PreprintCited by 372SARS-CoV-2 and COVID-19 ResearchCOVID-19 Clinical Research StudiesSARS-CoV-2 detection and testing

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Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

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Voloch, Carolina M, Silva F, Ronaldo da, de Almeida, Luiz G P, Cardoso, Cynthia C, Brustolini, Otavio J., Gerber, Alexandra L, Guimarães, Ana Paula de C, Mariani, Diana, Costa, Raissa Mirella da, Ferreira, Orlando C., Covid19-UFRJ Workgroup, LNCC-Workgroup, Cavalcanti, Adriana Cony, Frauches, Thiago Silva, de Mello, Claudia Maria Braga, Galliez, Rafael Mello, Faffe, Débora Souza, Castiñeiras, Terezinha M P P, Tanuri, Amilcar, de Vasconcelos, Ana Tereza R·2020·Journal of Virology

DOI 10.1101/2020.12.23.20248598PMC PMC8139668

Preprint — published as 10.1128/jvi.00119-21 · Paper page

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Abstract

In this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections. Article Summary Line: We identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.

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FIG 1 Phylogeny and timescale of P.2 lineage. (A) Maximum-likelihood tree of 1,377 SARS-CoV-2 genomes, including the 180 new Brazilian genomes generated in this work. We randomly sampled one genome/week/country from available samples in GISAID with collection dates ranging from May to November. Brazilian sequences with collection dates from May to November were all added to the data set (see Table S2). We ran IQTree 2.0.3 (10) under a general time-reversible (GTR) model of nucleotide substitution (11) with empirical base frequencies and invariant sites. Tips are colored according to their origin. Genomes generated from this work are red, other Brazilian genomes are blue, and genomes from other countries are not colored. Gray areas represent the three clades where Brazilian viruses are concentrated. The emergent lineage identified in this work, P.2, is in a dark-gray box and highlighted with red branches. The approximate likelihood ratio test (aLRT) support value for the branch holding P.2 monophyly is shown. (B) A time-scaled tree of clade II was estimated under a strict molecular clock in BEAST v.1.10.4 (12) using the GTR+I (11) nucleotide substitution model and assuming an exponential growth tree prior and a normal prior for the clock rate (mean = 8 × 10−4 and standard deviation = 0.1 × 10−5). The convergence of the Markov chain Monte Carlo chains, which were run at least for 50 million generations and sampled every 1,000th step, was inspected using Tracer v.1.7.1 (13). Maximum clade credibility (MCC) summary trees were generated using TreeAnnotator v.1.10.4 (12). Red circles in the tip nodes represent genomes generated in this work, and blue circles indicate other Brazilian samples. P.2 is identified by the red branches and highlighted in a gray box. The posterior probability of the branch holding P.2 monophyly is shown.CC BY · PubMed Central

FIG 2 Phylogeny of B.1.1.28 and its alias lineages (P.1 and P.2). Maximum-likelihood tree of 993 SARS-CoV-2 genomes. We downloaded all B.1.1.28, P.1, and P.2 high-coverage genomes available in GISAID on 11 February 2021. The phylogeny was estimated using IQTree 2.0.3 (10) under a GTR+F+R3 model chosen by ModelFinder. Brazilian genomes are not tip colored. Viruses from other countries are colored according to their geographical origin (dark blue, South America; light blue, North America; dark green, Europe; light green, Africa; brown, Asia; and orange, Oceania). Gray areas highlight P.1 and P.2 lineages. The aLRT support value for the branch holding P.1 and P.2 monophyly is shown. The tree is rooted with 3 B.1.1 genomes. The chart shows the single nucleotide polymorphisms (SNPs) that characterize P.1 and P.2 lineages.CC BY · PubMed Central

