1
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Lam C, Johnson-Mackinnon J, Basile K, Fong W, Suster CJ, Gall M, Agius J, Chandra S, Draper J, Martinez E, Drew A, Wang Q, Chen SC, Kok J, Dwyer DE, Sintchenko V, Rockett RJ. A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs. Microbiol Spectr 2023; 11:e0220223. [PMID: 37966271 PMCID: PMC10715188 DOI: 10.1128/spectrum.02202-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance system and highlights the importance of ongoing monitoring and the identification and implementation of improvements to whole genome sequencing methods to enhance public health responses to pathogen outbreaks.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Kerri Basile
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Carl J.E. Suster
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander Drew
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C. Chen
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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2
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Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreño JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburquerque B, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Paniz-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun 2023; 14:3235. [PMID: 37270625 PMCID: PMC10239218 DOI: 10.1038/s41467-023-38867-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
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Affiliation(s)
- Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Schaefer
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopi Patel
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Polanco
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angela A Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aria Rooker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian Cognigni
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Floda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nima Assad
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jian Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Levy A Sominsky
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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3
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Renuka Kumar G, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. Nat Commun 2023; 14:2308. [PMID: 37085489 PMCID: PMC10120482 DOI: 10.1038/s41467-023-37787-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (~30 kb). Here, we present a plasmid-based viral genome assembly and rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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Affiliation(s)
- Taha Y Taha
- Gladstone Institutes, San Francisco, CA, USA.
| | - Irene P Chen
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | - Hannah S Martin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Bryan H Bach
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Stacia Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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4
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Paulino-Ramírez R, López P, Mueses S, Cuevas P, Jabier M, Rivera-Amill V. Genomic Surveillance of SARS-CoV-2 Variants in the Dominican Republic and Emergence of a Local Lineage. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:ijerph20085503. [PMID: 37107785 PMCID: PMC10138544 DOI: 10.3390/ijerph20085503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus that evolves over time, leading to new variants. In the current study, we assessed the genomic epidemiology of SARS-CoV-2 in the Dominican Republic. A total of 1149 SARS-CoV-2 complete genome nucleotide sequences from samples collected between March 2020 and mid-February 2022 in the Dominican Republic were obtained from the Global Initiative on Sharing All Influenza Data (GISAID) database. Phylogenetic relationships and evolution rates were analyzed using the maximum likelihood method and the Bayesian Markov chain Monte Carlo (MCMC) approach. The genotyping details (lineages) were obtained using the Pangolin web application. In addition, the web tools Coronapp, and Genome Detective Viral Tools, among others, were used to monitor epidemiological characteristics. Our results show that the most frequent non-synonymous mutation over the study period was D614G. Of the 1149 samples, 870 (75.74%) were classified into 8 relevant variants according to Pangolin/Scorpio. The first Variants Being Monitored (VBM) were detected in December 2020. Meanwhile, in 2021, the variants of concern Delta and Omicron were identified. The mean mutation rate was estimated to be 1.5523 × 10-3 (95% HPD: 1.2358 × 10-3, 1.8635 × 10-3) nucleotide substitutions per site. We also report the emergence of an autochthonous SARS-CoV-2 lineage, B.1.575.2, that circulated from October 2021 to January 2022, in co-circulation with the variants of concern Delta and Omicron. The impact of B.1.575.2 in the Dominican Republic was minimal, but it then expanded rapidly in Spain. A better understanding of viral evolution and genomic surveillance data will help to inform strategies to mitigate the impact on public health.
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Affiliation(s)
- Robert Paulino-Ramírez
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Correspondence:
| | - Pablo López
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
| | - Sayira Mueses
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Paula Cuevas
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
| | - Maridania Jabier
- Instituto de Medicina Tropical y Salud Global, Universidad Iberoamericana, Research Hub, Santo Domingo 22333, Dominican Republic
- Servicio Nacional de Salud (SNS), Ministry of Health, Santo Domingo 10201, Dominican Republic
| | - Vanessa Rivera-Amill
- RCMI Center for Research Resources, Ponce Research Institute, Ponce, PR 00716-2348, USA (V.R.-A.)
