Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Open accessPreprint — published as 10.1128/jvi.00119-21 · Paper page
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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The panel also included circulating variant residues K417N, Y453F, S477R, N501Y, and D614G, some linked to rapidly rising case counts.
“Additionally, K417N, Y453F, S477R, N501Y, and D614G represent circulating variants some of which have been associated with rapidly increasing case numbers14,15,19,33–35.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [35]
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Heida, R., Hinrichs, W. L. J., & Frijlink, H. W. (2021) · Expert Review of Vaccines · doi:10.1080/14760584.2021.1903878 · Cited by 92 · see citing works
Case, J. B., Chen, R. E., Cao, L., Ying, B., Winkler, E. S., Johnson, M., Goreshnik, I., Pham, M. N., Shrihari, S., Kafai, N. M., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.008 · Cited by 73 · see citing works
Ferrareze, P. A. G., Franceschi, V. B., Mayer, A. D. M., Caldana, G. D., Zimerman, R. A., & Thompson, C. E. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.104941 · Cited by 82 · see citing works
Bekliz, M., Adea, K., Vetter, P., Eberhardt, C. S., Hosszu-Fellous, K., Vu, D., Puhach, O., Essaidi-Laziosi, M., Waldvogel‐Abramowski, S., Stephan, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31556-1 · Cited by 85 · see citing works
Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses
Nathan, A., Rossin, E. J., Kaseke, C., Park, R. J.-H., Khatri, A., Koundakjian, D., Urbach, J. M., Singh, N. K., Bashirova, A. A., Tano-Menka, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.029 · Cited by 84 · see citing works
“…Polack et al., 2020; Sadoff et al., 2021), the emergence of the B.1.1.7 alpha (Tang et al., 2020), B.1.351 beta (Tegally et al., 2021), P.1 gamma (Voloch et al., 2020), and B.1.617.2 delta variants (Cherian et al., 2021) has raised substantial new concerns due to their increased transmissibility…”
InfluentialIntroduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK
Toovey, O. T. R., Harvey, K. N., Bird, P. W., & Tang, J. W.-T. (2021) · Journal of Infection · doi:10.1016/j.jinf.2021.01.025 · Cited by 74 · see citing works
One Year of SARS-CoV-2: Genomic Characterization of COVID-19 Outbreak in Qatar
Benslimane, F. M., Al-Khatib, H. A., Al-Jamal, O., Albatesh, D., Boughattas, S., Ahmed, A. A., Bensaad, M., Younuskunju, S., Mohamoud, Y. A., Badr, M. A., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.768883 · Cited by 66 · see citing works
“Only a few samples -collected in March 2021- intermixed with genomes from Greece, South Africa, and the USA (Figure 5B).”
BackgroundInfluentialEmergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda
Bugembe, D. L., Phan, M. V. T., Ssewanyana, I., Semanda, P., Nansumba, H., Dhaala, B., Nabadda, S. N., O’Toole, A. N., Rambaut, A., Kaleebu, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00933-9 · Cited by 103 · see citing works
Fred, S. M., Kuivanen, S. H., Uğurlu, H., Casarotto, P. C., Levanov, L., Saksela, K., Vapalahti, O. P., & Ċastrén, E. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.755600 · Cited by 67 · see citing works
“…of an Emergent SARS-CoV-2 Lineage in Manaus, 2021; Phylogenetic Relationship of SARS-CoV-2 Sequences from Amazonas with Emerging Brazilian Variants Harboring Mutations E484K and N501Y in the Spike Protein - SARS-CoV-2 Coronavirus /NCoV-2019 Genomic Epidemiology, 2021; Voloch et al., 2020).”
