprint), Gamma-derived variants have continued to spread and accumulate new mutations – including changes in the Spike glycoprotein with a possible potentiating effect, such as deletions in the N-terminal domain (NTD; associated with evasion of antibody action and the ability to cause reinfection or vaccine escape) or structural changes at the S1/S2 junction (associated with more efficient cell invasion). These variants of the P.1 Lineage were given the name Gama+, and their transmission in the state of Amazonas and eventual spread to other states was the object of concern of specialists and authorities.
With the arrival in Brazil of another VOC, Delta (B.1.617.2, initially detected in the Indian Peninsula), in parallel with the concern about the establishment and dominance of the Gamma-derived VOC samples, it was also hypothesized that their spread and dominance in the epidemiological scenario was enough to stop the spread of Delta.
In this post, published on the expert virology forum Virological.Org, researchers from the Fiocruz Genomics Network report the results of analysis of 1132 complete genomes of SARS-CoV-2 isolated from clinical patient samples collected between July 1st and October 15th, 2021 – a sample corresponding to 4.5% of confirmed cases in the state for the period. Genomic surveillance saw a sharp drop in the prevalence of Gamma and Gamma+ VOC samples, as well as an increase in the prevalence of Delta VOC, which went from 1% of all samples in July to 89% in October. During this period, the introduction of VOI Mu (B.1.621, initially detected in Colombia) into the state also occurred, although it remained at a low prevalence according to the Network sampling (less than 1% of samples between August and September, and not detected in October). It is important to note that the spread of VOC Delta occurred in a period when the total number of cases in Amazonas decreased, probably due to the combination of natural and vaccine immune barriers (hybrid immune barrier).
Still, the results indicate that VOC Delta had the ability to replace, by ecological competition, the Gamma, Gamma+ and Mu variants in the state of Amazonas, even taking into account that this Federative Unit corresponds to one of the locations in the world with one of the highest hybrid immune barriers.
Naveca, F. G., Nascimento, V., Souza, V., Corado, A. L., Nascimento, F., Mejía, M., Brandão, M. J., Silva, A. V., Benzaken, A. S., Silva, G., Gonçalves, L., Luz, S. L. B., Cortés, J. J. C., Nieto, J. C. G., Vesga, K. N. R., Fernandes, C., Amorim, T., Mattos, T., Abdalla, L., Santos, J. H., Wallau, G. L., Delatorre, E., Arantes, I., Siqueira, M. M., Resende, P. C., Gräf, T. & Bello, G. The SARS-CoV-2 variant Delta displaced the variants Gamma and Gamma plus in Amazonas, Brazil
Early-stage research at the Fiocruz Genomics Network investigates the emergence and evolution of the P.1 (Gamma) lineage
As of late 2020, several countries around the world reported the detection of SARS-CoV-2 variants containing worrisome mutations in the S protein gene. Many of these variants, such as B.1.1.7 in the UK and B.1.351 in South Africa have spread very quickly, even reaching other countries as early as 2021, and have been classified as Variants of Concern (VOC). The first Brazilian VOC, P.1, was identified in the state of Amazonas and also spread rapidly throughout Brazil and abroad – the first cases being reported in patients returning to Japan from Brazil. One hypothesis about the emergence of VOCs holds that mutations have been accumulating in individuals with persistent SARS-CoV-2 infections, perhaps in patients with weakened immune systems. Alternatively, the process of emergence of VOCs may have been gradual, occurring as the virus circulated in the community.
This post on Virological.Org – a forum for sharing data among virological researchers – reports on the study and comparison of the genome of P.1 and two genetically related variants of this VOC (called P.1-like-I and P.1-like-II), proposing a new evolutionary history for P.1 and hypotheses about its emergence. Based on the presence of shared mutations between P.1 and P.1-like samples, the publication points to a gradual history of mutation accumulation in P.1, more consistent with its gradually emergence. In this process, the gradual evolution of the B.1.1.28 lineage circulating in Amazonas accumulated mutations that ensured the success of the virus and its circulation in the population with partial immunity. The scenario of uncontrolled transmission, therefore, is an important factor for the emergence of variants with an arsenal of mutations, which can give these lineages greater transmissibility or the ability to cause infections even in patients with antibodies against the novel coronavirus.
Gräf, T., Bello, G., Venas, T. M. M. et al. Identification of SARS-CoV-2 P.1-related lineages in Brazil provides new insights about the mechanisms of emergence of Variants of Concern
Preliminary study by the Genomics Network describes the identification and some characteristics of the N.10 variant genome
Since the arrival of the novel coronavirus in Brazil until April 2021, at least three occasions have been identified in which the lineages circulating in the country have given rise, through the accumulation of mutations, to variants of high epidemiological relevance. Of these, one was classified as a variant of concern (VOC) and named P.1 according to the PANGO nomenclature system, while two others (named P.2 and N.9) were classified as variants of interest (VOI). All three variants have the E484K mutation in the receptor-binding domain (RBD) of the Spike glycoprotein (S protein), which enables viral particles to bind to human cells, a mutation that is apparently important for antibody escape and reinfection of individuals who have already been infected with other coronavirus lineages. The variant has this modification and a number of other important mutations that further enhance the ability of the lineage to evade antibodies generated after natural infection or vaccination.