- Basic Sciences Department, School of Medicine, Ponce Health Sciences University, Ponce, PR 00716-2348, USA
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5
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Taha TY, Chen IP, Hayashi JM, Tabata T, Walcott K, Kimmerly GR, Syed AM, Ciling A, Suryawanshi RK, Martin HS, Bach BH, Tsou CL, Montano M, Khalid MM, Sreekumar BK, Kumar GR, Wyman S, Doudna JA, Ott M. Rapid assembly of SARS-CoV-2 genomes reveals attenuation of the Omicron BA.1 variant through NSP6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.525914. [PMID: 36798416 PMCID: PMC9934579 DOI: 10.1101/2023.01.31.525914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across the world and effectively evaded immune responses, its viral fitness in cell and animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent viral genomes is challenging because of the length of the viral genome (30kb). Here, we designed a plasmid-based viral genome assembly and resc ue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons in a single ligation reaction with >80% efficiency. Fully sequenced replicons and infectious viral stocks can be generated in 1 and 3 weeks, respectively. By testing a series of naturally occurring viruses as well as Delta-Omicron chimeric replicons, we show that Omicron nonstructural protein 6 harbors critical attenuating mutations, which dampen viral RNA replication and reduce lipid droplet consumption. Thus, pGLUE overcomes remaining barriers to broadly study SARS-CoV-2 replication and reveals deficits in nonstructural protein function underlying Omicron attenuation.
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6
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Tallei TE, Alhumaid S, AlMusa Z, Fatimawali, Kusumawaty D, Alynbiawi A, Alshukairi AN, Rabaan AA. Update on the omicron sub-variants BA.4 and BA.5. Rev Med Virol 2023; 33:e2391. [PMID: 36017597 PMCID: PMC9539252 DOI: 10.1002/rmv.2391] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/28/2023]
Abstract
Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID-19). However, new Omicron sub-variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID-19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of BiologyFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Saad Alhumaid
- Administration of Pharmaceutical CareAl‐Ahsa Health ClusterMinistry of HealthAl‐AhsaSaudi Arabia
| | - Zainab AlMusa
- Infectious Disease SectionInternal Medicine DepartmentKing Fahad Specialist HospitalDammamSaudi Arabia
| | - Fatimawali
- Pharmacy Study ProgramFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Diah Kusumawaty
- Department of BiologyFaculty of Mathematics and Natural Sciences EducationUniversitas Pendidikan IndonesiaBandungIndonesia
| | - Ahlam Alynbiawi
- Infectious Diseases SectionMedical Specialties DepartmentKing Fahad Medical CityRiyadhSaudi Arabia
| | - Abeer N. Alshukairi
- Department of MedicineKing Faisal Specialist Hospital and Research CenterJeddahSaudi Arabia
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Ali A. Rabaan
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
- Molecular Diagnostic LaboratoryJohns Hopkins Aramco HealthcareDhahranSaudi Arabia
- Department of Public Health and NutritionThe University of HaripurHaripurPakistan
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7
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Hou X, Gao J, Wang Y. Epistatic Variations in the Omicron Receptor Binding Domain Can Enhance Host Recognition: An In Silico Assessment and Prediction. J Phys Chem Lett 2022; 13:8808-8815. [PMID: 36106917 DOI: 10.1021/acs.jpclett.2c02209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The hypermutated receptor binding domain (RBD) of the Omicron (B.1.1.529) lineage exhibits a different binding interface with human angiotensin-converting enzyme 2 (ACE2) relative to that of the wild-type Wuhan Hu-1, yet how the altered interaction will affect viral evolution is largely unknown. Here, we used molecular dynamics simulation to characterize the binding features of the Omicron BA.1/hACE2 complex and used free energy perturbation calculations to assess the ongoing and putative variations. The complex reveals a substantial rearrangement of the interfacial hydrogen-bond network: R493 of RBD forms a dynamic electrostatic interaction with both E35 and D38 of hACE2, which prohibits the hydrogen bonds of R498-D38 and Y449-D38. Whereas most circulating mutations minimally affect RBD binding to hACE2, the charge-altering mutation R493Q attenuates the affinity by abolishing the electrostatic interaction. However, the potential variants H505Y or N417K/R493Q could restore and gain even greater binding affinities than BA.1 as a result of their optimized interaction network and epistasis effects.