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Predicting the unpredictable: how dynamic COVID-19 policies and restrictions challenge model forecastsPreprint
Houdroge, F., Palmer, A. Y., Delport, D., Walsh, T., Kelly, S. L., Hainsworth, S. W., Abeysuriya, R., Stuart, R. M., Kerr, C. C., COPLAN, P. M., et al. (2021) · medRxiv · doi:10.1101/2021.09.30.21264273
Dissecting Molecular Determinants of Mutational Escape Mechanisms in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Atomistic Simulations and Ensemble-Based Deep Mutational Scanning of Protein Stability and Binding InteractionsPreprint
Verkhivker, G. M., Agajanian, S., Öztaş, D. Y., & Gupta, G. (2021) · Preprints.org · doi:10.20944/preprints202107.0295.v1 · Cited by 1
Atomistic Simulations and Deep Mutational Scanning of Protein Stability and Binding Interactions in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms
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“[15], [16] - This variant contain N501Y (More transmission) and E484K (Escape of antibody) and K417N.”
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“Not least, the emergence of SARS-CoV-2 variants were detected in the state at 92 the time (13), although its transmissibility has not been proven to be major, nor has it 93 been a homogeneous event in the country.”
Background
Accuracy of SARS-CoV-2 molecular laboratory testing: insight on recurrence infection and the new emergent strains
Al-Griw, H. H. (2021) · Current Research in Microbiology and Infection · doi:10.31559/crmi2021.2.1.2
“These are the P.2, the lineage of SARS-CoV-2, originated from B.1.1.28, reported from 180 sequenced samples obtained from different municipalities in the state of Rio de Janeiro from April to December 2020 and was distinguished by five lineage-defining mutations (C100U/ C28253U/ G28628U/ G28975U/ C29754U) (Voloch et a…”
Influential
Detection of the new SARS-CoV-2 variant B.1.526 with the Spike E484K mutation in South AmericaPreprint
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Preventive behavior against covid-19 and its relationship with the social and health conditions of older adults
Dias, I. R., Janhaque, V. R., Vilas-Boas, V. A., Fusco, S. D. F. B., & Nunes, D. P. (2024) · Revista Brasileira de Geriatria e Gerontologia · doi:10.1590/1981-22562023026.230088.en
Limited Temporary Effect of Several Social Relaxation Events on the COVID-19 Series: An Analysis Based on Primary Data
Alonso, F. D. O. M., Sabino, B. D., de Oliveira, M. S. C., Knackfuss, F. B., & Varella, R. B. (2021) · Journal of Clinical Immunology & Microbiology · doi:10.46889/jcim.2021.2204
“Not least, the emergence of SARS-CoV-2 variants were detected in the state at the time, although its transmissibility has not been proven to be major [11].”
Background
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Cele, S., Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., Wilkinson, E., Naidoo, Y., et al. (2021) · doi:10.1101/2021.01.26.21250224 · Cited by 651
“Through genomic surveillance of the severe acute respiratory syndrome-related coronavirus 2 (SARS22 CoV-2), a number of new variants have recently been identified with multiple mutations in the spike 23 glycoprotein [1, 2, 3].”
Background

Authors: Voloch, C. M., Silva F, R. D., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., Costa, R. M. D., Ferreira, O. C., Workgroup, C.-U., LNCC-Workgroup, Cavalcanti, A. C., Frauches, T. S., de Mello, C. M. B., Galliez, R. M., Faffe, D. S., Castiñeiras, T. M. P. P., Tanuri, A., & de Vasconcelos, A. T. R.
Affiliations: Universidade Federal do Rio de Janeiro (BR)
Laboratório Nacional de Computação Científica (BR)
Secretaria de Estado de Saúde do Rio de Janeiro (BR)
ORCID: Voloch, Carolina M
Silva F, Ronaldo da
de Almeida, Luiz G P
Cardoso, Cynthia C
Brustolini, Otavio J.
Gerber, Alexandra L
Guimarães, Ana Paula de C
Mariani, Diana
Ferreira, Orlando C.
Galliez, Rafael Mello
Faffe, Débora Souza
Castiñeiras, Terezinha M P P
Tanuri, Amilcar
de Vasconcelos, Ana Tereza R
Venue: Journal of Virology
Publisher: openRxiv
Published: 2020-12-26
Volume: 95
Issue: 10
ISSN: 0022-538X (ISSN-L)
DOI: 10.1101/2020.12.23.20248598
PMC: PMC8139668
OpenAlex: W3135409471
Cited by: 372
References: 31
Citations by year: 2026: 5 · 2025: 8 · 2024: 25 · 2023: 34 · 2022: 93 · 2021: 206
FWCI: 28.43
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
Locations: Journal of Virology (publishedVersion, cc-by)
medRxiv (acceptedVersion)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Funders: Ministério da Ciência, Tecnologia e Inovação (01.20.0029.000462/20, 303170/2017-4, 404096/2020-4)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (= 404,096/2020–4, # 303170/2017-4)
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (E-26/202.791/2019, E-26/010.002278/2019, E-26/, E‐26/210.178/2020, E-26/210, =E-26/210.179/2020, E-26/202.903/20, E-26/010.002434/2019)
Financiadora de Estudos e Projetos (01.20.0029.000462/20)
Instituto Serrapilheira
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
Keywords: SARS-CoV-2, novel viral lineages, genomic profiling, phylogenetic analysis, genetic divergence, Rio de Janeiro, COVID-19 pandemic

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Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

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