The present publication (on the virology research discussion forum Virological.org, not yet reviewed by other research groups) describes the identification of a third VOI, N.10. Derived from lineage B.1.1.33 – the same lineage that gave rise to N.9 – N.10 was identified in samples from the state of Maranhão, and in addition to the E484K mutation, it has another mutation in the RBD of protein S, and several amino acid changes and deletions in another portion of the protein, called N-terminal domain (or NTD). Mutations in NTD have already been associated with an increased ability of lineages such as P.1 to evade antibody-mediated immune response, which makes this variant, present in 23% of the January 2021 samples from Maranhão analyzed, a possible cause for warning in the near future, especially if a significant increase in its prevalence is observed.
Resende, P. C., Gräf, T., Lima Neto, L. G. et al. Identification of a new B.1.1.33 SARS-CoV-2 Variant of Interest (VOI) circulating in Brazil with mutation E484K and multiple deletions in the amino (N)-terminal domain of the Spike protein
Initial work by scientists at the Fiocruz Genomics Network focuses on the mutations role in the Spike glycoprotein (S) of the novel coronavirus in its evolution and spread
The Spike glycoprotein of the novel coronavirus SARS-CoV-2, also called S protein, is involved in binding and invasion of human cells through the interaction of a portion called RBD (Receptor Binding Domain) with a protein present in some human cell types called ACE2 (Angiotensin Converting Enzyme 2). Antibodies produced naturally after SARS-CoV-2 infection capable of binding to portions of the S protein, most notably the RBD and NTD (N-terminal domain), have the potential to neutralize the virus’ ability to initiate infection. Thus, mutations in the genes for protein S may confer the ability to evade the antibody-mediated immune response, favoring strains carrying these mutations in the face of evolutionary pressure presented by immunity in the population.
The present publication (posted on the virology research discussion forum Virological.org) addresses, based on 11 samples, how lineages presenting convergent mutations in the RBD domain (present in VOC P.1 and VOIs P.2 and N.9) can escape the action of polyclonal antibodies and cause reinfections in the presence of other mutations in protein S. A series of amino acid insertions and deletions in another domain of protein S, termed NTD (found mainly in samples of the P.1 variant and, to a lesser extent, in non-P.1 and P.2 samples of lineage B.1.1.28, as well as in a P.2), seems to have a synergistic action with the changes in RBD, in terms of their ability to cause reinfection even in the presence of neutralizing antibodies generated in response to protein S from lineages that do not have these mutations. Besides explaining the mechanisms of this immune escape, the publication discusses how the wide dissemination of the novel Coronavirus in Brazil has enabled the emergence of lineages with mutations that give them adaptive advantages, such as changes in the S protein.
Resende, P. C., Naveca, F. G., Lins, R. D. et al. The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the Spike protein
(Initial version) N9: A new variant of SARS-CoV-2 identified for the first time between 2020 and early 2021, in samples from ten Brazilian states
(Permanently published under DOI: 10.1039/D1CC01747K)
The SARS-CoV-2 pandemic in Brazil was dominated by two main lineages throughout 2020 and early 2021. Among these lineages, B.1.1.28 has already given rise to two important variants carrying mutations in the Spike glycoprotein (S protein), such as the E484K amino acid substitution in the receptor-binding domain (RBD), implicated as a major factor in the neutralization escape by antibodies against the virus. These lineages are the variant of interest P.2 and the variant of concern (VOC) Gamma. P.1, which probably emerged in December 2020, has spread rapidly throughout the state of Amazonas and reached other regions of the country, and has additional mutations that appear to give the variant an increased ability to cause reinfection, and higher viral loads in patients.
This posting on the virology research discussion forum Virological.Org describes the first Brazilian variant positive for the E484K mutation derived from lineage B.1.1.33, the other dominant lineage in Brazil. VOI N.9 probably emerged in August 2020, and its discovery from samples from ten states (São Paulo, Santa Catarina, Amazonas, Pará, Bahia, Maranhão, Paraíba, Pernambuco, Piauí and Sergipe) collected between November 2020 and February 2021 confirms its rapid spread throughout the national territory, reflecting a hardship in ensuring social isolation and distance, and containing the people flow between different Brazilian regions. Despite this rapid spread, N.9 appears to have a low prevalence, corresponding to approximately 3% of samples on a national scale. In addition to carrying the E484K mutation in protein S, N.9 also has four other non-synonymous mutations that define the lineage.