Wang, Y., Xu, C., Wang, Y., Qin, H., Zhang, C., Li, Z., Xu, S., Zuo, Q., Liu, C., Huang, Z. W., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27350-0 · Cited by 83 · see citing works
Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail
Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., et al. (2021) · doi:10.1101/2021.01.27.428529 · Cited by 55 · see citing works
Jette, C. A., Cohen, A. A., Gnanapragasam, P. N. P., Muecksch, F., Lee, Y. E., Huey‐Tubman, K. E., Schmidt, F., Hatziioannou, T., Bieniasz, P. D., Nussenzweig, M. C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109760 · Cited by 99 · see citing works
Vega‐Magaña, N., Sánchez-Sánchez, R., Hernández‐Bello, J., Venancio-Landeros, A. A., Rodríguez, M. P., Vega-Zepeda, R. A., Galindo-Ornelas, B., Díaz-Sánchez, M., García‐Chagollán, M., Ojeda, G. M., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.672562 · Cited by 67 · see citing works
Intra-host evolution during SARS-CoV-2 prolonged infection
Voloch, C. M., Francisco, R. D. S., de Almeida, L. G. P., Brustolini, O. J. B., Cardoso, C. C., Gerber, A. L., Guimarães, A. P. D. C., Leitão, I. D. C., Mariani, D., Ota, V. A., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab078 · Cited by 98 · see citing works
Self-citationSARS-CoV-2 new variants: Characteristic features and impact on the efficacy of different vaccines
Khan, A., Khan, T., Ali, S., Aftab, S., Wang, Y., Wang, Q., Khan, M., Suleman, M., Ali, S., Heng, W., et al. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.112176 · Cited by 75 · see citing works
Cobre, A. D. F., Stremel, D. P., Noleto, G. R., Fachi, M. M., Surek, M., Wiens, A., Tonin, F. S., & Pontarolo, R. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104531 · Cited by 63 · see citing works
Jette, C. A., Cohen, A. A., Gnanapragasam, P. N. P., Muecksch, F., Lee, Y., Huey-Tubman, K. E., Schmidt, F., Hatziioannou, T., Bieniasz, P., Nussenzweig, M., et al. (2021) · bioRxiv · doi:10.1101/2021.04.23.441195 · Cited by 54 · see citing works
“…SARS-CoV-2, SARS-CoV-2 RBD mutants, SARS-CoV-2 variants (Annavajhala et al., 2021; Faria et al., 2021; Rambaut et al., 2020; Tegally et al., 2020; Voloch et al., 2020; West et al., 2021; Zhang et al., 2021), and sarbecovirus strains known to infect human ACE2-expressing target cells (SARS-CoV-2,…”
InfluentialBroad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro
Zeng, L., Liu, Y., Wrynla, X. H., Abbott, T. R., Han, M., Zhu, Y., Chemparathy, A. G., Lin, X., Chen, X., Wang, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30546-7 · Cited by 52 · see citing works
Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil
Clemens, S. A. C., Folegatti, P. M., Emary, K. R. W., Weckx, L. Y., Ratcliff, J., Bibi, S., Mendes, A. V. A., Milan, E. P., Pittella, A. M., Schwarzbold, A. V., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25982-w · Cited by 57 · see citing works
CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern
Liang, Y., Lin, H., Zou, L., Zhao, J., Li, B., Wang, H., Lu, J., Sun, J., Yang, X., Deng, X., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01017-21 · Cited by 78 · see citing works
Fedry, J., Hurdiss, D. L., Wang, C., Li, W.-T., Obal, G., Drulyte, I., Du, W., Howes, S., van Kuppeveld, F. V., Förster, F. G., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf5632 · Cited by 50 · see citing works
The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants
Rothenberger, S., Hurdiss, D. L., Walser, M., Malvezzi, F., Mayor, J., Ryter, S., Moreno, H., Liechti, N., Bosshart, A., Iss, C., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01382-3 · Cited by 72 · see citing works
Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants
Gupta, D., Sharma, P., Singh, M., Kumar, M., Ethayathulla, A. S., & Kaur, P. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04008-0 · Cited by 52 · see citing works
“It was first reported in the state of Rio de Janeiro, Brazil [63].”
BackgroundSuleman, M., Yousafi, Q., Ali, J., Ali, S. S., Hussain, Z., Ali, S., Waseem, M., Iqbal, A., Ahmad, S., Khan, A., et al. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104936 · Cited by 48 · see citing works
“Efforts to disclose the genomic organization of SARS-CoV-2 have revealed that the virus consists of sixteen nonstructural proteins (NSP1 – NSP16) and four structural proteins (S protein, E protein, N protein, and M protein) [17,18].”
