Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil

Resende, Paola Cristina; Delatorre, Edson; Gräf, Tiago; Mir, Daiana; Motta, Fernando Couto; Appolinario, Luciana; Paixão, Ariane Gomes; Mendonça, Ana Carolina da Fonseca; Ogrzewalska, Maria; Caetano, Bráulia Costa; Wallau, Gabriel Luz; Docena, Cássio; Santos, Mirleide Cordeiro dos; Ferreira, Jessylene de Almeida; Júnior, Edivaldo Costa Sousa; Silva, Sandro Patroca da; Fernandes, Sandra Bianchini; Vianna, Lucas A.; Souza, Larissa da Costa; Ferro, Jean F G; Nardy, Vanessa Brandão; Santos, Cliomar Alves do; Riediger, Irina Nastassja; Debur, Maria do Carmo; Croda, Júlio; Oliveira, Wanderson Kleber de; Abreu, André Luiz de; Bello, Gonzalo; Siqueira, Marilda M.

doi:10.3389/fmicb.2020.615280

Cited by 72 publications

(78 citation statements)

References 60 publications

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“…In the first episode, we detected the lineage B.1.1.33, whereas lineage P.2 (alias for B.1.1.28.2) was detected in the third clinical specimen (from the second episode) (Figure 1), according to PANGO lineage classification (10). The SARS-CoV-2 B.1.1.33 lineage was also detected in other samples from the state of Paraíba (Figure 1) and represent the most prevalent viral variant circulating in Brazil during the early epidemic phase (11,12). Of note, sequences recovered from the reinfection case and from 2 additional cases in the state of Paraíba harbor the substitution S-E484K (G23012A) and were classified as lineage P.2, which was initially detected in the state of Rio de Janeiro (13).…”

Section: Genomic Findingsmentioning

confidence: 75%

Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June–October 2020

Resende¹,

Bezerra²,

Vasconcelos³

et al. 2021

Emerg. Infect. Dis.

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T he effi ciency and persistence of natural protective immunity caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination are currently unknown. Reinfection cases have been reported in different countries ( 1), but the differentiation between cases of reinfection and viral persistence remains a challenge. The detection of 2 coronavirus disease (COVID-19) episodes >90 days apart and caused by 2 different lineages of SARS-CoV-2 remains the most reliable evidence of reinfection (2). In this article, we describe a reinfection case and highlight details about the genomic features of the 2 COVID-19 episodes. In addition, we demonstrate that the virus in the second episode was related to the emerging variant of interest (VOI) designated as lineage P.2, which is currently circulating throughout Brazil.

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Section: Genomic Findingsmentioning

confidence: 75%

Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June–October 2020

Resende¹,

Bezerra²,

Vasconcelos³

et al. 2021

Emerg. Infect. Dis.

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“…The B.1.1.33 lineage was studied in further details using 190 genomes from 13 Brazilian states, showing its variable abundance in different states (ranging from 2% in Pernambuco to 80% in Rio de Janeiro), and its moderate prevalence in South American countries (5-18%). Surprisingly, this lineage was firstly detected in early-March in other American countries ( e. g ., Argentina, Canada, and USA), and additional analysis suggest that an intermediate lineage (B.1.1.33-like) most probably arose in Europe and was later disseminated to Brazil, where its spread gave origin to lineage B.1.1.33 (Resende et al 2021) and possibly seeded secondary outbreaks in Argentina and Uruguay (Resende et al 2021; Mir et al 2021).…”

Section: Discussionmentioning

confidence: 97%

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

Pag

et al. 2021

Preprint

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The COVID-19 pandemic has already reached approximately 110 million people and it is associated with 2.5 million deaths worldwide. Brazil is the third worst-hit country, with approximately 10.2 million cases and 250 thousand deaths. Unprecedented international efforts have been established in order to share information about epidemiology, viral evolution and transmission dynamics. However, sequencing facilities and research investments are very heterogeneous across different regions and countries across the globe. The understanding of the SARS-CoV-2 biology is a vital part for the development of effective strategies for public health care and disease management. This work aims to analyze the available genomes sequenced in Brazil between February 2020 and February 2021, in order to identify mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in the Brazilian territory by using phylogenetics and phylodynamics analyses from high-quality genomes. We describe heterogeneous and episodic sequencing efforts, the progression of the different lineages along time, evaluating mutational spectra and frequency oscillations derived from the prevalence of novel and specific lineages across different Brazilian regions. We found at least seven major (1-7) and two minor clades (4.2 and 5.3) related to the six most prevalent Brazilian lineages and described its distribution across the Brazilian territory. The emergence and recent frequency shift of lineages (P.1 and P.2) containing mutations of concern in the spike protein (e. g., E484K, N501Y) draws attention due to their association with immune evasion and enhanced receptor binding affinity. Improvements in genomic surveillance are of paramount importance and should be extended in Brazil to better inform policy makers and enable precise evidence-based decisions to fight the COVID-19 pandemic.

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“…Previous phylogenetic analyses revealed the circulation of different predominant SARS-CoV-2 lineages in Brazil (B.1.1.28 and B.1.1.33) 8,9 and Uruguay (A.5 and B.1) 10,11 thus supporting independent viral seeding events and little viral exchanges between these neighboring countries during the very early phase of the epidemic. However, most Uruguayan SARS-CoV-2 samples previously analyzed were from Montevideo, the capital city of the country and there is only scarce information concerning the virus strains circulating in Uruguayan localities bordering Brazil…”

Section: Introductionmentioning

confidence: 88%

Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border

Mir

Rego

Resende

et al. 2021

Preprint

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SummaryBackgroundUruguay is one of the few countries in the Americas that successfully contained the COVID-19 epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of SARS-CoV-2 strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this ∼1,100 km uninterrupted dry frontier.MethodsUsing complete SARS-CoV-2 genomes from the Uruguayan-Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May-July) of the pandemic.FindingsPhylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan suburban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America.InterpretationAlthough Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems are crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world.Research in contextEvidence before this studySince the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of coronavirus disease 19 (COVID-19), was first detected in South America on February 26, 2020, it has rapidly spread through the region, causing nearly 350,000 deaths by December, 2020. In contrast to most American countries, Uruguay avoided an early exponential growth of SARS-CoV-2 cases and during the first six months of the pandemic it registered the lowest incidence of SARS-CoV-2 cases and deaths among South American countries. The intensive cross-border human mobility through the ∼1,100 km uninterrupted dry frontier between Uruguay and Brazil, might poses a major challenge for long-term control of the epidemic in Uruguay. Previous genomic studies conducted in Uruguay have analyzed sequences mostly sampled at the capital city, Montevideo, and detected prevalent SARS-CoV-2 lineages different from those described in Brazil, thus finding no evidence of frequent viral exchanges between these countries.Added value of this studyHere we present the first genomic study of SARS-CoV-2 strains detected in different Uruguayan and Brazilian localities along the bordering region. The samples analyzed include 30% (n = 59) of all laboratory confirmed SARS-CoV-2 cases from Uruguayan departments at the Brazilian border between March and July, 2020, as well as 68 SARS-CoV-2 sequences from individuals diagnosed in the southernmost Brazilian state of Rio Grande do Sul between March and August, 2020. We demonstrate that SARS-CoV-2 viral lineages that widely spread in the Southeastern Brazilian region (B.1.1.28 and B.1.1.33) were also responsible for most viral infections in Rio Grande do Sul and neighboring Uruguayan localities. We further uncover that major outbreaks detected in Uruguayan localities bordering Brazil in May and June, 2020, were originated from two independent introduction events of the Brazilian SARS-CoV-2 lineage B.1.1.33, unlike previous outbreaks in the Uruguayan metropolitan region that were seeded by European SARS-CoV-2 lineages.Implications of all the available evidenceOur findings confirm that although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, dissemination of SARS-CoV-2 across the Uruguayan-Brazilian frontier was not fully suppressed and had the potential to ignite local transmission chains in Uruguay. These findings also highlight the relevance of implementing bi-national public health cooperation workforces combining epidemiologic and genomic data to monitor the viral spread throughout this kind of highly permeable dry frontiers around the world.

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Evolutionary Dynamics and Dissemination Pattern of the SARS-CoV-2 Lineage B.1.1.33 During the Early Pandemic Phase in Brazil

Cited by 72 publications

References 60 publications

Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June–October 2020

Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June–October 2020

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border

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