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Article ; Online: Towards SARS-CoV-2 serotypes?

Simon-Loriere, Etienne / Schwartz, Olivier

2022 Volume 20, Issue 4, Page(s) 187–188

MeSH term(s)	COVID-19 ; Humans ; SARS-CoV-2 ; Serogroup ; Spike Glycoprotein, Coronavirus
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-02-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2139054-X
ISSN	1740-1534 ; 1740-1526
ISSN (online)	1740-1534
ISSN	1740-1526
DOI	10.1038/s41579-022-00708-x
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Article ; Online: SARS-CoV-2 Omicron emergence urges for reinforced One-Health surveillance.

Montagutelli, Xavier / van der Werf, Sylvie / Rey, Felix A / Simon-Loriere, Etienne

EMBO molecular medicine

2022 Volume 14, Issue 3, Page(s) e15558

Abstract: SARS-CoV-2 Omicron harbors substitutions in the receptor binding domain of the spike which strongly suggest its capacity to infect rodents. Wild animal reservoirs could favor the emergence of new variants with risks of spillback to humans and should be ... ...

Abstract	SARS-CoV-2 Omicron harbors substitutions in the receptor binding domain of the spike which strongly suggest its capacity to infect rodents. Wild animal reservoirs could favor the emergence of new variants with risks of spillback to humans and should be closely monitored.
MeSH term(s)	Animals ; COVID-19/epidemiology ; COVID-19/virology ; Humans ; One Health ; Population Surveillance ; Protein Binding ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-01-27
Publishing country	England
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202115558
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Article ; Online: Drivers of Dengue Intrahost Evolution.

Simon-Lorière, Etienne / Vignuzzi, Marco

Cell host & microbe

2017 Volume 22, Issue 3, Page(s) 260–261

Abstract: RNA viruses circulate as rapidly evolving swarms of related variants, and their evolutionary dynamics within hosts may be key to understanding virus emergence. In this issue of Cell Host & Microbe, Parameswaran et al. (2017) combine next-generation ... ...

Abstract	RNA viruses circulate as rapidly evolving swarms of related variants, and their evolutionary dynamics within hosts may be key to understanding virus emergence. In this issue of Cell Host & Microbe, Parameswaran et al. (2017) combine next-generation sequencing and functional studies to characterize viral populations in acute dengue infections.
MeSH term(s)	Dengue/virology ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; RNA Viruses
Language	English
Publishing date	2017-09-14
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	2278004-X
ISSN	1934-6069 ; 1931-3128
ISSN (online)	1934-6069
ISSN	1931-3128
DOI	10.1016/j.chom.2017.08.015
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Article ; Online: Humoral immune escape by current SARS-CoV-2 variants BA.2.86 and JN.1, December 2023.

Jeworowski, Lara M / Mühlemann, Barbara / Walper, Felix / Schmidt, Marie L / Jansen, Jenny / Krumbholz, Andi / Simon-Lorière, Etienne / Jones, Terry C / Corman, Victor M / Drosten, Christian

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2024 Volume 29, Issue 2

Abstract: Variant BA.2.86 and its descendant, JN.1, of SARS-CoV-2 are rising in incidence across Europe and globally. We isolated recent JN.1, BA.2.86, EG.5, XBB.1.5 and earlier variants. We tested live virus neutralisation of sera taken in September 2023 from ... ...

Abstract	Variant BA.2.86 and its descendant, JN.1, of SARS-CoV-2 are rising in incidence across Europe and globally. We isolated recent JN.1, BA.2.86, EG.5, XBB.1.5 and earlier variants. We tested live virus neutralisation of sera taken in September 2023 from vaccinated and exposed healthy persons (n = 39). We found clear neutralisation escape against recent variants but no specific pronounced escape for BA.2.86 or JN.1. Neutralisation escape corresponds to recent variant predominance but may not be causative of the recent upsurge in JN.1 incidence.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Europe/epidemiology ; Health Status ; Antibodies, Viral ; Antibodies, Neutralizing
Chemical Substances	Antibodies, Viral ; Antibodies, Neutralizing
Language	English
Publishing date	2024-01-12
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2024.29.2.2300740
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Article ; Online: SARS-CoV-2 infection in domestic rats after transmission from their infected owner

Montagutelli, Xavier / Decaudin, Bérénice / Beretta, Maxime / Mouquet, Hugo / Simon-Lorière, Etienne

bioRxiv

Abstract: We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that ... ...

Abstract	We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.
Keywords	covid19
Language	English
Publishing date	2022-10-13
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.10.13.512053
Database	COVID19

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Article ; Online: SARS-CoV-2 infection in domestic rats after transmission from their infected owner

Montagutelli, Xavier / Decaudin, Berenice / Beretta, Maxime / Mouquet, Hugo / Simon-Loriere, Etienne

bioRxiv

Abstract	We report the transmission of SARS-CoV-2 Omicron variant from a COVID-19 symptomatic individual to two domestic rats, one of which developed severe symptoms. Omicron carries several mutations which permit rodent infection. This report demonstrates that pet, and likely wild, rodents could therefore contribute to SARS-CoV-2 spread and evolution.
Keywords	covid19
Language	English
Publishing date	2022-10-13
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.10.13.512053
Database	COVID19

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Article ; Online: Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15.

Fernandez-Garcia, Maria Dolores / Simon-Loriere, Etienne / Kebe, Ousmane / Sakuntabhai, A / Ndiaye, Kader

Scientific reports

2020 Volume 10, Issue 1, Page(s) 6759

Abstract: Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To ... ...

