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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“During October 2020, the first cases of the lineage P.2 were detected in Pernambuco, and at the time, P.2 was considered a variant of interest (VOI Zeta) due to specific spike mutations and increasing prevalence in Brazil (38, 39).”
Background
RT-LAMP Multicenter Study for SARS-CoV-2 Genome Molecular Detection in Brazilian Swab and Saliva Samples
da Costa, V. D., Santos, A. C., da Silva, L. L., Wiggers, W. J., Ivantes, C. A. P., Lima, D. M., Colares, J. K. B., Dall’Acqua, D. S. V., Motta-Castro, A. R. C., Dávila, A. M. R., et al. (2023) · Diagnostics · doi:10.3390/diagnostics13020210 · Cited by 8
“28, named gamma and zeta, emerged in the Brazilian states of Amazonas and Rio de Janeiro, respectively [41,42].”
Background
Investigation of target sequencing of SARS-CoV-2 and immunogenic GWAS profiling in host cells of COVID-19 in Vietnam
Hoang, T. H., Vu, G. M., Tran, M. H., Tran, T. T. H., Le, Q. D., Tran, K. V., Nguyen, T. T., Nguyen, L., Tran, T. H., Ta, V. T., et al. (2022) · BMC Infectious Diseases · doi:10.1186/s12879-022-07415-1 · Cited by 5
The past, present and future of genomics and bioinformatics: A survey of Brazilian scientists
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“…of the SARS-CoV-2 virus, which caused the COVID-19 pandemic (Araujo et al. , 2020; Jesus et al. , 2020), and to study the spread of the virus in the country since March 2020 (Candido et al. , 2020; Silva Francisco Jr et al. , 2020; Buss et al. , 2021; Faria et al. , 2021; Voloch et al. , 2021).”
First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission
Sola‐Campoy, P. J., Buenestado‐Serrano, S., Pérez‐Lago, L., Rodríguez‐Grande, C., Catalán, P., Andrés-Zayas, C., Alcalá, L., Losada, C., Rico-Luna, C., Muñóz, P., et al. (2022) · Enfermedades infecciosas y microbiologia clinica (English ed ) · doi:10.1016/j.eimce.2021.05.015
Protective Immunity against Gamma and Zeta Variants after Inactivated SARS-CoV-2 Virus Immunization
Fumagalli, M. J., de Castro-Jorge, L. A., Fraga‐Silva, T. F. D. C., de Azevedo, P. O., Capato, C. F., Rattis, B. A. D. C., Hojo-Souza, N. S., Floriano, V. G., de Castro, J. T., Ramos, S. G., et al. (2021) · Viruses · doi:10.3390/v13122440 · Cited by 9
Genome sequencing of SARS-CoV-2 reveals the prevalence of variant B 1.1.7 in Egypt
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Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics
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Simultaneous evaluation of antibodies that inhibit SARS-CoV-2 RBD variants with a novel competitive multiplex assay
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“As we enter the second year of the SARS68 CoV-2 pandemic, and promising vaccines are rolled out (4, 5), the ongoing 69 transmission along with the emergence of new variants with multiple mutations at key 70 residues in the spike glycoprotein (6-8), has resulted in the continued implementation 71 of stringent public he…”
Comparative spatial–temporal analysis of SARS-CoV-2 lineages B.1.1.33 and BQ.1.1 Omicron variant across pandemic phases
Ardisson, J. S., Monfardini, M. V., Athaydes, B. R., Vargas, A. M. C., Torezani, R., Ribeiro‐Rodrigues, R., Spano, L. C., Paneto, G. G., Delatorre, E. O., von Zeidler, S. V., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-95140-5 · Cited by 4
Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture
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Self-citation
SARS-CoV-2 variants from COVID-19 positive cases in the Free State province, South Africa from July 2020 to December 2021
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“This variant emerged in July 2020 in the Brazilian state of Rio de Janeiro and exhibited the E484K mutation in the spike region (with the absence of N501Y mutation) (32).”
Background
COVID-19 in the municipalities of Botucatu and Serrana, São Paulo, Brazil, the effects of lethality and mortality
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Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia
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“Most mutations that were responsible for variants classification occurred in S protein, but several other emerging mutations were observed in both coding and non-coding sequences of other genes especially NSP12, NSP9 and N proteins (Khailany et al., 2020).”
Rescuing the Host Immune System by Targeting the Immune Evasion Complex ORF8-IRF3 in SARS-CoV-2 Infection with Natural Products Using Molecular Modeling Approaches
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Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability
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Structural Insights of SARS-CoV-2 Spike Protein from Delta and Omicron VariantsPreprint
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“glycoprotein w/o ACE2 receptor in the closed (pre fusion) and open (post fusion) conformers [14, 19-21].”
Background
Early detection of community acquired of SARS-CoV-2 lineage B.1.351 in Hong Kong
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Detection of anti‐SARS‐CoV‐2 antibodies in dried blood spots utilizing manual or automated spot extraction and electrochemiluminescence immunoassay (ECLIA)
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Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology
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Sword of Damocles or choosing well. Population genetics sheds light into the future of the COVID-19 pandemic and SARS-CoV-2 new mutant strainsPreprint
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BRET-based biosensors for SARS-CoV-2 oligonucleotide detection
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“In early 2021, The most popular variants were the British variant [20], the Indian variant [21], the South African variant [22], and the Brazilian variant [23].”
