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Paronetto O, Allioux C, Diméglio C, Lobjois L, Jeanne N, Ranger N, Boineau J, Pucelle M, Demmou S, Abravanel F, Chapuy-Regaud S, Izopet J, Lhomme S. Characterization of virus‒host recombinant variants of the hepatitis E virus. J Virol 2024:e0029524. [PMID: 38712945 DOI: 10.1128/jvi.00295-24] [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] [Received: 02/13/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Hepatitis E virus is a single-strand, positive-sense RNA virus that can lead to chronic infection in immunocompromised patients. Virus-host recombinant variants (VHRVs) have been described in such patients. These variants integrate part of human genes into the polyproline-rich region that could introduce new post-translational modifications (PTMs), such as ubiquitination. The aim of this study was to characterize the replication capacity of different VHRVs, namely, RNF19A, ZNF787, KIF1B, EEF1A1, RNA18, RPS17, and RPL6. We used a plasmid encoding the Kernow strain, in which the fragment encoding the S17 insertion was deleted (Kernow p6 delS17) or replaced by fragments encoding the different insertions. The HEV RNA concentrations in the supernatants and the HepG2/C3A cell lysates were determined via RT-qPCR. The capsid protein ORF2 was immunostained. The effect of ribavirin was also assessed. The HEV RNA concentrations in the supernatants and the cell lysates were higher for the variants harboring the RNF19A, ZNF787, KIF1B, RPS17, and EEF1A1 insertions than for the Kernow p6 del S17, while it was not with RNA18 or RPL6 fragments. The number of ORF2 foci was higher for RNF19A, ZNF787, KIF1B, and RPS17 than for Kernow p6 del S17. VHRVs with replicative advantages were less sensitive to the antiviral effect of ribavirin. No difference in PTMs was found between VHRVs with a replicative advantage and those without. In conclusion, our study showed that insertions did not systematically confer a replicative advantage in vitro. Further studies are needed to determine the mechanisms underlying the differences in replicative capacity. IMPORTANCE Hepatitis E virus (HEV) is a major cause of viral hepatitis. HEV can lead to chronic infection in immunocompromised patients. Ribavirin treatment is currently used to treat such chronic infections. Recently, seven virus-host recombinant viruses were characterized in immunocompromised patients. These viruses have incorporated a portion of a human gene fragment into their genome. We studied the consequences of these insertions on the replication capacity. We found that these inserted fragments could enhance virus replication for five of the seven recombinant variants. We also showed that the recombinant variants with replicative advantages were less sensitive to ribavirin in vitro. Finally, we found that the mechanisms leading to such a replicative advantage do not seem to rely on the post-translational modifications introduced by the human gene fragment that could have modified the function of the viral protein. The mechanisms involved in improving the replication of such recombinant viruses remain to be explored.
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Affiliation(s)
- Olivia Paronetto
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Claire Allioux
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Chloé Diméglio
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Lhorane Lobjois
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Nicolas Jeanne
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Noémie Ranger
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Jérôme Boineau
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Mélanie Pucelle
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Sofia Demmou
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Florence Abravanel
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Sabine Chapuy-Regaud
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Jacques Izopet
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Sébastien Lhomme
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), UMR 5051 (CNRS), UMR 1291 (INSERM), Université Toulouse III-Paul Sabatier, Toulouse, France
- Laboratoire de Virologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
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Vellas C, Latour J, Trémeaux P, Ranger N, Ferrer V, Harter A, Carcenac R, Boyer P, Demmou S, Claraz P, Kamar N, Izopet J. Molecular evolution of omicron variant in immunocompromised individuals with chronic SARS-CoV-2 infection. J Infect 2023; 87:e89-e93. [PMID: 37783375 DOI: 10.1016/j.jinf.2023.09.011] [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: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Affiliation(s)
- Camille Vellas
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III (University of Toulouse III), Toulouse Institute for Infectious and Inflammatory Diseases, F-31300, France; Université Toulouse III Paul Sabatier, F-31300, France.