Abstract	Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15.
MeSH term(s)	Genome, Viral/genetics ; Genomics ; Humans ; Metagenomics/methods ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Paralysis/genetics ; Paralysis/virology ; Parechovirus/genetics ; Parechovirus/isolation & purification ; Parechovirus/pathogenicity ; Sequence Analysis, DNA ; Whole Genome Sequencing
Language	English
Publishing date	2020-04-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-63467-w
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Article ; Online: Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages.

Touret, Franck / Giraud, Emilie / Bourret, Jérôme / Donati, Flora / Tran-Rajau, Jaouen / Chiaravalli, Jeanne / Lemoine, Frédéric / Agou, Fabrice / Simon-Lorière, Etienne / van der Werf, Sylvie / de Lamballerie, Xavier

iScience

2023 Volume 26, Issue 4, Page(s) 106413

Abstract: The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them ... ...

Abstract	The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1, and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1, and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1, and XBB variants.
Language	English
Publishing date	2023-03-15
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106413
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Article ; Online: Untargeted metagenomic sequencing identifies Toscana virus in patients with idiopathic meningitis, southern Spain, 2015 to 2019.

Gámbaro, Fabiana / Pérez, Ana Belén / Prot, Matthieu / Agüera, Eduardo / Baidaliuk, Artem / Sánchez-Seco, María Paz / Martínez-Martínez, Luis / Vázquez, Ana / Fernandez-Garcia, María Dolores / Simon-Loriere, Etienne

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2023 Volume 28, Issue 45

Abstract: BackgroundVarious pathogens, including bacteria, fungi, parasites, and viruses can lead to meningitis. Among viruses causing meningitis, Toscana virus (TOSV), a phlebovirus, is transmitted through sandfly bites. TOSV infection may be suspected if ... ...

Abstract	BackgroundVarious pathogens, including bacteria, fungi, parasites, and viruses can lead to meningitis. Among viruses causing meningitis, Toscana virus (TOSV), a phlebovirus, is transmitted through sandfly bites. TOSV infection may be suspected if patients with enterovirus- and herpesvirus-negative aseptic (non-bacterial) meningitis recall recent insect bites. Other epidemiological factors (season, rural area) may be considered. The broad range of possible meningitis aetiologies poses considerable diagnosis challenges. Untargeted metagenomic next-generation sequencing (mNGS) can potentially identify pathogens, which are not considered or detected in routine diagnostic panels.AimIn this retrospective, single-centre observational study, we investigated mNGS usefulness to understand the cause of meningitis when conventional approaches fail.MethodsCerebrospinal fluid (CSF) samples from patients hospitalised in southern Spain in 2015-2019 with aseptic meningitis and no aetiology found by conventional testing, were subjected to mNGS. Patients' demographic characteristics had been recorded and physicians had asked them about recent insect bites. Obtained viral genome sequences were phylogenetically analysed.ResultsAmong 23 idiopathic cases, TOSV was identified in eight (all male; median age: 39 years, range: 15-78 years). Five cases lived in an urban setting, three occurred in autumn and only one recalled insect bites. Phylogenetic analysis of TOSV segment sequences supported one intra-genotype reassortment event.ConclusionsOur study highlights the usefulness of mNGS for identifying viral pathogens directly in CSF. In southern Spain, TOSV should be considered regardless of recalling of insect bites or other epidemiological criteria. Detection of a disease-associated reassortant TOSV emphasises the importance of monitoring the spread and evolution of phleboviruses in Mediterranean countries.
MeSH term(s)	Humans ; Male ; Adult ; Sandfly fever Naples virus/genetics ; Insect Bites and Stings ; Phylogeny ; Retrospective Studies ; Spain/epidemiology ; Meningitis
Language	English
Publishing date	2023-11-09
Publishing country	Sweden
Document type	Observational Study ; Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2023.28.45.2200913
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Article ; Online: APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak.

Suspène, Rodolphe / Raymond, Kyle A / Boutin, Laetitia / Guillier, Sophie / Lemoine, Frédéric / Ferraris, Olivier / Tournier, Jean-Nicolas / Iseni, Frédéric / Simon-Lorière, Etienne / Vartanian, Jean-Pierre

The Journal of infectious diseases

2023 Volume 228, Issue 10, Page(s) 1421–1429

Abstract: Background: On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the 2 different lineages present in the 2021 and ... ...

Abstract	Background: On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the 2 different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5'GpA context, indicative of APOBEC3 cytidine deaminase activity. Methods: By using a sensitive polymerase chain reaction (differential DNA denaturation PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients. Results: We demonstrate that G->A hypermutated MPXV genomes can be recovered experimentally from APOBEC3 transfection followed by MPXV infection. Here, among the 7 human APOBEC3 cytidine deaminases (A3A-A3C, A3DE, A3F-A3H), only APOBEC3F was capable of extensively deaminating cytidine residues in MPXV genomes. Hyperedited genomes were also recovered in ∼42% of analyzed patients. Moreover, we demonstrate that substantial repair of these mutations occurs. Upon selection, corrected G->A mutations escaping drift loss contribute to the MPXV evolution observed in the current epidemic. Conclusions: Stochastic or transient overexpression of the APOBEC3F gene exposes the MPXV genome to a broad spectrum of mutations that may be modeling the mutational landscape after multiple cycles of viral replication.
MeSH term(s)	Humans ; Monkeypox virus/genetics ; Cytidine Deaminase/genetics ; Mutation ; Disease Outbreaks ; Cytidine ; Cytosine Deaminase/chemistry ; Cytosine Deaminase/genetics
Chemical Substances	Cytidine Deaminase (EC 3.5.4.5) ; Cytidine (5CSZ8459RP) ; APOBEC3F protein, human (EC 3.5.4.1) ; Cytosine Deaminase (EC 3.5.4.1)
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiad165
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