Resende, P. C., Naveca, F. G., Lins, R. D., Dezordi, F. Z., Ferraz, M. V. F., Moreira, E. G., Coêlho, D. F., Motta, F. C., Paixão, A. C. D., Appolinario, L., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab069 · Cited by 46 · see citing works
Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants
Jacot, D., Pillonel, T., Greub, G., & Bertelli, C. (2021) · Journal of Clinical Microbiology · doi:10.1128/jcm.00944-21 · Cited by 42 · see citing works
Liu, H., Yuan, M., Huang, D.-L., Bangaru, S., Zhao, F.-Z., Lee, C. D., Peng, L., Barman, S., Zhu, X.-Y., Nemazee, D., et al. (2021) · Cell Host and Microbe · doi:10.1016/j.chom.2021.04.005 · Cited by 46 · see citing works
“…mutations in both human and mink populations give rise to concerns about viral escape from current vaccines and therapeutics in development (Andreano et al., 2020; Greaney et al., 2021a; Kemp et al., 2021; Mallapaty, 2020; Oude Munnink et al., 2021; Tegally et al., 2021; Voloch et al., 2021).”
BackgroundGreaney, A. J., Starr, T. N., Barnes, C., et al. (2021) · bioRxiv · doi:10.1101/2021.03.17.435863 · Cited by 45 · see citing works
Resende, P. C., Gräf, T., Paixão, A. C. D., Appolinario, L., Lopes, R. S., Mendonça, A. C. D. F., da Rocha, A. S. B., Motta, F. C., Neto, L. G. L., Khouri, R., et al. (2021) · Viruses · doi:10.3390/v13050724 · Cited by 43 · see citing works
“2, first described in samples from October 2020 in the state of Rio de Janeiro, was distinguished by the presence of the S:E484K mutation in RBD and other four lineage-defining mutations outside the S protein [6].”
BackgroundSelf-citationBugembe, D., V.T.Phan, M., Ssewanyana, I., et al. (2021) · medRxiv · doi:10.1101/2021.02.08.21251393 · Cited by 45 · see citing works
“1 (7) ) and applied the 250 same profileHMM analysis.”
MethodLong, S. W., Olsen, R. J., Christensen, P. A., Subedi, S., Olson, R., Davis, J. J., Saavedra, M. O., Yerramilli, P., Pruitt, L., Reppond, K., et al. (2021) · American Journal Of Pathology · doi:10.1016/j.ajpath.2021.03.004 · Cited by 46 · see citing works
Peng, J., Liu, J., Mann, S. A., Mitchell, A. M., Laurie, M. T., Sunshine, S., Pilarowski, G., Ayscue, P., Kistler, A., Vanaerschot, M., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab283 · Cited by 41 · see citing works
Verkhivker, G. M., Agajanian, S., Oztas, D., et al. (2021) · bioRxiv · doi:10.1101/2021.04.13.439743 · Cited by 42
Neutralizing activity of Sputnik V vaccine sera against SARS-CoV-2 variantsPreprint
Ikegame, S., Siddiquey, M. N. A., Hung, C.-T., Haas, G. D., Brambilla, L., Oguntuyo, K. Y., Kowdle, S., Vilardo, A. E., Edelstein, A., Perandones, C., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-400230/v1 · Cited by 27 · see citing works
“For example, a B.1.526 sub-lineage carrying E484K in recent weeks has expanded more rapidly than B.1.1.7 (Annavajhala et al. , 2021; West et al. , 2021), which may be indicative of the ability of S: E484K variants to penetrate herd immunity.”
InfluentialMartins, A. F., Zavascki, A. P., Wink, P. L., Volpato, F. C. Z., Monteiro, F. L., Rosset, C., de Paris, F., Ramos, Á., & Barth, A. L. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.12.2100276 · Cited by 60 · see citing works
Gorman, M. J., Patel, N., Guebre‐Xabier, M., Zhu, A. L., Atyeo, C. G., Pullen, K. M., Loos, C., Goez-Gazi, Y., Carrion, R., Tian, J.-H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.05.429759 · Cited by 29 · see citing works
Upadhyay, V., Lucas, A., Panja, S., Miyauchi, R., & Mallela, K. M. G. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101208 · Cited by 41 · see citing works
Gawish, R., Starkl, P. M., Pimenov, L., Hladik, A., Lakovits, K., Oberndorfer, F., Cronin, S. J., Ohradanova‐Repic, A., Wirnsberger, G., Agerer, B., et al. (2022) · eLife · doi:10.7554/elife.74623 · Cited by 58 · see citing works
“Upon adaptation to humans, SARS-CoV-2 evolution gave rise to multiple variants including novel SARS-CoV-2 variants of concern (VOCs), characterized by increased transmissibility and/or virulence, or reduced effectiveness of countermeasures such as vaccinations or antibody therapies (WHO, 2021a).”