| | - Justine Latour
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Pauline Trémeaux
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Noémie Ranger
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Vénicia Ferrer
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Agnès Harter
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Romain Carcenac
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Pauline Boyer
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Sofia Demmou
- CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
| | - Pauline Claraz
- Institut Universitaire du Cancer (University Cancer Institute), Service de Pharmacie (Pharmacy Department), Toulouse F-31100, France
| | - Nassim Kamar
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III (University of Toulouse III), Toulouse Institute for Infectious and Inflammatory Diseases, F-31300, France; Université Toulouse III Paul Sabatier, F-31300, France; CHU de Toulouse, Département de Néphrologie, Dialyse et Transplantation d'Organes (Department of Nephrology, Dialysis and Organ Transplantation), Toulouse F-31400, France
| | - Jacques Izopet
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III (University of Toulouse III), Toulouse Institute for Infectious and Inflammatory Diseases, F-31300, France; Université Toulouse III Paul Sabatier, F-31300, France; CHU de Toulouse (Toulouse University Hospital), Laboratoire de Virologie (Virology Laboratory), Toulouse F-31300, France
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3
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Trémeaux P, Latour J, Ranger N, Ferrer V, Harter A, Carcenac R, Boyer P, Demmou S, Nicot F, Raymond S, Izopet J. SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing. Microbiol Spectr 2023; 11:e0049323. [PMID: 37260377 PMCID: PMC10434069 DOI: 10.1128/spectrum.00493-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023] Open
Abstract
Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping. We identified 17 co-infections with SARS-CoV-2 strains belonging to different clades in 6829 samples sequenced between January and October, 2022 (prevalence 0.25%). There were 3 Delta/Omicron co-infections and 14 Omicron/Omicron co-infections (4 cases of 21K/21L, 1 case of 21L/22A, 2 cases of 21L/22B, 4 cases of 22A/22B, 2 cases of 22B/22C and 1 case of 22B/22E). Four of these patients (24%) also harbored recombinant minor haplotypes, including one with a recombinant virus that was selected in the viral quasispecies over the course of his chronic infection. While co-infections remain rare among SARS-CoV-2-infected individuals, long-read SMRT sequencing is a useful tool for detecting them as well as recombinant events, providing the basis for assessing their clinical impact, and a precise indicator of epidemic evolution. IMPORTANCE SARS-CoV-2 variants have been responsible for the successive waves of infection over the 3 years of pandemic. While co-infection followed by recombination is one driver of virus evolution, there have been few reports of co-infections, mainly between Delta and Omicron variants or between the first 2 Omicron variants 21K_BA.1 and 21L_BA.2. The 17 co-infections we detected during 2022 included cases with the recent clades of Omicron 22A, 22B, 22C, and 22E; 24% harbored recombinant variants. This study shows that long-read SMRT sequencing is well suited to SARS-CoV-2 genomic surveillance.
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Affiliation(s)
- Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Vénicia Ferrer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Agnès Harter
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Boyer
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291 – CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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4
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Narat V, Salmona M, Kampo M, Heyer T, Rachik AS, Mercier-Delarue S, Ranger N, Rupp S, Ambata P, Njouom R, Simon F, Le Goff J, Giles-Vernick T. Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis. Nat Commun 2023; 14:3674. [PMID: 37339968 DOI: 10.1038/s41467-023-39455-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, MNHN/CNRS/Univ. Paris Cité, Paris, France
| | - Maud Salmona
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Mamadou Kampo
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | | | | | | | - Noémie Ranger
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Stephanie Rupp
- Department of Anthropology, City University of NewYork - Lehman College, NewYork, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Virology, AP-HP, Hôpital Saint Louis, Paris, France
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Virology, AP-HP, Hôpital Saint Louis, Paris, France.
- INSIGHT U976, INSERM, Université Paris Cité, Paris, France.
| | - Tamara Giles-Vernick
- Anthropology and Ecology of Disease Emergence Unit, Institut Pasteur, Université Paris Cité, Paris, France.