Resende, P. C., Gräf, T., Paixão, A. C. D. et al. A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil
Preliminary: Fiocruz Genomics Network describes a case of reinfection by VOC P.1 (Gama) in Amazonas, and analyses derived from the study of the genome of this variant
The emergence of Variant of Concern (VOC) P.1 in the state of Amazonas in December 2020 brought about a number of concerns and relevant research questions, with respect to understanding the role of changes in the P.1 protein – and other characteristics of the virus – in its increased transmissibility, as well as the possibility that this set of mutations conferred the sample the ability to escape the immune response acquired after an infection or vaccination, allowing reinfections. In this posting on the scientific virology discussion forum, Virological.org, the first confirmed case of reinfection caused by VOC P.1 is presented, and preliminary data from genome analyses of P.1 lineage samples from the reinfected patient and several other patients are presented. These analyses point to 21 lineage-defining mutations characteristic of P.1, including 11 amino acid changes in the Spike glycoprotein (S protein), responsible for the initial stage of infection, relative to the B.1 lineage that had affected the patient months before reinfection. Possibly some of the 11 characteristic changes of P.1 are involved in the ability of this lineage to reinfect patients who would already be immune to the disease after a first infection event.
Naveca, F. G., Costa, C., Nascimento, V. et al. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil
Initial research work conducted by members of the Fiocruz Genomics Network explores the genome of 69 samples from Amazonas, and describes the emergence of P.1 (Gamma) in the state
Understanding the phylogenetic relationships between different samples of a virus during an epidemic event is important not only to understand the evolution of the virus in molecular terms, but also to understand how different convergent mutations can arise independently. In this posting on the virology research discussion forum Virological.org, analysis of 69 SARS-CoV-2 samples collected in the state of Amazonas demonstrates the circulation of two lineages in the state, circulating widely until November 2020, and showing no mutations of interest in the S protein genes, as well as the local emergence of a variant of the B.1.1.28 strain – later named P.1 – detected in travelers from Japan who probably contracted it on a visit to Manaus in December 2020. This variant contains a number of changes in the S protein that elected it as a variant of concern (VOC), and it became dominant in the state in a short time span. The analysis of the genomes, and their comparison with samples from other regions of Brazil, allows us to infer that the process that resulted in the Amazonian variant is not the same that gave rise to the lineage detected in Rio de Janeiro, despite some mutations in common between the two, probably the result of convergent evolution.
Naveca, F. G., Nascimento, V., Souza, V. et al. Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein
(Initial Version) Variants of the virus causing COVID-19 circulating in Brazil are able to cause infections in people who already have antibodies for the disease
(Permanently published under DOI: 10.1039/D1CC01747K)
The first case of reinfection by the novel coronavirus formally recognized by the Ministry of Health was on December 9th, 2020. The present publication on the specialist discussion forum for virological research, Virological.Org, describes a range of information and research findings derived from this reinfection, and draws conclusions about the significance of this event for pandemic surveillance and control in Brazil.
The case affected a 37-year-old health professional, who was seeing patients in Paraíba, although she lived in Rio Grande do Norte. The patient had two clinical episodes compatible with SARS-CoV-2 infection separated by 116 days (onset of symptoms of the first infection: June 17th; second infection: October 11th) and, after sequencing and comparison between samples from these two events, reinfection was found, since the first infection was caused by a virus compatible with the B.1.1.33 lineage and the second infection was caused by a virus compatible with the B.1.1.28 lineage. This second agent of infectious agent also had an amino acid substitution in the S E484K protein, associated with antibodies escape ability generated in response to infection and SARS-CoV-2 vaccination. In addition to demonstrating the circulation of variants capable of causing reinfection in Brazil, the publication also shows the circulation of the B.1.1.28 (E484K) lineage outside the state of Rio de Janeiro, where it is believed – based on reconstructions – that the lineage initially originated.
Resende, P. C., Bezerra, J. F., Vasconcelos, R. H. T. et al. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020
Research in preliminary stage of the Genomics Network aims to understand the relationships between novel Coronavirus samples in 6 Brazilian states and to trace the history of virus introductions in the country
This publication, posted on the expert virology forum Virological.Org, is the result of the sequence analysis of 81 complete SARS-CoV-2 genomes derived from samples collected in 6 Brazilian Federative Units between February and April 2020. Through phylogenetic analysis tools, and comparison with samples obtained in other countries around the world, it was possible for the research group to trace the introduction history of the virus in Brazilian territory, as well as to highlight and understand aspects of its community transmission in the country. The results of the study suggest that the novel coronavirus was introduced into Brazil from Europe around February 4th, and that by about February 23rd it had branched into a new lineage, provisionally named B.1.1.BR. The evidence also indicates that, even before the detection of the first imported case of SARS-CoV-2 in the country, this Brazilian lineage was already circulating in the population through community transmission (when it is no longer possible to identify the transmission chain due to its wide dissemination in the community).
Resende, P. C., Delatorre, E., Gräf, T. et al. Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil