1
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Ferrier CH, Ruis C, Zadelhoff D, Robe PAJT, van Zandvoort MJE. IDEAL monitoring of musical skills during awake craniotomy: From step 1 to step 2. J Neuropsychol 2024; 18 Suppl 1:48-60. [PMID: 37916937 DOI: 10.1111/jnp.12347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 11/03/2023]
Abstract
The aim of awake brain surgery is to perform a maximum resection on the one hand, and to preserve cognitive functions, quality of life and personal autonomy on the other hand. Historically, language and sensorimotor functions were most frequently monitored. Over the years other cognitive functions, including music, have entered the operation theatre. Cases about monitoring musical abilities during awake brain surgery are emerging, and a systematic method how to monitor music would be the next step. According to the IDEAL framework for surgical innovations our study aims to present future recommendation based on a systematic literature search (PRISMA) in combination with lessons learned from three case reports from our own clinical practice with professional musicians (n = 3). We plead for structured procedures including individual tailored tasks. By embracing these recommendations, we can both improve clinical care and unravel music functions in the brain.
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Affiliation(s)
- C H Ferrier
- Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C Ruis
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Experimental Psychology/Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - D Zadelhoff
- Experimental Psychology/Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - P A J T Robe
- Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J E van Zandvoort
- Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Experimental Psychology/Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
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2
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McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger MT, Hinrichs AS, O'Toole AN, Ruis C, Turakhia Y, Rambaut A, Corbett-Detig R. A framework for automated scalable designation of viral pathogen lineages from genomic data. Nat Microbiol 2024; 9:550-560. [PMID: 38316930 PMCID: PMC10847047 DOI: 10.1038/s41564-023-01587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024]
Abstract
Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Adriano de Bernardi Schneider
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- RNA Forecast e.U., Vienna, Austria
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Aine Niamh O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
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3
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Ruis C, Weimann A, Tonkin-Hill G, Pandurangan AP, Matuszewska M, Murray GGR, Lévesque RC, Blundell TL, Floto RA, Parkhill J. Mutational spectra are associated with bacterial niche. Nat Commun 2023; 14:7091. [PMID: 37925514 PMCID: PMC10625568 DOI: 10.1038/s41467-023-42916-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
As observed in cancers, individual mutagens and defects in DNA repair create distinctive mutational signatures that combine to form context-specific spectra within cells. We reasoned that similar processes must occur in bacterial lineages, potentially allowing decomposition analysis to detect both disruption of DNA repair processes and exposure to niche-specific mutagens. Here we reconstruct mutational spectra for 84 clades from 31 diverse bacterial species and find distinct mutational patterns. We extract signatures driven by specific DNA repair defects using hypermutator lineages, and further deconvolute the spectra into multiple signatures operating within different clades. We show that these signatures are explained by both bacterial phylogeny and replication niche. By comparing mutational spectra of clades from different environmental and biological locations, we identify niche-associated mutational signatures, and then employ these signatures to infer the predominant replication niches for several clades where this was previously obscure. Our results show that mutational spectra may be associated with sites of bacterial replication when mutagen exposures differ, and can be used in these cases to infer transmission routes for established and emergent human bacterial pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gemma G R Murray
- Parasites and Microbes Programme, Wellcome Sanger Institute; Wellcome Genome Campus, Cambridge, UK
| | - Roger C Lévesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec City, Québec, Canada
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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4
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On YY, Figueroa W, Fan C, Ho PM, Bényei ÉB, Weimann A, Ruis C, Floto AR, Welch M. Impact of transient acquired hypermutability on the inter- and intra-species competitiveness of Pseudomonas aeruginosa. ISME J 2023; 17:1931-1939. [PMID: 37666975 PMCID: PMC10579334 DOI: 10.1038/s41396-023-01503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/06/2023]
Abstract
Once acquired, hypermutation is unrelenting, and in the long-term, leads to impaired fitness due to its cumulative impact on the genome. This raises the question of why hypermutators arise so frequently in microbial ecosystems. In this work, we explore this problem by examining how the transient acquisition of hypermutability affects inter- and intra-species competitiveness, and the response to environmental insults such as antibiotic challenge. We do this by engineering Pseudomonas aeruginosa to allow the expression of an important mismatch repair gene, mutS, to be experimentally controlled over a wide dynamic range. We show that high levels of mutS expression induce genomic stasis (hypomutation), whereas lower levels of induction lead to progressively higher rates of mutation. Whole-genome sequence analyses confirmed that the mutational spectrum of the inducible hypermutator is similar to the distinctive profile associated with mutS mutants obtained from the airways of people with cystic fibrosis (CF). The acquisition of hypermutability conferred a distinct temporal fitness advantage over the wild-type P. aeruginosa progenitor strain, in both the presence and the absence of an antibiotic selection pressure. However, over a similar time-scale, acquisition of hypermutability had little impact on the population dynamics of P. aeruginosa when grown in the presence of a competing species (Staphylococcus aureus). These data indicate that in the short term, acquired hypermutability primarily confers a competitive intra-species fitness advantage.