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5
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Migueres M, Dimeglio C, Mansuy JM, Abravanel F, Raymond S, Latour J, Jeanne N, Ranger N, Lhomme S, Saune K, Tremeaux P, Izopet J. Influence of Nasopharyngeal Viral Load on the Spread of the Omicron BA.2 Variant. Clin Infect Dis 2023; 76:e514-e517. [PMID: 35796540 DOI: 10.1093/cid/ciac563] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 11/14/2022] Open
Abstract
We used variant typing polymerase chain reaction to describe the evolution of severe acute respiratory syndrome coronavirus 2 Omicron sublineages between December 2021 and mid-March 2022. The selective advantage of the BA.2 variant over BA.1 is not due to greater nasopharyngeal viral loads.
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Affiliation(s)
- Marion Migueres
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Chloé Dimeglio
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Jean-Michel Mansuy
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France
| | - Florence Abravanel
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Stéphanie Raymond
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Justine Latour
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France
| | - Nicolas Jeanne
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France
| | - Noémie Ranger
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France
| | - Sébastien Lhomme
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Karine Saune
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Pauline Tremeaux
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France
| | - Jacques Izopet
- Laboratoire de virologie, Institut fédératif de Biologie, Hôpital Purpan, CHU Toulouse, 31300 Toulouse, France.,Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291-CNRS UMR5051, 31300 Toulouse, France.,Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
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Raymond S, Jeanne N, Nicot F, Dimeglio C, Carcenac R, Harter A, Ranger N, Martin-Blondel G, Delobel P, Izopet J. HIV-1 resistance genotyping by ultra-deep sequencing and 6-month virological response to first-line treatment. J Antimicrob Chemother 2023; 78:346-353. [PMID: 36449383 DOI: 10.1093/jac/dkac391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVES To evaluate the routine use of the Sentosa ultra-deep sequencing (UDS) system for HIV-1 polymerase resistance genotyping in treatment-naïve individuals and to analyse the virological response (VR) to first-line antiretroviral treatment. METHODS HIV drug resistance was determined on 237 consecutive samples from treatment-naïve individuals using the Sentosa UDS platform with two mutation detection thresholds (3% and 20%). VR was defined as a plasma HIV-1 virus load <50 copies/mL after 6 months of treatment. RESULTS Resistance to at least one antiretroviral drug with a mutation threshold of 3% was identified in 29% and 16% of samples according to ANRS and Stanford algorithms, respectively. The ANRS algorithm also revealed reduced susceptibility to at least one protease inhibitor (PI) in 14.3% of samples, to one reverse transcriptase inhibitor in 12.7%, and to one integrase inhibitor (INSTI) in 5.1%. For a mutation threshold of 20%, resistance was identified in 24% and 13% of samples according to ANRS and Stanford algorithms, respectively. The 6 months VR was 87% and was similar in the 58% of patients given INSTI-based treatment, in the 16% given PI-based treatment and in the 9% given NNRTI-based treatment. Multivariate analysis indicated that the VR was correlated with the baseline HIV virus load and resistance to at least one PI at both 3% and 20% mutation detection thresholds (ANRS algorithm). CONCLUSIONS The Vela UDS platform is appropriate for determining antiretroviral resistance in patients on a first-line antiretroviral treatment. Further studies are needed on the use of UDS for therapeutic management.
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Affiliation(s)
- Stéphanie Raymond
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
| | - Guillaume Martin-Blondel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300France
| | - Pierre Delobel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300France
| | - Jacques Izopet
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM UMR 1291 - CNRS UMR 5051, Toulouse, France.,CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300France
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7
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [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: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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Nicot F, Trémeaux P, Latour J, Jeanne N, Ranger N, Raymond S, Dimeglio C, Salin G, Donnadieu C, Izopet J. Whole-genome sequencing of SARS-CoV-2: Comparison of target capture and amplicon single molecule real-time sequencing protocols. J Med Virol 2022; 95:e28123. [PMID: 36056719 PMCID: PMC9539136 DOI: 10.1002/jmv.28123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS-CoV-2.
