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  1. Artikel ; Online: Asfarviruses and Closely Related Giant Viruses.

    Hannat, Sihem / La Scola, Bernard / Andreani, Julien / Aherfi, Sarah

    Viruses

    2023  Band 15, Heft 4

    Abstract: Acanthamoeba polyphaga ... ...

    Abstract Acanthamoeba polyphaga mimivirus
    Mesh-Begriff(e) Swine ; Animals ; Giant Viruses ; Phylogeny ; African Swine Fever Virus/genetics ; Viruses/genetics ; Mimiviridae/genetics ; DNA Viruses/genetics ; Genome, Viral
    Sprache Englisch
    Erscheinungsdatum 2023-04-20
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15041015
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: High penetration of doravirine in the central nervous system: What are the benefits?

    Banti, Estelle / Dhiver, Catherine / Aherfi, Sarah / Motte, Anne / Solas, Caroline

    Infectious diseases now

    2021  Band 52, Heft 2, Seite(n) 116–117

    Mesh-Begriff(e) Central Nervous System ; Humans ; Pyridones ; Triazoles/therapeutic use
    Chemische Substanzen Pyridones ; Triazoles ; doravirine (913P6LK81M)
    Sprache Englisch
    Erscheinungsdatum 2021-10-01
    Erscheinungsland France
    Dokumenttyp Letter
    ISSN 2666-9919
    ISSN (online) 2666-9919
    DOI 10.1016/j.idnow.2021.09.006
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  3. Artikel: Fatal Fulminant Hepatitis E in a Diabetic Patient on Metformin.

    Peroni, Erika / Mora, Pierre / Motte, Anne / Gerolami, René / Aherfi, Sarah / Colson, Philippe

    Diagnostics (Basel, Switzerland)

    2022  Band 12, Heft 10

    Abstract: Hepatitis E is mostly autochthonous in Western developed countries, eating pig-derived products being the most frequently documented source. Hepatitis E virus (HEV) infection is usually asymptomatic or self-limiting, but it can cause acute liver failure. ...

    Abstract Hepatitis E is mostly autochthonous in Western developed countries, eating pig-derived products being the most frequently documented source. Hepatitis E virus (HEV) infection is usually asymptomatic or self-limiting, but it can cause acute liver failure. HEV serological testing was performed using EUROIMMUN immunoenzymatic assays. HEV RNA in the serum was determined using an in-house real-time reverse transcriptase PCR procedure. The HEV genotype was determined through phylogenetic analysis after Sanger sequencing was performed using an in-house procedure. The case patient, an immunocompetent patient in his 60s with type 2 diabetes and no documented chronic liver disease, was hospitalized in February 2021 in an intensive care unit due to an initially unexplained coma. He presented metformin overdose and fulminant hepatitis E (HEV RNA in the serum was 4,140,000 copies/mL) that evolved toward death. The HEV genotype was 3f. We identified eight previous hepatitis E in diabetic patients, but with no metformin excessive plasma concentration, in the literature. Three patients were liver transplant recipients and three died. HEV infection can be severe and life-threatening in diabetic patients, which warrants HEV testing in this special population in the case of an altered general condition and/or liver cytolysis.
    Sprache Englisch
    Erscheinungsdatum 2022-09-30
    Erscheinungsland Switzerland
    Dokumenttyp Case Reports
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics12102385
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  4. Artikel ; Online: Genome Sequences of Two New Pandoravirus Strains Isolated from Brazil and France.

    Brahim Belhaouari, Djamal / Hannat, Sihem / Rodrigues, Rodrigo / Aherfi, Sarah / La Scola, Bernard / Andreani, Julien

    Microbiology resource announcements

    2022  Band 11, Heft 7, Seite(n) e0013122

    Abstract: Pandoraviruses are giant viruses of amoebas with a wide range of genome sizes (1.5 to 2.5 Mbp) and 1-μm ovoid viral particles. Here, we report the isolation, genome sequencing, and annotation of two new strains from the proposed family Pandoraviridae: ... ...

    Abstract Pandoraviruses are giant viruses of amoebas with a wide range of genome sizes (1.5 to 2.5 Mbp) and 1-μm ovoid viral particles. Here, we report the isolation, genome sequencing, and annotation of two new strains from the proposed family Pandoraviridae: Pandoravirus belohorizontensis and Pandoravirus aubagnensis.
    Sprache Englisch
    Erscheinungsdatum 2022-06-22
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00131-22
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  5. Artikel ; Online: Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences.

    Bader, Wahiba / Delerce, Jeremy / Aherfi, Sarah / La Scola, Bernard / Colson, Philippe

    International journal of molecular sciences

    2022  Band 23, Heft 24

    Abstract: The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been ... ...