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Affiliation(s)
- Yue Yuan On
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Catherine Fan
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Currently based at Epoch Biodesign, Oxford, UK
| | - Pok-Man Ho
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Aaron Weimann
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Andres R Floto
- Heart Lung Research Institute, University of Cambridge, Cambridge, UK
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
- Cambridge University Hospitals Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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5
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Roemer C, Sheward DJ, Hisner R, Gueli F, Sakaguchi H, Frohberg N, Schoenmakers J, Sato K, O'Toole Á, Rambaut A, Pybus OG, Ruis C, Murrell B, Peacock TP. SARS-CoV-2 evolution in the Omicron era. Nat Microbiol 2023; 8:1952-1959. [PMID: 37845314 DOI: 10.1038/s41564-023-01504-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023]
Abstract
Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have markedly diversified. Here we review the evolutionary trajectories and processes that underpin the emergence of these lineages, and identify the most prevalent sublineages. We discuss the potential origins of second-generation BA.2 lineages. Simple and complex recombination, antigenic drift and convergent evolution have enabled SARS-CoV-2 to accumulate mutations that alter its antigenicity. We also discuss the potential evolutionary trajectories of SARS-CoV-2 in the future.
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Affiliation(s)
- Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ryan Hisner
- University of Cape Town, Rondebosch, South Africa
| | | | | | | | | | - Kenta Sato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Áine O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK.
- The Pirbright Institute, Woking, UK.
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6
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Sanderson T, Hisner R, Donovan-Banfield I, Hartman H, Løchen A, Peacock TP, Ruis C. A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes. Nature 2023; 623:594-600. [PMID: 37748513 PMCID: PMC10651478 DOI: 10.1038/s41586-023-06649-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Molnupiravir, an antiviral medication widely used against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), acts by inducing mutations in the virus genome during replication. Most random mutations are likely to be deleterious to the virus and many will be lethal; thus, molnupiravir-induced elevated mutation rates reduce viral load1,2. However, if some patients treated with molnupiravir do not fully clear the SARS-CoV-2 infections, there could be the potential for onward transmission of molnupiravir-mutated viruses. Here we show that SARS-CoV-2 sequencing databases contain extensive evidence of molnupiravir mutagenesis. Using a systematic approach, we find that a specific class of long phylogenetic branches, distinguished by a high proportion of G-to-A and C-to-T mutations, are found almost exclusively in sequences from 2022, after the introduction of molnupiravir treatment, and in countries and age groups with widespread use of the drug. We identify a mutational spectrum, with preferred nucleotide contexts, from viruses in patients known to have been treated with molnupiravir and show that its signature matches that seen in these long branches, in some cases with onward transmission of molnupiravir-derived lineages. Finally, we analyse treatment records to confirm a direct association between these high G-to-A branches and the use of molnupiravir.
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Affiliation(s)
| | - Ryan Hisner
- Department of Bioinformatics, University of Cape Town, Cape Town, South Africa
| | - I'ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, National Institute for Health and Care Research, Liverpool, UK
| | | | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- The Pirbright Institute, Pirbright, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
- Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, Cambridge, UK.
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7
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de Sain AM, van Zandvoort MJE, Mantione MHM, Huenges Wajer IMC, Willems PWA, Robe PA, Ruis C. A timeline of cognitive functioning in glioma patients who undergo awake brain tumor surgery: a response to Mahajan et al. and their letter to the editor. Acta Neurochir (Wien) 2023; 165:2501-2502. [PMID: 37351674 DOI: 10.1007/s00701-023-05689-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Affiliation(s)
- A M de Sain
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS, Utrecht, the Netherlands.
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands.
| | - M J E van Zandvoort
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS, Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - M H M Mantione
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - I M C Huenges Wajer
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS, Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - P W A Willems
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - P A Robe
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
| | - C Ruis
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS, Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, the Netherlands
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8
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Wajer IMCH, Kal J, Robe PA, van Zandvoort MJE, Ruis C. Awake craniotomy does not lead to increased psychological complaints. Acta Neurochir (Wien) 2023; 165:2505-2512. [PMID: 37225975 PMCID: PMC10477129 DOI: 10.1007/s00701-023-05615-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
BACKGROUND Patients with brain tumours are increasingly treated by using the awake craniotomy technique. Some patients may experience anxiety when subjected to brain surgery while being fully conscious. However, there has been only limited research into the extent to which such surgeries actually result in anxiety or other psychological complaints. Previous research suggests that undergoing awake craniotomy surgery does not lead to psychological complaints, and that post-traumatic stress disorders (PTSD) are uncommon following this type of surgery. It must be noted, however, that many of these studies used small random samples. METHOD In the current study, 62 adult patients completed questionnaires to identify the degree to which they experienced anxiety, depressive and post-traumatic stress complaints following awake craniotomy using an awake-awake-awake procedure. All patients were cognitively monitored and received coaching by a clinical neuropsychologist during the surgery. RESULTS In our sample, 21% of the patients reported pre-operative anxiety. Four weeks after surgery, 19% of the patients reported such complaints, and 24% of the patients reported anxiety complaints after 3 months. Depressive complaints were present in 17% (pre-operative), 15% (4 weeks post-operative) and 24% (3 months post-operative) of the patients. Although there were some intra-individual changes (improvement or deterioration) in the psychological complaints over time, on group-level postoperative levels of psychological complaints were not increased relative to the preoperative level of complaints. The severity of post-operative PTSD-related complaints were rarely suggestive of a PTSD. Moreover, these complaints were seldom attributed to the surgery itself, but appeared to be more related to the discovery of the tumour and the postoperative neuropathological diagnosis. CONCLUSIONS The results of the present study do not indicate that undergoing awake craniotomy is associated with increased psychological complaints. Nevertheless, psychological complaints may well exist as a result of other factors. Consequently, monitoring the patient's mental wellbeing and offering psychological support where necessary remain important.
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Affiliation(s)
- I M C Huenges Wajer
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands.
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands.
| | - J Kal
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - P A Robe
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J E van Zandvoort
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
| | - C Ruis
- Department of Neurology and Neurosurgery, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Experimental Psychology, Helmholtz Institute, Utrecht University, Utrecht, The Netherlands
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9
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de Sain A, Mantione M, Wajer IH, van Zandvoort M, Willems P, Robe P, Ruis C. A timeline of cognitive functioning in glioma patients who undergo awake brain tumor surgery. Acta Neurochir (Wien) 2023; 165:1645-1653. [PMID: 37097374 PMCID: PMC10227103 DOI: 10.1007/s00701-023-05588-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND The purpose of awake brain tumor surgery is to maximize the resection of the tumor and to minimize the risk of neurological and cognitive impairments. The aim of this study is to gain understanding of the development of possible postoperative cognitive deficits after awake brain tumor surgery in patients with suspected gliomas, by comparing preoperative, early postoperative, and late postoperative functioning. A more detailed timeline will be helpful in informing candidates for surgery about what to expect regarding their cognitive functioning. METHODS Thirty-seven patients were included in this study. Cognitive functioning was measured by means of a broad cognitive screener preoperatively, days after surgery and months after surgery in patients who underwent awake brain tumor surgery with cognitive monitoring. The cognitive screener included tests for object naming, reading, attention span, working memory, inhibition, inhibition/switching, and visuoperception. We performed a Friedman ANOVA to analyze on group level. RESULTS Overall, no significant differences were found between preoperative cognitive functioning, early postoperative cognitive functioning, and late postoperative cognitive functioning, except for performances on the inhibition task. Directly after surgery, patients were significantly slower on this task. However, in the following months after surgery, they returned to their preoperative level. CONCLUSION The timeline of cognitive functioning after awake tumor surgery appeared overall stable in the early and late postoperative phase, except for inhibition, which is more difficult in the first days after awake brain tumor surgery. This more detailed timeline of cognitive functioning, in combination with future research, can possibly be contributing in informing patients and caregivers what to expect after awake brain tumor surgery.
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Affiliation(s)
- A.M. de Sain
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - M.H.M. Mantione
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - I.M.C. Huenges Wajer
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - M.J.E. van Zandvoort
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - P.W.A. Willems
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - P.A. Robe
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - C. Ruis
- Department of Experimental Psychology, Utrecht University, Heidelberglaan 1, 3584 CS Utrecht, the Netherlands
- Department of Neurology & Neurosurgery, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
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10
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Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA. A lung-specific mutational signature enables inference of viral and bacterial respiratory niche. Microb Genom 2023; 9. [PMID: 37185044 DOI: 10.1099/mgen.0.001018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luis M Polo
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Maria Soledad Alvarez
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Ye Cheng
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
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11
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 2022; 610:154-160. [PMID: 35952712 PMCID: PMC9534748 DOI: 10.1038/s41586-022-05200-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine and Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Kamran Khan
- BlueDot, Toronto, Ontario, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario, Canada
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.
- Pandemic Sciences Institute, University of Oxford, Oxford, UK.
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12
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Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Makatini Z, Moyo S, Amoako DG, Baxter C, Althaus CL, Anyaneji UJ, Kekana D, Viana R, Giandhari J, Lessells RJ, Maponga T, Maruapula D, Choga W, Matshaba M, Mbulawa MB, Msomi N, Naidoo Y, Pillay S, Sanko TJ, San JE, Scott L, Singh L, Magini NA, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht FK, Venter M, Chiloane G, McIntyre C, O'Toole A, Ruis C, Peacock TP, Roemer C, Kosakovsky Pond SL, Williamson C, Pybus OG, Bhiman JN, Glass A, Martin DP, Jackson B, Rambaut A, Laguda-Akingba O, Gaseitsiwe S, von Gottberg A, de Oliveira T. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med 2022; 28:1785-1790. [PMID: 35760080 PMCID: PMC9499863 DOI: 10.1038/s41591-022-01911-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - 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
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - 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
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 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
| | - Dikeledi Kekana
- 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
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Wonderful Choga
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Mpaphi B Mbulawa
- 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
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 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
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 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, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nonkululeko A Magini
- 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, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Graeme Dor
- National Priority Program of the National Health Laboratory Service, 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
| | - 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
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florette K Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Georginah Chiloane
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Caitlyn McIntyre
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - 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 N 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
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Lancet Laboratories, 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
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
| | - 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
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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13
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Gutierrez B, Castelán Sánchez HG, Candido DDS, Jackson B, Fleishon S, Houzet R, Ruis C, Delaye L, Faria NR, Rambaut A, Pybus OG, Escalera-Zamudio M. Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America. Cell Host Microbe 2022; 30:1112-1123.e3. [PMID: 35853454 PMCID: PMC9212848 DOI: 10.1016/j.chom.2022.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/18/2022] [Accepted: 06/16/2022] [Indexed: 02/09/2023]
Abstract
Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation thus far. Here, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages to investigate the possibility of virus recombination among them. Our analyses reveal well-supported phylogenetic differences between the Orf1ab region encoding viral non-structural proteins and the rest of the genome, including Spike (S) protein and remaining reading frames. By accounting for several deletions in NSP6, Orf3a, and S, we conclude that the B.1.628 major cluster, now designated as lineage XB, originated from a recombination event between viruses of B.1.631 and B.1.634 lineages. This scenario is supported by the spatiotemporal distribution of these lineages across the USA and Mexico during 2021, suggesting that the recombination event originated in this geographical region. This event raises important questions regarding the role and potential effects of recombination on SARS-CoV-2 evolution.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
| | - Hugo G Castelán Sánchez
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Darlan da Silva Candido
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Luis Delaye
- Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México; Departamento de Ingeniería Genética, Unidad Irapuato, CINVESTAV, Irapuato, Mexico
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK; Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK; The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK; Department of Pathobiology, Royal Veterinary College, London, UK.
| | - Marina Escalera-Zamudio
- Department of Zoology, University of Oxford, Oxford, UK; Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex), México.
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14
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. medRxiv 2021:2021.12.14.21267606. [PMID: 34981069 PMCID: PMC8722612 DOI: 10.1101/2021.12.14.21267606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases 1-3 . The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions 4,5 . Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta's invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- contributed equally as first authors
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Rosario Evans Pena
- Department of Zoology, University of Oxford, Oxford, UK
- contributed equally as first authors
| | - Ben C Lambert
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - David M Aanensen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
- jointly supervised this work
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- jointly supervised this work
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- jointly supervised this work
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15
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McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O'Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Res Sq 2021:rs.3.rs-1159614. [PMID: 34981043 PMCID: PMC8722606 DOI: 10.21203/rs.3.rs-1159614/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations; however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta’s invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.
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Affiliation(s)
- John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sumali Bajaj
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Ben C Lambert
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Rhys Inward
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Samir Bhatt
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Erik Volz
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Neo Wu
- Google, Mountain View, CA, USA
| | | | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | | | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- UK Health Security Agency, London, UK
| | | | | | | | | | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre of Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Isaac I Bogoch
- Divisions of Internal Medicine & Infectious Diseases, Toronto General Hospital, University Health Network, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
| | - Kamran Khan
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | | | | | - David M Aanensen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Thomas Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff, UK
- Quadram Institute, Norwich, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Marc A Suchard
- Departments of Biostatistics, Biomathematics and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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16
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Beale MA, Marks M, Cole MJ, Lee MK, Pitt R, Ruis C, Balla E, Crucitti T, Ewens M, Fernández-Naval C, Grankvist A, Guiver M, Kenyon CR, Khairullin R, Kularatne R, Arando M, Molini BJ, Obukhov A, Page EE, Petrovay F, Rietmeijer C, Rowley D, Shokoples S, Smit E, Sweeney EL, Taiaroa G, Vera JH, Wennerås C, Whiley DM, Williamson DA, Hughes G, Naidu P, Unemo M, Krajden M, Lukehart SA, Morshed MG, Fifer H, Thomson NR. Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis. Nat Microbiol 2021; 6:1549-1560. [PMID: 34819643 PMCID: PMC8612932 DOI: 10.1038/s41564-021-01000-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022]
Abstract
Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.
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Affiliation(s)
- Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Michael Marks
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK
| | - Michelle J Cole
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Min-Kuang Lee
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Rachel Pitt
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Christopher Ruis
- Molecular Immunity Unit, MRC-Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eszter Balla
- Bacterial STIs Reference Laboratory, Department of Bacteriology, National Public Health Centre, Budapest, Hungary
| | - Tania Crucitti
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Michael Ewens
- Brotherton Wing Clinic, Brotherton Wing, Leeds General Infirmary, Leeds, UK
| | - Candela Fernández-Naval
- Microbiology Department, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Grankvist
- National Reference Laboratory for STIs, Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Malcolm Guiver
- Laboratory Network, Manchester, UK Health Security Agency, Manchester Royal Infirmary, Manchester, UK
| | - Chris R Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerpen, Belgium
| | - Rafil Khairullin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ranmini Kularatne
- Centre for HIV and STI, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Maider Arando
- STI Unit Vall d'Hebron-Drassanes, Infectious Diseases Department, Hospital Vall d'Hebron, Barcelona, Spain
| | - Barbara J Molini
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrey Obukhov
- Tuvan Republican Skin and Venereal Diseases Dispensary, Ministry of Health of Tuva Republic, Kyzyl, Russia
| | - Emma E Page
- Virology Department, Old Medical School, Leeds Teaching Hospitals Trust, Leeds, UK
| | - Fruzsina Petrovay
- Bacterial STIs Reference Laboratory, Department of Bacteriology, National Public Health Centre, Budapest, Hungary
| | | | | | | | - Erasmus Smit
- Clinical Microbiology Department, Queen Elizabeth Hospital, Birmingham, UK
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Emma L Sweeney
- The University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jaime H Vera
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Christine Wennerås
- National Reference Laboratory for STIs, Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Prenilla Naidu
- Alberta Precision Laboratories, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mel Krajden
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sheila A Lukehart
- Departments of Medicine/Infectious Diseases and Global Health, University of Washington, Seattle, WA, USA
| | - Muhammad G Morshed
- British Columbia Centre for Disease Control, Public Health Laboratory, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Helen Fifer
- Blood Safety, Hepatitis, STI and HIV Division, UK Health Security Agency, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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17
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Ruis C, Bryant JM, Bell SC, Thomson R, Davidson RM, Hasan NA, van Ingen J, Strong M, Floto RA, Parkhill J. Dissemination of Mycobacterium abscessus via global transmission networks. Nat Microbiol 2021; 6:1279-1288. [PMID: 34545208 PMCID: PMC8478660 DOI: 10.1038/s41564-021-00963-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023]
Abstract
Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of global transmission networks of M. abscessus. How and when these clones emerged and spread globally is unclear. Here, we use evolutionary analyses of isolates from individuals both with and without CF to reconstruct the population history, spatiotemporal spread and recent transmission networks of the DCCs. We demonstrate synchronous expansion of six unrelated DCCs in the 1960s, a period associated with major changes in CF care and survival. Each of these clones has spread globally as a result of rare intercontinental transmission events. We show that the DCCs, but not environmentally acquired isolates, exhibit a specific smoking-associated mutational signature and that current transmission networks include individuals both with and without CF. We therefore propose that the DCCs initially emerged in non-CF populations but were then amplified and spread through the CF community. While individuals with CF are probably the most permissive host, non-CF individuals continue to play a key role in transmission networks and may facilitate long-distance transmission.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Scott C Bell
- Children's Health Research Institute, The University of Queensland, Brisbane, Australia
- Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | - Rachel Thomson
- Gallipoli Medical Research Institute, The University of Queensland, Brisbane, Australia
| | - Rebecca M Davidson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Nabeeh A Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jakko van Ingen
- Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK.
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK.
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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18
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Kraemer MUG, Hill V, Ruis C, Dellicour S, Bajaj S, McCrone JT, Baele G, Parag KV, Battle AL, Gutierrez B, Jackson B, Colquhoun R, O'Toole Á, Klein B, Vespignani A, Volz E, Faria NR, Aanensen DM, Loman NJ, du Plessis L, Cauchemez S, Rambaut A, Scarpino SV, Pybus OG. Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science 2021; 373:889-895. [PMID: 34301854 PMCID: PMC9269003 DOI: 10.1126/science.abj0113] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022]
Abstract
Understanding the causes and consequences of the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern is crucial to pandemic control yet difficult to achieve because they arise in the context of variable human behavior and immunity. We investigated the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based polymerase chain reaction data. We identified a multistage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explored how B.1.1.7 spread was shaped by nonpharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.
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Affiliation(s)
- Moritz U G Kraemer
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
| | - Verity Hill
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Department of Zoology, University of Oxford, Oxford, UK
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
| | - Simon Dellicour
- Network Science Institute, Northeastern University, Boston, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sumali Bajaj
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - John T McCrone
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Guy Baele
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Kris V Parag
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Anya Lindström Battle
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bernardo Gutierrez
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ben Jackson
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Áine O'Toole
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Brennan Klein
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Alessandro Vespignani
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Network Science Institute, Northeastern University, Boston, USA
| | - Erik Volz
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Nuno R Faria
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - David M Aanensen
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J Loman
- Molecular Immunity Unit, Department of Medicine, Cambridge University, Cambridge, UK
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Louis du Plessis
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
- Department of Zoology, University of Oxford, Oxford, UK
| | - Simon Cauchemez
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Andrew Rambaut
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel V Scarpino
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
- Network Science Institute, Northeastern University, Boston, USA
- Vermont Complex Systems Center, University of Vermont, Burlington, USA
- Santa Fe Institute, Santa Fe, USA
| | - Oliver G Pybus
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil.
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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19
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Bryant JM, Brown KP, Burbaud S, Everall I, Belardinelli JM, Rodriguez-Rincon D, Grogono DM, Peterson CM, Verma D, Evans IE, Ruis C, Weimann A, Arora D, Malhotra S, Bannerman B, Passemar C, Templeton K, MacGregor G, Jiwa K, Fisher AJ, Blundell TL, Ordway DJ, Jackson M, Parkhill J, Floto RA. Stepwise pathogenic evolution of Mycobacterium abscessus. Science 2021; 372:372/6541/eabb8699. [PMID: 33926925 DOI: 10.1126/science.abb8699] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.
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Affiliation(s)
- Josephine M Bryant
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Karen P Brown
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Sophie Burbaud
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Isobel Everall
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Wellcome Sanger Institute, Hinxton, UK
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Daniela Rodriguez-Rincon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dorothy M Grogono
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Chelsea M Peterson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Deepshikha Verma
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Ieuan E Evans
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Aaron Weimann
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Divya Arora
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.,Scientific Computing Department, Science and Technology Facilities Council, Harwell, UK
| | - Bridget Bannerman
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.,University of Cambridge Centre for AI in Medicine, Cambridge, UK
| | - Charlotte Passemar
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kerra Templeton
- Queen Elizabeth University Hospital, NHS Greater Glasgow & Clyde, Glasgow, Scotland, UK
| | - Gordon MacGregor
- Queen Elizabeth University Hospital, NHS Greater Glasgow & Clyde, Glasgow, Scotland, UK
| | - Kasim Jiwa
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute and Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Diane J Ordway
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins CO, USA
| | - Julian Parkhill
- Wellcome Sanger Institute, Hinxton, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK. .,University of Cambridge Centre for AI in Medicine, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
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20
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Rambaut A, Holmes EC, O'Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L, Pybus OG. Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2021; 6:415. [PMID: 33514928 PMCID: PMC7845574 DOI: 10.1038/s41564-021-00872-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An Addendum to this paper has been published: https://doi.org/10.1038/s41564-021-00872-5.
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Affiliation(s)
- Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia.
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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21
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du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021; 371:708-712. [PMID: 33419936 PMCID: PMC7877493 DOI: 10.1126/science.abf2946] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
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Affiliation(s)
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Jordan Ashworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas R Connor
- School of Biosciences, Cardiff University, Cardiff, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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22
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Ruis C, Lindesmith LC, Mallory ML, Brewer-Jensen PD, Bryant JM, Costantini V, Monit C, Vinjé J, Baric RS, Goldstein RA, Breuer J. Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence. Virus Evol 2020; 6:veaa067. [PMID: 33381305 PMCID: PMC7751145 DOI: 10.1093/ve/veaa067] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesized that new GII.4 pandemic viruses arise when previously circulating pandemic or pre-pandemic variants undergo substitutions in antigenic regions that enable evasion of host population immunity, as described by conventional models of antigenic drift. In contrast, we show here that the acquisition of new genetic and antigenic characteristics cannot be the proximal driver of new pandemics. Pandemic GII.4 viruses diversify and spread over wide geographical areas over several years prior to simultaneous pandemic emergence of multiple lineages, indicating that the necessary sequence changes must have occurred before diversification, years prior to pandemic emergence. We confirm this result through serological assays of reconstructed ancestral virus capsids, demonstrating that by 2003, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics.
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Affiliation(s)
- Christopher Ruis
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Lisa C Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Josephine M Bryant
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Veronica Costantini
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christopher Monit
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK.,Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children, London, UK
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23
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Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 2020; 21:180. [PMID: 32698896 PMCID: PMC7376924 DOI: 10.1186/s13059-020-02090-4] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/02/2020] [Indexed: 02/03/2023] Open
Abstract
Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .
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Affiliation(s)
- Gerry Tonkin-Hill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK. .,Department of Biostatistics, University of Oslo, Blindern, 0317, Norway.