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Affiliation(s)
- Florence Nicot
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | | | - Justine Latour
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Nicolas Jeanne
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Noémie Ranger
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Stéphanie Raymond
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Chloé Dimeglio
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Gérald Salin
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Cécile Donnadieu
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Jacques Izopet
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
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Dimeglio C, Loubes JM, Migueres M, Sauné K, Trémeaux P, Lhomme S, Ranger N, Latour J, Mansuy JM, Izopet J. Influence of vaccination and prior immunity on the dynamics of Omicron BA.1 and BA.2 sub-variants. J Infect 2022; 84:834-872. [PMID: 35307410 PMCID: PMC8926943 DOI: 10.1016/j.jinf.2022.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023]
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10
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Vellas C, Del Bello A, Gaube G, Tremeaux P, Jeanne N, Ranger N, Martin-Blondel G, Delobel P, Kamar N, Izopet J. Impact of Casirivimab-Imdevimab on SARS-CoV-2 delta variant nasopharyngeal virus load and Spike quasispecies. Open Forum Infect Dis 2022; 9:ofac093. [PMID: 35299988 PMCID: PMC8903465 DOI: 10.1093/ofid/ofac093] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background The increasing use of monoclonal antibodies (mAbs) to treat coronavirus disease 2019 raises questions about their impact on the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mAb-resistant variants. We assessed the impact of Casirivimab-Imdevimab on SARS-CoV-2 mutations associated with reduced mAb activity in treated patients. Methods We measured the nasopharyngeal (NP) viral load and sequenced the haplotypes of spike gene of 50 patients infected with the SARS-CoV-2 delta variant and treated with Casirivimab-Imdevimab using single-molecule real-time sequencing. Results The NP SARS-CoV-2 viral load of patients treated with Casirivimab-Imdevimab decreased from 8.13 (interquartile range [IQR], 7.06–8.59) log10 copies/mL pretreatment to 3.67 (IQR, 3.07–5.15) log10 copies/mL 7 days later (P < .001). Of the 36 patients for whom follow-up timepoints Spike sequencing were available, none of the Spike mutations that reduced mAb activity were detected. Conclusions Casirivimab-Imdevimab is an effective treatment for patients infected with the SARS-CoV-2 delta variant. Despite selective pressure on SARS-CoV-2 Spike quasispecies, we detected no key mutations that reduced mAb activity in our patients.
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Affiliation(s)
- Camille Vellas
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, F-31300 France
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
| | - Arnaud Del Bello
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
- CHU de Toulouse, Département de Néphrologie, Dialyse et Transplantation d'Organes, Toulouse, F-31300 France
| | - Géraldine Gaube
- CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Pauline Tremeaux
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Nicolas Jeanne
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Noémie Ranger
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Guillaume Martin-Blondel
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
- CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Pierre Delobel
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
- CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Nassim Kamar
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
- CHU de Toulouse, Département de Néphrologie, Dialyse et Transplantation d'Organes, Toulouse, F-31300 France
| | - Jacques Izopet
- CHU de Toulouse, Laboratoire de Virologie, Toulouse, F-31300 France
- INSERM UMR1291 - CNRS UMR5051 - Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, F-31300 France
- Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
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11
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Fromentin M, Bridier-Nahmias A, Legoff J, Mercier-Delarue S, Ranger N, Vuillard C, Do Vale J, Zucman N, Alberdi A, Ricard JD, Roux D. The 16S rRNA lung microbiome in mechanically ventilated patients: a methodological study. Exp Lung Res 2021; 48:23-34. [PMID: 34963427 DOI: 10.1080/01902148.2021.2021327] [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: 10/19/2022]
Abstract
PURPOSE Characterization of the respiratory tract bacterial microbiome is in its infancy when compared to the gut microbiota. To limit bias mandates a robust methodology. Specific amplification of the hypervariable (V) region of the 16SrRNA gene is a crucial step. Differences in accuracy exist for one V region to another depending on the sampled environment. We aimed to assess the impact of the primer sequences targeting the V4 region currently used for gut microbiota studies in respiratory samples. Materials and methods: The original 515 F-806R primer pair targets the V4 region of the 16SrRNA gene. We compared two different 515 F-806R primer pairs before Illumina 250 paired-end sequencing for bacterial microbiome analyses of respiratory samples from critically-ill ventilated patients. "S-V4" for "Stringent V4" primer pair is used in two ongoing international projects "the Integrative Human microbiome project (iHMP)" and "the Earth microbiome project (EMP)." "R-V4" for "Relaxed V4" primer pair has been modified to reduce biases against specific environmental taxa. The optimal method was determined by concordance with conventional microbiology. Results: Twenty samples from three patients who developed a ventilator-associated pneumonia (VAP) and four who did not (control ventilated patients) were sequenced. Highly different results were obtained. "S-V4" provided the best agreement with the conventional microbiology for endotracheal aspirate: 89% as compared to 56% for "R-V4." The main difference related to poor Enterobacteriaceae detection with "R-V4" primers. Conclusions: Accuracy of the bacterial lung microbiome composition was highly dependent on the primers used for amplification of the 16 s rRNA hypervariable sequence. This work validates for future lung microbiome studies the use of the 515 F-806R "S-V4" primer pair associated to Illumina® MiSeq paired-end sequencing.