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Affiliation(s)
- Xudong Hou
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
| | - Jiali Gao
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, People's Republic of China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yingjie Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, People's Republic of China
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8
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Gesto JSM, Cabanelas A, Farjun B, dos Santos MC, Fidalgo-Neto AA, Kuriyama SN, Souza TML. Implemented occupational health surveillance limits the spread of SARS-CoV-2 Omicron at the workplace. Front Med (Lausanne) 2022; 9:910176. [PMID: 36111122 PMCID: PMC9468326 DOI: 10.3389/fmed.2022.910176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has put an enormous pressure on human societies, at both health and economic levels. Early diagnosis of SARS-CoV-2, the causative agent of 2019 coronavirus disease (COVID-19), has proved an efficient method to rapidly isolate positive individuals and reduce transmission rates, thus alleviating its negative impact on society’s well-being and economic growth. In this work, through a coordinated and centralized effort to monitor SARS-CoV-2 circulation in companies from the State of Rio de Janeiro, Brazil, we have detected and linked an early rise of infection rates in January 2022 to the introduction of the Omicron variant of concern (VoC) (BA.1). Interestingly, when the Omicron genomic isolates were compared to correlates from public datasets, it was revealed that introduction events were multiple, with possible migration routes mapping to: Mali; Oman and United States; and Italy, Latin America, and United States. In addition, we have built a haplotype network with our genomic dataset and found no strong evidence of transmission chains, between and within companies. Considering Omicron’s particularly high transmissibility, and that most of our samples (>87%) arose from 3 out of 10 companies, these findings suggest that workers from such environments were exposed to SARS-CoV-2 outside their company boundaries. Thus, using a mixed strategy in which quick molecular diagnosis finds support in comprehensive genomic analysis, we have shown that a successfully implemented occupational health program should contribute to document emerging VoC and to limit the spread of SARS-CoV-2 at the workplace.
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Affiliation(s)
- João Silveira Moledo Gesto
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Adriana Cabanelas
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | - Bruna Farjun
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
| | | | | | - Sergio N. Kuriyama
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- SENAI Innovation Institute for Green Chemistry, Rio de Janeiro, Brazil
- *Correspondence: Sergio N. Kuriyama,
| | - Thiago Moreno L. Souza
- SESI Innovation Center for Occupational Health, Rio de Janeiro, Brazil
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
- National Institute of Science and Technology for Innovation on Diseases of Neglected Populations (INCT/IDN), Rio de Janeiro, Brazil
- Thiago Moreno L. Souza,
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9
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Brynjolfsson SF, Sigurgrimsdottir H, Gudlaugsson O, Kristjansson M, Kristinsson KG, Ludviksson BR. Determining SARS-CoV-2 non-infectivity state-A brief overview. Front Public Health 2022; 10:934242. [PMID: 36033758 PMCID: PMC9412020 DOI: 10.3389/fpubh.2022.934242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/18/2022] [Indexed: 01/25/2023] Open
Abstract
From the beginning of the COVID-19 pandemic, it has claimed over 6 million lives, and globally the pandemic rages with detrimental consequences, with the emergence of new more infectious and possibly virulent variants. A clinical obstacle in this battle has been to determine when an infected individual has reached a non-infectious state. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) can be transmitted under diverse circumstances, and various rules and regulations, along with different testing methods, have been applied in an attempt to confine the transmission. However, that has proven to be a difficult task. In this review, we take together recently published data on infectivity and transmission of SARS-CoV-2 and have combined it with the clinical experience that physicians in Iceland have accumulated from the pandemic. In addition, we suggest guidelines for determining when patients with COVID-19 reach a non-infectious state based on a combination of clinical experience, scientific data, and proficient use of available tests. This review has addressed some of the questions regarding contagiousness and immunity against SARS-CoV-2.