    Abstract The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of the mapping of NGS reads. We compared intra-sample genetic diversity and global genetic diversity available from Nextstrain. Hierarchical clustering of all samples based on the intra-sample genetic diversity was performed and visualized with the Morpheus web application. NGS mapping data from 110 SARS-CoV-2-positive respiratory samples characterized by a mean depth of 169 NGS reads/nucleotide position and for which consensus genomes that had been obtained were classified into 15 viral lineages were analyzed. Mean intra-sample nucleotide diversity was 0.21 ± 0.65%, and 5357 positions (17.9%) exhibited significant (>4%) diversity, in ≥2 genomes for 1730 (5.8%) of them. ORF10, spike, and N genes had the highest number of positions exhibiting diversity (0.56%, 0.34%, and 0.24%, respectively). Nine hot spots of intra-sample diversity were identified in the SARS-CoV-2 NSP6, NSP12, ORF8, and N genes. Hierarchical clustering delineated a set of six genomes of different lineages characterized by 920 positions exhibiting intra-sample diversity. In addition, 118 nucleotide positions (0.4%) exhibited diversity at both intra- and inter-patient levels. Overall, the present study illustrates that the SARS-CoV-2 consensus genome sequences are only an incomplete and imperfect representation of the entire viral population infecting a patient, and that quasispecies analysis may allow deciphering more accurately the viral evolutionary pathways.
    Mesh-Begriff(e) Humans ; SARS-CoV-2/genetics ; Quasispecies ; COVID-19/epidemiology ; COVID-19/genetics ; Pandemics ; Consensus ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Nucleotides
    Chemische Substanzen Nucleotides
    Sprache Englisch
    Erscheinungsdatum 2022-12-10
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232415658
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  6. Artikel ; Online: Hepatitis delta treatment with bulevirtide in real life: a case report.

    Giordan, Marc-Antoine / Bengone Abogourin, Jessica Grace / Aherfi, Sarah / Allemand, Isabelle / Colson, Philippe

    International journal of antimicrobial agents

    2022  Band 59, Heft 5, Seite(n) 106562

    Mesh-Begriff(e) Antiviral Agents/therapeutic use ; Hepatitis B virus ; Hepatitis Delta Virus ; Humans ; Lipopeptides
    Chemische Substanzen Antiviral Agents ; Lipopeptides ; bulevirtide
    Sprache Englisch
    Erscheinungsdatum 2022-03-04
    Erscheinungsland Netherlands
    Dokumenttyp Letter ; Comment
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2022.106562
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  7. Artikel ; Online: Simple Wastewater Preparation Protocol Applied to Monitor the Emergence of the Omicron 21L/BA.2 Variant by Genome Sequencing.

    Wurtz, Nathalie / Boussier, Maelle / Souville, Louis / Penant, Gwilherm / Lacoste, Alexandre / Colson, Philippe / La Scola, Bernard / Aherfi, Sarah

    Viruses

    2023  Band 15, Heft 2

    Abstract: Detecting and monitoring viruses in wastewater samples have been reported as useful ways of tracking SARS-CoV-2 epidemic trends. However, there is currently no unanimously recognised method of processing samples to identify and quantify SARS-CoV-2 ... ...

    Abstract Detecting and monitoring viruses in wastewater samples have been reported as useful ways of tracking SARS-CoV-2 epidemic trends. However, there is currently no unanimously recognised method of processing samples to identify and quantify SARS-CoV-2 variants in wastewater. We aimed to implement a method that was as simple as possible in order to be used universally. In a study performed between January 2022 and June 2022 in the city of Marseille, France, we first evaluated the impact of the sample preservation strategy. We then compared ultracentrifugation to ultrafiltration and several steps of filtration to determine the optimal approach for virus concentration. As a proof-of-concept, the definitive protocol was applied to next-generation sequencing of SARS-CoV-2 in wastewater to monitor the emergence of the Omicron variant in the city. For sewage water to be processed in the week following the sampling, storage at +4 °C is sufficient, with less than 1 Ct loss. Filtration with a 5 µm syringe filter, then with a 0.8 µm filtration unit, followed by ultrafiltration was the optimal protocol, leading to an average increase of 3.24 Ct when the starting Ct was on average 38 in the wastewater. This made it possible to observe the emergence of the Omicron 21L/BA.2 variant after Omicron 21K/BA.1 by genome sequencing over a period ranging from 20 February to 10 April 2022 in agreement with observations based on patient data. To conclude, by using a simple method requiring only basic filters and a centrifuge as equipment, it is possible to accurately track the relative incidence rates and the emergence of SARS-CoV-2 variants based on sewage samples.
    Mesh-Begriff(e) Humans ; SARS-CoV-2/genetics ; Wastewater ; Sewage ; COVID-19/diagnosis ; COVID-19/epidemiology
    Chemische Substanzen Wastewater ; Sewage
    Sprache Englisch
    Erscheinungsdatum 2023-01-17
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15020268
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Hepatitis B Virus Genomics Knocking at the Door of Routine Diagnostic Laboratories.