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Affiliation(s)
- Melanie Fromentin
- AP-HP, Hôpital Cochin, service d'anesthésie réanimation, Paris, France.,INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France
| | - Antoine Bridier-Nahmias
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France
| | - Jérôme Legoff
- INSERM, U 976, HIPI Human Immunology, Pathophysiology & Immunotherapy, Université de Paris, Paris, France
| | - Severine Mercier-Delarue
- INSERM, U 976, HIPI Human Immunology, Pathophysiology & Immunotherapy, Université de Paris, Paris, France
| | - Noémie Ranger
- INSERM, U 976, HIPI Human Immunology, Pathophysiology & Immunotherapy, Université de Paris, Paris, France
| | - Constance Vuillard
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France.,AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Médecine Intensive Réanimation, Colombes, France
| | - Julien Do Vale
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France
| | - Noémie Zucman
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France.,AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Médecine Intensive Réanimation, Colombes, France
| | - Antonio Alberdi
- Plateforme Technologique de l'Institut de Recherche Saint Louis (IRSL) Hématologie, Immunologie, Oncologie, Université de Paris, Paris, France
| | - Jean-Damien Ricard
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France.,AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Médecine Intensive Réanimation, Colombes, France
| | - Damien Roux
- INSERM UMR 1137, IAME, Infection Antimicrobials Modelling Evolution, Université de Paris, Paris, France.,AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Médecine Intensive Réanimation, Colombes, France
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12
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Lhomme S, Latour J, Jeanne N, Trémeaux P, Ranger N, Migueres M, Salin G, Donnadieu C, Izopet J. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Viruses 2021; 13:v13122544. [PMID: 34960813 PMCID: PMC8707593 DOI: 10.3390/v13122544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
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Affiliation(s)
- Sébastien Lhomme
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
- Correspondence: ; Tel.: +33-5-67-69-04-24
| | - Justine Latour
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Pauline Trémeaux
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Noémie Ranger
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Marion Migueres
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Gérald Salin
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Cécile Donnadieu
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Jacques Izopet
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
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13
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Vellas C, Del Bello A, Debard A, Steinmeyer Z, Tribaudeau L, Ranger N, Jeanne N, Martin-Blondel G, Delobel P, Kamar N, Izopet J. Influence of treatment with neutralizing monoclonal antibodies on the SARS-CoV-2 nasopharyngeal load and quasispecies. Clin Microbiol Infect 2021; 28:139.e5-139.e8. [PMID: 34537363 PMCID: PMC8444376 DOI: 10.1016/j.cmi.2021.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/07/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 01/01/2023]
Abstract
Objectives To evaluate the impact of neutralizing monoclonal antibody (mAb) treatment and to determine whether the selective pressure of mAbs could facilitate the proliferation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with spike protein mutations that might attenuate mAb effectiveness. Patients and methods We evaluated the impact of mAbs on the nasopharyngeal (NP) viral load and virus quasispecies of mAb-treated patients using single-molecule real-time sequencing. The mAbs used were: Bamlanivimab alone (four patients), Bamlanivimab/Etesevimab (23 patients) and Casirivimab/Imdevimab (five patients). Results The NP SARS-CoV-2 viral load of mAb-treated patients decreased from 8.2 log10 copies/mL before administration to 4.3 log10 copies/mL 7 days after administration. Five immunocompromised patients given Bamlanivimab/Etesevimab were found to have mAb activity-reducing spike mutations. Two patients harboured SARS-CoV-2 variants with a Q493R spike mutation 7 days after administration, as did a third patient 14 days after administration. The fourth patient harboured a variant with a Q493K spike mutation 7 days post-treatment, and the fifth patient had a variant with a E484K spike mutation on day 21. The emergence of the spike mutation was accompanied by stabilization or rebound of the NP viral load in three of five patients. Conclusion Two-mAb therapy can drive the selection of resistant SARS-CoV-2 variants in immunocompromised patients. Patients given mAbs should be closely monitored and measures to limit virus spread should be reinforced.