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Affiliation(s)
- Siggeir F. Brynjolfsson
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,*Correspondence: Siggeir F. Brynjolfsson
| | - Hildur Sigurgrimsdottir
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Olafur Gudlaugsson
- Department of Infectious Diseases, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Mar Kristjansson
- Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Infectious Diseases, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Karl G. Kristinsson
- Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Clinical Microbiology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bjorn R. Ludviksson
- Department of Immunology, Landspitali—The National University Hospital of Iceland, Reykjavik, Iceland,Department of Medicine, Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Bjorn R. Ludviksson
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10
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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11
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Rajpal VR, Sharma S, Kumar A, Chand S, Joshi L, Chandra A, Babbar S, Goel S, Raina SN, Shiran B. "Is Omicron mild"? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies. J Med Virol 2022; 94:3521-3539. [PMID: 35355267 PMCID: PMC9088584 DOI: 10.1002/jmv.27749] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
SARS-CoV-2 Omicron with its lineages BA.1, BA.2, and BA.3 has triggered a fresh wave of Covid-19 infections. Though, Omicron has, so far, produced mild symptoms, its genome contains 60 mutations including 37 in the spike protein and 15 in the receptor-binding domain. Thirteen sites conserved in previous SARS-CoV-2 variants carry mutations in Omicron. Many mutations have shown evolution under positive selection. Omicron's giant mutational leap has raised concerns as there are signs of higher virus infectivity rate, pathogenesis, reinfection, and immune evasion. Preliminary studies have reported waning of immunity after two-dose primary vaccine regime, need for the boosters, folds reduction in vaccine effectiveness and neutralizing antibodies even after boosting and significant neutralization resistance with the therapeutic monoclonal, polyclonal, and convalescent antibodies against Omicron. The narrative that "Omicron is mild," therefore, needs time to be tested with a deeper, scientific dwelling into the facts.
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Affiliation(s)
| | - Shashi Sharma
- Division of VirologyDefence Research and Development EstablishmentGwaliorMadhya PradeshIndia
| | - Avinash Kumar
- Department of BotanyVinoba Bhave UniversityHazaribagJharkhandIndia
| | - Shweta Chand
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Lata Joshi
- Department of BotanyHansraj College, University of DelhiDelhiIndia
| | - Atika Chandra
- Department of BotanyMaitreyi College, University of DelhiDelhiIndia
| | - Sadhna Babbar
- Department of BotanySwami Shraddhanand College, University of DelhiDelhiIndia
| | | | - Soom Nath Raina
- Department of BiotechnologyAmity Institute of Biotechnology, Amity University Uttar PradeshNoidaUttar PradeshIndia
| | - Behrouz Shiran
- Department of Plant Breeding and BiotechnologyShahrekord UniversityShahrekordIran
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12
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Mortazavi SA, Jooyan N, Baha'addini Baigy Zarandi BF, Jooyan N, Faraz M, Mortazavi SMJ. Coming Out of Nowhere: The Paradox of the Birth of Omicron. J Biomed Phys Eng 2022; 12:325-326. [PMID: 36059290 PMCID: PMC9395623 DOI: 10.31661/jbpe.v0i0.2202-1456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/20/2022] [Indexed: 06/15/2023]
Affiliation(s)
| | - Najmeh Jooyan
- PhD, Department of Medical Physics and Engineering , School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Neda Jooyan
- MD, Aliasghar Teaching Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Faraz
- MSc, Department of Medical Physics and Engineering , School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Javad Mortazavi
- PhD, Department of Medical Physics and Engineering , School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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13
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Greco S, Gerdol M. Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage. Transbound Emerg Dis 2022; 69:e3408-e3415. [PMID: 35908169 PMCID: PMC9353284 DOI: 10.1111/tbed.14672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/17/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Although the major SARS‐CoV‐2 omicron lineages share over 30 non‐synonymous substitutions in the spike glycoprotein, they show several unique mutations that were acquired after their ancestral split. One of the most intriguing mutations associated with BA.1 is the presence of the inserted tripeptide Glu‐Pro‐Glu within the N‐terminal domain, at a site that had previously independently acquired short insertions in several other SARS‐CoV‐2 lineages. Although the functional implications of the small nucleotide sequences found at this insertion hotspot, named RIR1, are still unclear, we have previously hypothesized that they may play a compensatory role in counterbalancing minor fitness deficits associated with other co‐occurring spike non‐synonymous mutations. Here we show that similar insertion events have independently occurred at RIR1 at least 20 times in early 2022 within the BA.2 lineage, being occasionally associated with significant community transmission. One of these omicron sublineages, characterized by a Ser‐Gly‐Arg insertion in position 212, has been responsible of over 4,000 documented covid‐19 cases worldwide between January and July 2022, for the most part concentrated in Denmark, where it reached a national prevalence close to 4% (10% in the Nordjylland region) in mid‐May. Although the concurrent spread of the BA.2.12.1, BA.4 and BA.5 lineages led to the rapid decline of this BA.2 sublineage, the independent acquisition of several other RIR1 insertions on a BA.2 genomic background suggests that these events may provide a slight fitness advantage. Therefore, we they should be carefully monitored in the upcoming months in other emerging omicron‐related lineages, including BA.5. This article is protected by copyright. All rights reserved