    Colson, Philippe / Borentain, Patrick / Ravaux, Isabelle / Aherfi, Sarah

    The Journal of infectious diseases

    2019  Band 221, Heft 6, Seite(n) 1026–1029

    Mesh-Begriff(e) Hepatitis B/diagnosis ; Hepatitis B Antibodies ; Hepatitis B virus/genetics ; Humans ; Metagenomics
    Chemische Substanzen Hepatitis B Antibodies
    Sprache Englisch
    Erscheinungsdatum 2019-10-18
    Erscheinungsland United States
    Dokumenttyp Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiz544
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  9. Artikel ; Online: Isolation of 4000 SARS-CoV-2 shows that contagiousness is associated with viral load, not vaccine or symptomatic status.

    Boschi, Celine / Aherfi, Sarah / Houhamdi, Linda / Colson, Philippe / Raoult, Didier / Scola, Bernard La

    Emerging microbes & infections

    2021  Band 10, Heft 1, Seite(n) 2276–2278

    Abstract: Culture inoculation of 6722 nasopharyngeal samples since February 2020 allowed isolation of 3637 SARS-CoV-2 and confirmed that isolation rate is correlated to viral load, regardless symptomatology or vaccination status. Moreover, the delta variant is ... ...

    Abstract Culture inoculation of 6722 nasopharyngeal samples since February 2020 allowed isolation of 3637 SARS-CoV-2 and confirmed that isolation rate is correlated to viral load, regardless symptomatology or vaccination status. Moreover, the delta variant is associated with higher viral loads and therefore higher rates of viral isolation, explaining its greater contagiousness.
    Mesh-Begriff(e) Adult ; Aged ; Aged, 80 and over ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19/virology ; COVID-19 Vaccines/administration & dosage ; COVID-19 Vaccines/genetics ; COVID-19 Vaccines/immunology ; Female ; Humans ; Male ; Middle Aged ; Nasopharynx/virology ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Vaccination ; Viral Load
    Chemische Substanzen COVID-19 Vaccines
    Sprache Englisch
    Erscheinungsdatum 2021-11-18
    Erscheinungsland United States
    Dokumenttyp Letter
    ZDB-ID 2681359-2
    ISSN 2222-1751 ; 2222-1751
    ISSN (online) 2222-1751
    ISSN 2222-1751
    DOI 10.1080/22221751.2021.2008776
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  10. Artikel ; Online: SARS-CoV-2 Testing of Aircraft Wastewater Shows That Mandatory Tests and Vaccination Pass before Boarding Did Not Prevent Massive Importation of Omicron Variant into Europe.

    Le Targa, Lorlane / Wurtz, Nathalie / Lacoste, Alexandre / Penant, Gwilherm / Jardot, Priscilla / Annessi, Alexandre / Colson, Philippe / La Scola, Bernard / Aherfi, Sarah

    Viruses

    2022  Band 14, Heft 7

    Abstract: Background: Most new SARS-CoV-2 epidemics in France occurred following the importation from abroad of emerging viral variants. Currently, the risk of new variants being imported is controlled based on a negative screening test (PCR or antigenic) and ... ...

    Abstract Background: Most new SARS-CoV-2 epidemics in France occurred following the importation from abroad of emerging viral variants. Currently, the risk of new variants being imported is controlled based on a negative screening test (PCR or antigenic) and proof of up-to-date vaccine status, such as the International Air Transport Association travel pass.
    Methods: The wastewater from two planes arriving in Marseille (France) from Addis Ababa (Ethiopia) in December 2021 was tested by RT-PCR to detect SARS-CoV2 and screen for variants. These tests were carried out between landing and customs clearance and were then sequenced by MiSeq Illumina. Antigenic tests and sequencing by NovaSeq were carried out on respiratory samples collected from the 56 passengers on the second flight.
    Results: SARS-CoV-2 RNA suspected of being from the Omicron BA.1 variant was detected in the aircraft's wastewater. SARS-CoV2 RNA was detected in 11 [20%) passengers and the Omicron BA.1 variant was identified.
    Conclusion: Our work shows the efficiency of aircraft wastewater testing to detect SARS-CoV-2 cases among travellers and to identify the viral genotype. It also highlights the low efficacy of the current control strategy for flights entering France from outside Europe, which combines a requirement to produce a vaccine pass and proof of a negative test before boarding.
    Mesh-Begriff(e) Aircraft ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19 Testing ; Ethiopia ; Europe ; Humans ; RNA, Viral/analysis ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Vaccination ; Waste Water
    Chemische Substanzen RNA, Viral ; Waste Water
    Sprache Englisch
    Erscheinungsdatum 2022-07-09
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14071511
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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