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Affiliation(s)
- Camille Vellas
- CHU de Toulouse, Virology Laboratory, Toulouse, France; INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France.
| | - Arnaud Del Bello
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France; CHU de Toulouse, Département de Néphrologie, Dialyse et Transplantation d'Organes, Toulouse, France
| | - Alexa Debard
- CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | | | - Laure Tribaudeau
- Université Toulouse III Paul Sabatier, Toulouse, France; CHU de Toulouse, C.O.M.E.D.I.M.S, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Virology Laboratory, Toulouse, France
| | | | - Guillaume Martin-Blondel
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Pierre Delobel
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France; CHU de Toulouse, Service des Maladies Infectieuses et Tropicales, Toulouse, France
| | - Nassim Kamar
- INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France; CHU de Toulouse, Département de Néphrologie, Dialyse et Transplantation d'Organes, Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Virology Laboratory, Toulouse, France; INSERM UMR1291-CNRS UMR5051-Université Toulouse III, Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France
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14
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Migueres M, Lhomme S, Trémeaux P, Dimeglio C, Ranger N, Latour J, Dubois M, Nicot F, Miedouge M, Mansuy JM, Izopet J. Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants. J Clin Virol 2021; 143:104969. [PMID: 34509927 PMCID: PMC8411575 DOI: 10.1016/j.jcv.2021.104969] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 06/28/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 01/26/2023]
Abstract
Background The recent emergence of new SARS CoV-2 variants (variants of concern, VOC) that spread rapidly and may lead to immune escape has emphasized the urgent need to monitor and control their spread. Methods We analyzed 2018 SARS-CoV-2 positive specimens collected between February 9 and March 22, 2021 using the Thermofisher® TaqPath™ COVID-19 CE-IVD RT-PCR kit (TaqPath) and the ID solutions® ID™ SARS-CoV-2/UK/SA Variant Triplex RT-PCR (ID triplex) assay to screen for VOCs. Results The ID triplex assay identified 62.8% of them as VOCs: 61.8% B.1.1.7 and 0.9% B.1.351/P.1. The agreement between the ID triplex results for B.1.1.7 and the TaqPath S gene target failure (SGTF)/ S gene target late detection (SGTL) profile for this variant agreed very well (k = 0.86). A low virus load was the main cause of discrepancies. Sequencing discordant results with both assays indicated that the TaqPath assay detected the B.1.1.7 lineage slightly better. Both assays suggested that the virus loads of B.1.1.7 variants were significantly higher than those of non-B.1.1.7 strains. Only 10/20 B1.351/P.1 strains detected with the ID triplex assay were confirmed by sequencing. Conclusions We conclude that the SGTF/SGTL profiles identified using the TaqPath assay and ID triplex results are suitable for detecting the B.1.1.7 lineage. The ID triplex assay, which rapidly determines all three current VOCs simultaneously, could be a valuable tool for limiting virus spread by supporting contact-tracing and isolation.
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Affiliation(s)
- M Migueres
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - S Lhomme
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - P Trémeaux
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - C Dimeglio
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - N Ranger
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J Latour
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - M Dubois
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - F Nicot
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - M Miedouge
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J M Mansuy
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France
| | - J Izopet
- CHU Toulouse, Hôpital Purpan, Virology Laboratory, 31300, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM UMR1291 - CNRS UMR5051, Toulouse 31300, France; Université Toulouse III Paul-Sabatier, Toulouse, France
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15
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Dimeglio C, Milhes M, Loubes JM, Ranger N, Mansuy JM, Trémeaux P, Jeanne N, Latour J, Nicot F, Donnadieu C, Izopet J. Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2. Viruses 2021; 13:898. [PMID: 34066231 PMCID: PMC8151774 DOI: 10.3390/v13050898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as of 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how the spread of the virus in regions of France will vary depending on the proportions of variants and on the public health strategies adopted, including anti-COVID-19 vaccination. The proportion of SARS-CoV-2 variant B.1.1.7, which was not detected in early January, increased to become 60% of the forms of SARS-CoV-2 circulating in the Toulouse urban area at the beginning of February 2021, but there was no increase in positive nucleic acid tests. Our prediction model indicates that maintaining public health measures and accelerating vaccination are efficient strategies for the sustained control of SARS-CoV-2.
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Affiliation(s)
- Chloé Dimeglio
- INSERM UMR1291—CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France;
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Marine Milhes
- Genotoul-Genome & Transcriptome—Plateforme Génomique (GeT-PlaGe), US INRAe 1426, 31326 Castanet-Tolosan, France; (M.M.); (C.D.)
| | - Jean-Michel Loubes
- Institut de Mathématiques de Toulouse, Université de Toulouse, 31400 Toulouse, France;
| | - Noémie Ranger
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Jean-Michel Mansuy
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Pauline Trémeaux
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Nicolas Jeanne
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Justine Latour
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Florence Nicot
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
| | - Cécile Donnadieu
- Genotoul-Genome & Transcriptome—Plateforme Génomique (GeT-PlaGe), US INRAe 1426, 31326 Castanet-Tolosan, France; (M.M.); (C.D.)
| | - Jacques Izopet
- INSERM UMR1291—CNRS UMR5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), 31300 Toulouse, France;
- Virology Laboratory, Centre Hospitalier Universitaire de Toulouse, Hôpital Purpan, 31300 Toulouse, France; (N.R.); (J.-M.M.); (P.T.); (N.J.); (J.L.); (F.N.)
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16
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Nicot F, Dimeglio C, Migueres M, Jeanne N, Latour J, Abravanel F, Ranger N, Harter A, Dubois M, Lameiras S, Baulande S, Chapuy-Regaud S, Kamar N, Lhomme S, Izopet J. Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes. Front Microbiol 2021; 11:634430. [PMID: 33584599 PMCID: PMC7875884 DOI: 10.3389/fmicb.2020.634430] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 11/27/2020] [Accepted: 12/30/2020] [Indexed: 12/27/2022] Open
Abstract
Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, and HEV-3.3) have been identified but the overlaps between intra-subtype and inter-subtype p-distances make subtype classification inconsistent. Reference sequences have been proposed to facilitate communication between researchers and new putative subtypes have been identified recently. We have used the full or near full-length HEV-3 genome sequences available in the Genbank database (April 2020; n = 503) and distance analyses of clades HEV-3.1 and HEV-3.2 to determine a p-distance cut-off (0.093 nt substitutions/site) in order to define subtypes. This could help to harmonize HEV-3 genotyping, facilitate molecular epidemiology studies and investigations of the biological and clinical differences between HEV-3 subtypes.