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Affiliation(s)
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste
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14
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Harari S, Tahor M, Rutsinsky N, Meijer S, Miller D, Henig O, Halutz O, Levytskyi K, Ben-Ami R, Adler A, Paran Y, Stern A. Drivers of adaptive evolution during chronic SARS-CoV-2 infections. Nat Med 2022; 28:1501-1508. [PMID: 35725921 PMCID: PMC9307477 DOI: 10.1038/s41591-022-01882-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence. Analysis of mutations that arise in chronic SARS-CoV-2 infections shows both overlap and differences with mutations present in pandemic viral variants of concern, highlighting their distinct drivers of evolution.
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Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Maayan Tahor
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Natalie Rutsinsky
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Suzy Meijer
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Oryan Henig
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ora Halutz
- Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Katia Levytskyi
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Paran
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel. .,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel.
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15
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Kassianos G, Puig-Barberà J, Dinse H, Teufel M, Türeci Ö, Pather S. Addressing COVID-19 vaccine hesitancy. Drugs Context 2022; 11:2021-12-3. [PMID: 35814493 PMCID: PMC9225513 DOI: 10.7573/dic.2021-12-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
Immunization programmes have been globally recognized as one of the most successful medical interventions against infectious diseases. Despite the proven efficacy and safety profiles of coronavirus disease 2019 (COVID-19) vaccines, there are still a substantial number of people who express vaccine hesitancy. Factors that influence vaccine decision-making are heterogenous, complex, and context specific and may be caused or amplified by uncontrolled online information or misinformation. With respect to COVID-19, the recent emergence of novel variants of concern that give rise to milder disease also drives vaccine hesitancy. Healthcare professionals remain one of the most trusted groups to advise and provide information to those ambivalent about COVID-19 vaccination and should be equipped with adequate resources and information as well as practical guidance to empower them to effectively discuss concerns. This article seeks to summarize the currently available information to address the most common concerns regarding COVID-19 vaccination.
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Affiliation(s)
- George Kassianos
- Royal College of General Practitioners, London, UK
- The British Global and Travel Health Association, London, UK
| | - Joan Puig-Barberà
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Hannah Dinse
- University of Duisburg-Essen, Clinic for Psychosomatic Medicine and Psychotherapy, LVR University Hospital, Essen, Germany
| | - Martin Teufel
- University of Duisburg-Essen, Clinic for Psychosomatic Medicine and Psychotherapy, LVR University Hospital, Essen, Germany
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16
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Abstract
Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission. During its rapid spread in humans, SARS-CoV-2 has evolved independent new forms, the so-called "variants of concern," that are better optimized for human-to-human transmission. The most important adaptation of the bat coronavirus progenitor of both SARS-CoV-1 and SARS-CoV-2 for human infection (and other mammals) is the use of the angiotensin-converting enzyme 2 (ACE2) receptor. Relaxed structural constraints provide plasticity to SARS-related coronavirus spike protein permitting it to accommodate significant amino acid replacements of antigenic consequence without compromising the ability to bind to ACE2. Although the bulk of research has justifiably concentrated on the viral spike protein as the main determinant of antigenic evolution and changes in transmissibility, there is accumulating evidence for the contribution of other regions of the viral proteome to virus-host interaction. Whereas levels of community transmission of recombinants compromising genetically distinct variants are at present low, when divergent variants cocirculate, recombination between SARS-CoV-2 clades is being detected, increasing the risk that viruses with new properties emerge. Applying computational and machine learning methods to genome sequence data sets to generate experimentally verifiable predictions will serve as an early warning system for novel variant surveillance and will be important in future vaccine planning. Omicron, the latest SARS-CoV-2 variant of concern, has focused attention on step change antigenic events, "shift," as opposed to incremental "drift" changes in antigenicity. Both an increase in transmissibility and antigenic shift in Omicron led to it readily causing infections in the fully vaccinated and/or previously infected. Omicron's virulence, while reduced relative to the variant of concern it replaced, Delta, is very much premised on the past immune exposure of individuals with a clear signal that boosted vaccination protects from severe disease. Currently, SARS-CoV-2 has proven itself to be a dangerous new human respiratory pathogen with an unpredictable evolutionary capacity, leading to a risk of future variants too great not to ensure all regions of the world are screened by viral genome sequencing, protected through available and affordable vaccines, and have non-punitive strategies in place for detecting and responding to novel variants of concern.
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Affiliation(s)
- Amalio Telenti
- Vir Biotechnology, San Francisco, California 94158, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, USA
| | - Emma B Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
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17
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Barre A, Klonjkowski B, Benoist H, Rougé P. How Do Point Mutations Enhancing the Basic Character of the RBDs of SARS-CoV-2 Variants Affect Their Transmissibility and Infectivity Capacities? Viruses 2022; 14:783. [PMID: 35458513 PMCID: PMC9031512 DOI: 10.3390/v14040783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022] Open
Abstract
The spread of SARS-CoV-2 variants in the population depends on their ability to anchor the ACE2 receptor in the host cells. Differences in the electrostatic potentials of the spike protein RBD (electropositive/basic) and ACE2 receptor (electronegative/acidic) play a key role in both the rapprochement and the recognition of the coronavirus by the cell receptors. Accordingly, point mutations that result in an increase in electropositively charged residues, e.g., arginine and lysine, especially in the RBD of spike proteins in the SARS-CoV-2 variants, could contribute to their spreading capacity by favoring their recognition by the electronegatively charged ACE2 receptors. All SARS-CoV-2 variants that have been recognized as being highly transmissible, such as the kappa (κ), delta (δ) and omicron (o) variants, which display an enhanced electropositive character in their RBDs associated with a higher number of lysine- or arginine-generating point mutations. Lysine and arginine residues also participate in the enhanced RBD-ACE2 binding affinity of the omicron variant, by creating additional salt bridges with aspartic and glutamic acid residues from ACE2. However, the effects of lysine- and arginine-generating point mutations on infectivity is more contrasted, since the overall binding affinity of omicron RBD for ACE2 apparently results from some epistasis among the whole set of point mutations.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Bernard Klonjkowski
- UMR Virologie, INRA, ANSES, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France;
| | - Hervé Benoist
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Faculté de Pharmacie, Institut de Recherche et Développement, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (H.B.)
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18
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Kinikar AA, Vartak S, Dawre R, Valvi C, Kamath P, Sonkawade N, Pawar S, Bhagat V, A K, Nawale K, Deshmukh I, Das R, Kulkarni RK, Potdar V, Karyakarte R. Clinical Profile and Outcome of Hospitalized Confirmed Cases of Omicron Variant of SARS-CoV-2 Among Children in Pune, India. Cureus 2022; 14:e24629. [PMID: 35664398 PMCID: PMC9156401 DOI: 10.7759/cureus.24629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2022] [Indexed: 11/05/2022] Open
Abstract
Background The Omicron variant of SARS-CoV-2 infection was seen to be more infectious but less severe in children than adults with reduced hospitalization rates. There is a paucity of data on hospitalized children with confirmed Omicron variant. Objective We describe demographic, epidemiologic, clinical, radiological, laboratory features and outcomes of children with confirmed Omicron variant of SARS-CoV-2 infection admitted to a tertiary care teaching hospital in Pune, India. Methodology Children who tested positive for SARS-CoV-2 - Omicron variant and were admitted between 1st December 2021 and 28th February 2022 were included in the study. Results Out of a total of 37 Covid-positive children admitted during the study period, 16 underwent genome sequencing of which 14 were confirmed to be Omicron variant and two were Delta variant. The age range was one month to 12 years and seven (50%) were male. Common presenting features were fever (n=13, 93%), cough (n=7, 50%), seizures (n=7, 50%) and coryza (n=5, 36%). Comorbidities noted were epilepsy (n=3, 21%) and one each with Thalassemia Major, suspected inborn error of metabolism (IEM), operated anorectal malformation with hypospadias, chronic suppurative otitis media with complications (mastoiditis and facial nerve palsy), neonatal cholestasis and intracranial bleed with dural venous sinus thrombosis. Malnutrition was noted in 42%, pallor in 10 cases (71%). Severe anaemia (n=10, 71%), elevated ferritin (n=6, 43%), positive C-Reactive Protein (n=4, 28%) and deranged D-dimer (n=11, 78%) were noted. The Neutrophil to Lymphocyte ratio (NLR) was >3.3 in five (36%) children. Four (28%) had evidence of pneumonia on the chest radiograph. Oxygen therapy was needed in nine (64%) while two children (14%) required mechanical ventilation. There were two deaths (14%) in children with multiorgan dysfunction and refractory shock. Intravenous immunoglobulin and methylprednisolone were administered to one patient respectively (14%). The median hospital stay was 10 days (Interquartile range = 8). Conclusion Hospitalized children with Omicron variant of SARS-CoV-2 who have underlying comorbidities may have severe presentations needing ICU care. Mortality rates are low with appropriate ICU care.
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Affiliation(s)
- Aarti A Kinikar
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sagar Vartak
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rahul Dawre
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Chhaya Valvi
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Pragathi Kamath
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Naresh Sonkawade
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Sameer Pawar
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Vaishnavi Bhagat
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Kiruthiga A
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Komal Nawale
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Isha Deshmukh
- Pediatrics, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rashmita Das
- Microbiology, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
| | - Rajesh K Kulkarni
- Pediatrics, Postgraduate Institute, Yashwantrao Chavan Memorial (YCM) Hospital, Pune, IND
| | - Varsha Potdar
- Infectious Disease, Indian Council of Medical Research (ICMR) - National Institute of Virology, Pune, IND
| | - Rajesh Karyakarte
- Microbiology, Byramjee Jeejeebhoy (BJ) Government Medical College & Sassoon General Hospitals, Pune, IND
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Nikolaidis M, Papakyriakou A, Chlichlia K, Markoulatos P, Oliver SG, Amoutzias GD. Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF. Viruses 2022; 14:707. [PMID: 35458441 PMCID: PMC9025783 DOI: 10.3390/v14040707] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/13/2022] Open
Abstract
In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, 15341 Agia Paraskevi, Greece;
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece;
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK;
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
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20
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Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads rapidly and harbors many mutations in the spike protein, but the origin of this virus variant remains unclear. We address the role of unusual virus evolution mechanisms such as hypermutation, out-of-frame reading, and recombination. Rather, regular Darwinian evolution, that is, the repeated selection of beneficial spike mutations, seems to have led to the appearance of the grossly altered spike protein of the Omicron variant.
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21
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Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022; 603:679-686. [PMID: 35042229 PMCID: PMC8942855 DOI: 10.1038/s41586-022-04411-y] [Citation(s) in RCA: 1003] [Impact Index Per Article: 501.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/02/2023]
Abstract
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Affiliation(s)
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Phillip A Bester
- Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michaela Davids
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Deelan Doolabh
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diana Hardie
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Rageema Joseph
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Legodile Koopile
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Lesego Kuate-Lere
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Onalethatha Lesetedi-Mafoko
- Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Boitshoko Mahlangu
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Kamela Mahlakwane
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Gert Marais
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Kereng Masupu
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, USA
| | - Simnikiwe Mayaphi
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Nokuzola Mbhele
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Adriano Mendes
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Anele Mnguni
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kgomotso Moruisi
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Mosepele Mosepele
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Gerald Motsatsi
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Modisa S Motswaledi
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Thongbotho Mphoyakgosi
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Peter N Mwangi
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Noxolo Ntuli
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Martin Nyaga
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Lucier Olubayo
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Botshelo Radibe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Strydom
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Naume Tebeila
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Joseph Tsui
- Department of Zoology, University of Oxford, Oxford, UK
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Constantinos K Wibmer
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- PathCare Vermaak, Pretoria, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Florette Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Marietje Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- Lancet Laboratories, Johannesburg, South Africa
- Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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