| | - Neil MacAlasdair
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Christopher Ruis
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Medical Research Council (MRC)-Laboratory of Molecular Biology, Cambridge, UK
| | - Aaron Weimann
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Medical Research Council (MRC)-Laboratory of Molecular Biology, Cambridge, UK.,European Bioinformatics Institute, Cambridge, UK
| | - Gal Horesh
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK
| | | | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Simon D W Frost
- Microsoft Research, Redmond, 98052, WA, USA.,London School of Hygiene & Tropical Medicine, London, UK
| | - Jukka Corander
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.,Department of Biostatistics, University of Oslo, Blindern, 0317, Norway.,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, 00014, Finland
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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24
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Domman D, Ruis C, Dorman MJ, Shakya M, Chain PSG. Novel Insights Into the Spread of Enteric Pathogens Using Genomics. J Infect Dis 2020; 221:S319-S330. [PMID: 31538189 DOI: 10.1093/infdis/jiz220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/19/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daryl Domman
- Bioscience Division, Los Alamos National Laboratory, New Mexico
| | - Christopher Ruis
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, New Mexico
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25
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Monit C, Morris ER, Ruis C, Szafran B, Thiltgen G, Tsai MHC, Mitchison NA, Bishop KN, Stoye JP, Taylor IA, Fassati A, Goldstein RA. Positive selection in dNTPase SAMHD1 throughout mammalian evolution. Proc Natl Acad Sci U S A 2019; 116:18647-18654. [PMID: 31451672 PMCID: PMC6744909 DOI: 10.1073/pnas.1908755116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The vertebrate protein SAMHD1 is highly unusual in having roles in cellular metabolic regulation, antiviral restriction, and regulation of innate immunity. Its deoxynucleoside triphosphohydrolase activity regulates cellular dNTP concentration, reducing levels below those required by lentiviruses and other viruses to replicate. To counter this threat, some primate lentiviruses encode accessory proteins that bind SAMHD1 and induce its degradation; in turn, positive diversifying selection has been observed in regions bound by these lentiviral proteins, suggesting that primate SAMHD1 has coevolved to evade these countermeasures. Moreover, deleterious polymorphisms in human SAMHD1 are associated with autoimmune disease linked to uncontrolled DNA synthesis of endogenous retroelements. Little is known about how evolutionary pressures affect these different SAMHD1 functions. Here, we examine the deeper history of these interactions by testing whether evolutionary signatures in SAMHD1 extend to other mammalian groups and exploring the molecular basis of this coevolution. Using codon-based likelihood models, we find positive selection in SAMHD1 within each mammal lineage for which sequence data are available. We observe positive selection at sites clustered around T592, a residue that is phosphorylated to regulate SAMHD1 activity. We verify experimentally that mutations within this cluster affect catalytic rate and lentiviral restriction, suggesting that virus-host coevolution has required adaptations of enzymatic function. Thus, persistent positive selection may have involved the adaptation of SAMHD1 regulation to balance antiviral, metabolic, and innate immunity functions.
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Affiliation(s)
- Christopher Monit
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Bart Szafran
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Grant Thiltgen
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Ming-Han Chloe Tsai
- Retroviral Replication Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - N Avrion Mitchison
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom
| | - Kate N Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom;
| | - Richard A Goldstein
- Division of Infection and Immunity, University College London, WC1E 6BT London, United Kingdom;
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26
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Brown LAK, Ruis C, Clark I, Roy S, Brown JR, Albuquerque AS, Patel SY, Miller J, Karim MY, Dervisevic S, Moore J, Williams CA, Cudini J, Moreira F, Neild P, Seneviratne SL, Workman S, Toumpanakis C, Atkinson C, Burns SO, Breuer J, Lowe DM. A comprehensive characterization of chronic norovirus infection in immunodeficient hosts. J Allergy Clin Immunol 2019; 144:1450-1453. [PMID: 31415785 PMCID: PMC6843911 DOI: 10.1016/j.jaci.2019.07.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/11/2019] [Accepted: 07/18/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Li-An K Brown
- Department of Infectious Diseases, Royal Free London NHS Foundation Trust, London, United Kingdom; Department of Microbiology, Whittington Health NHS Trust, London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, London, United Kingdom; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Medical Research Council (MRC)-Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ian Clark
- Department of Histopathology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Adriana S Albuquerque
- Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, United Kingdom
| | - Smita Y Patel
- Oxford University Hospitals NHS Trust and NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Joanne Miller
- Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, Surrey, United Kingdom
| | - Mohammed Yousuf Karim
- Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, Surrey, United Kingdom; Pathology, Sidra Medicine, Doha, Qatar
| | - Samir Dervisevic
- Norfolk and Norwich University Hospital, Norwich, Norfolk, United Kingdom
| | - Jennifer Moore
- Norfolk and Norwich University Hospital, Norwich, Norfolk, United Kingdom
| | - Charlotte A Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Fernando Moreira
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Penny Neild
- St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Suranjith L Seneviratne
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sarita Workman
- Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Christos Toumpanakis
- Department of Gastroenterology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Claire Atkinson
- Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, United Kingdom
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, United Kingdom; Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - David M Lowe
- Institute of Immunity and Transplantation, University College London, Royal Free Campus, London, United Kingdom; Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom.