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Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study
Alves, H. J., de Araújo, J. L. F., Fonseca, P. L. C., Moreira, F. R. R., Menezes, D., Queiroz, D. C., Miguita, L., de Souza, R. M., Geddes, V. E. V., Costa, W. C., et al. (2022) · Viruses · doi:10.3390/v14122747 · Cited by 5
Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants
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SARS-CoV-2 B.1.214.1, B.1.214.2 and B.1.620 are predominant lineages between December 2020 and July 2021 in the Republic of Congo
Mapanguy, C. C. M., Batchi-Bouyou, A. L., Djontu, J. C., Pallerla, S. R., Ngoma, C. H., Linh, L. T. K., Rachakonda, S. P., Casadei, N., Angelov, A., Sonnabend, M., et al. (2022) · IJID Regions · doi:10.1016/j.ijregi.2022.03.009 · Cited by 5
SARS-CoV-2 Variant Determination Through SNP Assays in Samples From Industry Workers From Rio de Janeiro, Brazil
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Design, immunogenicity, and efficacy of a pan-sarbecovirus dendritic-cell targeting vaccine
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Lethality and mortality of COVID-19 in an important industrial center in latin america, region of grande abc, São Paulo, Brazil
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Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N
Al‐Jawabreh, A., Ereqat, S., Dumaidi, K., Al-Jawabreh, H., & Nasereddin, A. (2021) · BMC Research Notes · doi:10.1186/s13104-021-05874-4 · Cited by 4
A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-studyPreprint
Bhatia, S., Wardle, J., Nash, R. K., Nouvellet, P., & Cori, A. (2021) · medRxiv · doi:10.1101/2021.11.26.21266899 · Cited by 4
PCR-Sequencing Approaches to Assess Informative Mutations in SARS-Cov-2 Spike (S) and ORF7, ORF8 and N Genes Characterizing Variants of Concern and Variants of InterestPreprint
Vitiello, G. A. F., de Oliveira, I. M., Ivanski, F., Fermino, B. L., Gustani‐Buss, E., Bezerra, R. D. S., Buss, C. E., Ximenez, J. P. B., Paz, B. M., Gabriel, K. D. O. F., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-1072564/v1
Acquisition and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient
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Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with BrazilPreprint
Rego, N., Fernández-Calero, T., Arantes, I., Noya, V., Mir, D., Brandes, M., Zanetti, J., Arleo, M., Pereira-Flores, E., Possi, T., et al. (2021) · medRxiv · doi:10.1101/2021.07.05.21259760 · Cited by 3
“This variant harbors the E484K amino acid change in the receptor-binding domain (RBD) of the viral Spike among its five lineage-defining mutations [6].”
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The increase in SARS-CoV-2 lineages during 2020–2022 in a state in the Brazilian Northeast is associated with a number of cases
Freitas, M. T. D. S., Sena, L. O. C., Fukutani, K. F., dos Santos, C. A., Neto, F. D. C. B., Ribeiro, J. S., dos Reis, É. S., Balbino, V. D. Q., Leitao, S. P. D. S., Batista, M. V. D. A., et al. (2023) · Frontiers in Public Health · doi:10.3389/fpubh.2023.1222152 · Cited by 3
Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
Werbajh, S., Larocca, L., Carrillo, C., Stolowicz, F. G., Ogas, L., Pallotto, S., Cassará, S., Mammana, L., Zapiola, I., Bouzas, M. B., et al. (2023) · Viruses · doi:10.3390/v15091910 · Cited by 6
“1, which has 17 unique mutations, including three in the receptor binding domain of the spike protein [26], was first identified in four travelers from Brazil who were tested during routine screening at Haneda airport outside Tokyo, Japan.”
Background
Frequent and unpredictable changes in COVID-19 policies and restrictions reduce the accuracy of model forecasts
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. (2023) · Scientific Reports · doi:10.1038/s41598-023-27711-3 · Cited by 6
Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil
Assato, P. A., Clemente, L. G., Giovanetti, M., Ribeiro, G. D. C., Lima, A. R. J., Palmieri, M., de Moraes, L. N., Kashima, S. H., Fukumasu, H., Nogueira, M. L., et al. (2023) · Viruses · doi:10.3390/v15020327 · Cited by 3
Pharmacoinformatic approach to identify potential phytochemicals against SARS-CoV-2 spike receptor-binding domain in native and variants of concern
Chinnadurai, R. K., Ponne, S., Loganathan, C., Kumar, R., Palvannan, T., & Subramanian, B. (2022) · Molecular Diversity · doi:10.1007/s11030-022-10580-9 · Cited by 8
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BackgroundInfluential
SARS-CoV-2 variant N.9 identified in Rio de Janeiro, Brazil
Tort, L. F. L., Ribeiro, I. P., Menezes, L. S. R., dos Santos, A. A. C., Santos, M. P., Damasceno, L. S., Resende, P. C., Siqueira, M. M., Brasil, P., & Bonaldo, M. C. (2021) · Memórias do Instituto Oswaldo Cruz · doi:10.1590/0074-02760210166 · Cited by 3
Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics
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Analysis of amino acid change dynamics reveals SARS-CoV-2 variant emergence
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Emerging SARS-CoV-2 variants expand species tropism to rodentsPreprint
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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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