BackgroundResultInfluentialSimultaneous evaluation of antibodies that inhibit SARS-CoV-2 variants via multiplex assay
López, E., Haycroft, E. R., Adair, A., Mordant, F. L., O’Neill, M. T., Pymm, P., Redmond, S. J., Lee, W. S., Gherardin, N. A., Wheatley, A. K., et al. (2021) · JCI Insight · doi:10.1172/jci.insight.150012 · Cited by 38 · see citing works
“residues in the spike glycoprotein (6-8), has resulted in the continued implementation 74 of stringent public health measures to control infection in many parts of the world.”
BackgroundLamarca, A. P., de Almeida, L. G. P., Francisco, R. D. S., Agnez‐Lima, L. F., Scortecci, K. C., Perez, V. P., Brustolini, O. J. B., Sousa, E. S. S., Secco, D., Santos, Â., et al. (2021) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0009835 · Cited by 33 · see citing works
Self-citationQasem, A., Shaw, A. M., Elkamel, E., & Naser, S. A. (2021) · Current Issues in Molecular Biology · doi:10.3390/cimb43020053 · Cited by 42 · see citing works
Booster dose of mRNA vaccine augments waning T cell and antibody responses against SARS-CoV-2
Kurt, F. G. Ö., Lepper, A., Gerhards, C., Roemer, M., Lasser, S., Arkhypov, I., Bitsch, R., Bugert, P., Altevogt, P., Gouttefangeas, C., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1012526 · Cited by 46 · see citing works
“Emergence of different variants has generated concern about the effectiveness of immunity after vaccination (18, 19).”
BackgroundMeyers, L. M., Gutiérrez, A. H., Boyle, C., Terry, F. E., McGonnigal, B., Salazar, A. Μ., Princiotta, M. F., Martin, W. D., Groot, A. S. D., & Moise, L. (2021) · npj Vaccines · doi:10.1038/s41541-021-00331-6 · Cited by 43 · see citing works
50 Years of structural immunology
Wilson, I. A., & Stanfield, R. L. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100745 · Cited by 43 · see citing works
Junejo, Y., Özaslan, M., Safdar, M., Khailany, R. A., Rehman, S. U., Yousaf, W., & Khan, M. A. (2020) · Gene Reports · doi:10.1016/j.genrep.2020.100752 · Cited by 46 · see citing works
“All non-coding mutations are within 3′UTR or 5′UTR regions that have C>T changes (Rozhgar et al., 2020).”
A simple reverse genetics method to generate recombinant coronaviruses
Mélade, J., Piorkowski, G., Touret, F., Fourié, T., Driouich, J., Cochin, M., Bouzidi, H. S., Coutard, B., Nougaırède, A., & de Lamballerie, X. N. (2022) · EMBO Reports · doi:10.15252/embr.202153820 · Cited by 44 · see citing works
Verkhivker, G. M., Agajanian, S., Oztas, D., et al. (2021) · bioRxiv · doi:10.1101/2021.02.21.432165 · Cited by 36
Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Franceschi, V. B., Caldana, G. D., Mayer, A. D. M., Cybis, G. B., Neves, C. A. M., Ferrareze, P. A. G., Demoliner, M., de Almeida, P. R., Gularte, J. S., Hansen, A. W., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07708-w · Cited by 35 · see citing works
“Phylodynamics inferences pointed that this lineage emerged in early July, approximately four months before the detection of its first genomes [53].”
- 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
- Venue
- Journal of Virology
- Publisher
- openRxiv
- Published
- 2020-12-26
- Volume
- 95
- Issue
- 10
- ISSN
- 0022-538X (ISSN-L)
- PMC
- PMC8139668
- OpenAlex
- W3135409471
- Cited by
- 372
- References
- 31
- Citations by year
- 2026: 5 · 2025: 8 · 2024: 25 · 2023: 34 · 2022: 93 · 2021: 206 · 2013: 1
- 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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