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27
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Ruis C, Brown LAK, Roy S, Atkinson C, Williams R, Burns SO, Yara-Romero E, Jacobs M, Goldstein R, Breuer J, Lowe DM. Mutagenesis in Norovirus in Response to Favipiravir Treatment. N Engl J Med 2018; 379:2173-2176. [PMID: 30485769 DOI: 10.1056/nejmc1806941] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Li-An K Brown
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sunando Roy
- University College London, London, United Kingdom
| | | | | | | | | | - Michael Jacobs
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | | | | | - David M Lowe
- University College London, London, United Kingdom
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28
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van Kessel E, Snijders TJ, Baumfalk AE, Ruis C, van Baarsen KM, Broekman ML, van Zandvoort MJE, Robe PA. P01.146 Neurocognitive changes after awake surgery for diffuse glioma; a retrospective cohort study. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- E van Kessel
- University Medical Center Utrecht, Utrecht, Netherlands
| | - T J Snijders
- University Medical Center Utrecht, Utrecht, Netherlands
| | - A E Baumfalk
- University Medical Center Utrecht, Utrecht, Netherlands
| | - C Ruis
- University Medical Center Utrecht, Utrecht, Netherlands
| | | | - M L Broekman
- Leiden University Medical Center, Leiden, Netherlands
- Haaglanden Medical Center, The Hague, Netherlands
| | - M J E van Zandvoort
- University Medical Center Utrecht, Utrecht, Netherlands
- Helmhotz Institute, Utrecht University, Utrecht, Netherlands
| | - P A Robe
- University Medical Center Utrecht, Utrecht, Netherlands
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29
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Ruis C, Roy S, Brown JR, Allen DJ, Goldstein RA, Breuer J. The emerging GII.P16-GII.4 Sydney 2012 norovirus lineage is circulating worldwide, arose by late-2014 and contains polymerase changes that may increase virus transmission. PLoS One 2017; 12:e0179572. [PMID: 28662035 PMCID: PMC5491022 DOI: 10.1371/journal.pone.0179572] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/31/2017] [Indexed: 11/18/2022] Open
Abstract
Noroviruses are a leading cause of human gastroenteritis worldwide. The norovirus genotype GII.4 is the most prevalent genotype in the human population and has caused six pandemics since 1995. A novel norovirus lineage containing the GII.P16 polymerase and pandemic GII.4 Sydney 2012 capsid was recently detected in Asia and Germany. We demonstrate that this lineage is also circulating within the UK and USA and has been circulating since October 2014 or earlier. While the lineage does not contain unique substitutions in the capsid, it does contain polymerase substitutions close to positions known to influence polymerase function and virus transmission. These polymerase substitutions are shared with a GII.P16-GII.2 virus that dominated outbreaks in Germany in Winter 2016. We suggest that the substitutions in the polymerase may have resulted in a more transmissible virus and the combination of this polymerase and the pandemic GII.4 capsid may result in a highly transmissible virus. Further surveillance efforts will be required to determine whether the GII.P16-GII.4 Sydney 2012 lineage increases in frequency over the coming months.
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Affiliation(s)
- Christopher Ruis
- Division of Infection and Immunity, University College London, London, United Kingdom
- * E-mail:
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Julianne R. Brown
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children, London, United Kingdom
| | - David J. Allen
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Virus Reference Department, National Infections Service, Public Health England, London, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, United Kingdom
| | - Richard A. Goldstein
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children, London, United Kingdom
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30
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Brown JR, Roy S, Ruis C, Yara Romero E, Shah D, Williams R, Breuer J. Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. J Clin Microbiol 2016; 54:2530-7. [PMID: 27487952 PMCID: PMC5035417 DOI: 10.1128/jcm.01052-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 01/11/2023] Open
Abstract
Norovirus full-genome sequencing is challenging due to sequence heterogeneity among genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and transcriptome sequencing (RNA-Seq), which nonspecifically sequences all RNA, including host and bacterial RNA, in stool specimens. Target enrichment uses a panel of custom-designed 120-mer RNA baits that are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, which overcomes the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimize the sequencing of nontarget RNA. SureSelect target enrichment and Illumina sequencing were used to sequence full genomes from 507 norovirus-positive stool samples with reverse transcription-real-time PCR cycle threshold (CT) values of 10 to 43. Sequencing on an Illumina MiSeq system in batches of 48 generated, on average, 81% on-target reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, and GII.17. When outliers were accounted for, we generated >80% genome coverage for all positive samples, regardless of CT values. A total of 164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain; 164/164 samples were successfully sequenced, compared to 158/164 samples that were amplified by PCR. Four of the samples that failed capsid PCR analysis had low titers, which suggests that target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity among norovirus genomes.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Erika Yara Romero
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Divya Shah
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Judy Breuer
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom Division of Infection and Immunity, University College London, London, United Kingdom
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Brown J, Roy S, Shah D, Ruis C, Williams R, Yara Romero E, Breuer J. Norovirus molecular epidemiology in a paediatric UK hospital: Unexpected diversity, seasonality and sources of infection. J Clin Virol 2016. [DOI: 10.1016/j.jcv.2016.08.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Brown J, Ruis C, Tutill H, Depledge D, Christiansen M, Breuer J. SureSelect target enrichment: A robust and sensitive method for sequencing of whole norovirus genomes direct from clinical specimens. J Clin Virol 2015. [DOI: 10.1016/j.jcv.2015.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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