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Affiliation(s)
- Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France
| | - Marion Migueres
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Justine Latour
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Florence Abravanel
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Noémie Ranger
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Martine Dubois
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France
| | - Sonia Lameiras
- Institut Curie Genomics of Excellence Platform, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence Platform, Institut Curie Research Center, Paris, France
| | - Sabine Chapuy-Regaud
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Nassim Kamar
- INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France.,CHU de Toulouse, Hôpital Rangueil, Service de Néphrologie, Dialyse et Transplantation d'Organe, Toulouse, France
| | - Sébastien Lhomme
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Centre National de Référence du Virus de l'Hépatite E, Toulouse, France.,INSERM, U1043, Toulouse, France.,Department of Virology, Université Toulouse III Paul-Sabatier, Toulouse, France
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Narat V, Amato KR, Ranger N, Salmona M, Mercier-Delarue S, Rupp S, Ambata P, Njouom R, Simon F, Giles-Vernick T, LeGoff J. A multi-disciplinary comparison of great ape gut microbiota in a central African forest and European zoo. Sci Rep 2020; 10:19107. [PMID: 33154444 PMCID: PMC7645722 DOI: 10.1038/s41598-020-75847-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 01/01/2023] Open
Abstract
Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition of gut bacteriome and suggest consequences for human and animal health. Gut bacteriome comparisons across different environments diverge in their results, showing no generalizable patterns linking habitat and dietary degradation with bacterial diversity. The challenge in drawing general conclusions from such studies lies in the broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S ribosomal RNA gene sequencing to characterize intestinal microbiota of free-ranging sympatric chimpanzees and gorillas in southeastern Cameroon and sympatric chimpanzees and gorillas in a European zoo. We conducted participant-observation and semi-structured interviews among people living near these great apes to understand better their feeding habits and habitats. Unexpectedly, bacterial diversity (ASV, Faith PD and Shannon) was higher among zoo gorillas than among those in the Cameroonian forest, but zoo and Cameroonian chimpanzees showed no difference. Phylogeny was a strong driver of species-specific microbial composition. Surprisingly, zoo gorilla microbiota more closely resembled that of zoo chimpanzees than of Cameroonian gorillas. Zoo living conditions and dietary similarities may explain these results. We encourage multidisciplinary approach integrating environmental sampling and anthropological evaluation to characterize better diverse environmental conditions of such investigations.
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Affiliation(s)
- Victor Narat
- Eco-anthropologie, UMR7206 CNRS/MNHN/Université de Paris, Site du Musée de L'Homme, Paris, France
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, USA
- Humans and the Microbiome, CIFAR, Toronto, Canada
| | - Noémie Ranger
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Maud Salmona
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France
| | | | - Stephanie Rupp
- Department of Anthropology, City University of New York - Lehman College, New York, NY, USA
| | - Philippe Ambata
- Ministry of Agriculture and Rural Development, Yaounde, Cameroon
| | | | - François Simon
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France
| | - Tamara Giles-Vernick
- Institut Pasteur, Anthropology and Ecology of Disease Emergence Unit, Paris, France.
- Humans and the Microbiome, CIFAR, Toronto, Canada.
| | - Jérôme LeGoff
- Université de Paris, Equipe INSIGHT, Inserm U976, 75010, Paris, France.
- Département des Agents Infectieux, Virologie et Greffes, AP-HP, Hôpital Saint-Louis, 75010, Paris, France.
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18
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Ranger N, Travers E. TU-C-19A-01: “Leaning In” to Equal Opportunity for Women: The Responsibility of Individuals, Employers and Organizations. Med Phys 2014. [DOI: 10.1118/1.4889263] [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: 11/07/2022] Open
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Michel-Kerjan E, Hochrainer-Stigler S, Kunreuther H, Linnerooth-Bayer J, Mechler R, Muir-Wood R, Ranger N, Vaziri P, Young M. Catastrophe risk models for evaluating disaster risk reduction investments in developing countries. Risk Anal 2013; 33:984-999. [PMID: 23237737 DOI: 10.1111/j.1539-6924.2012.01928.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Major natural disasters in recent years have had high human and economic costs, and triggered record high postdisaster relief from governments and international donors. Given the current economic situation worldwide, selecting the most effective disaster risk reduction (DRR) measures is critical. This is especially the case for low- and middle-income countries, which have suffered disproportionally more economic and human losses from disasters. This article discusses a methodology that makes use of advanced probabilistic catastrophe models to estimate benefits of DRR measures. We apply such newly developed models to generate estimates for hurricane risk on residential structures on the island of St. Lucia, and earthquake risk on residential structures in Istanbul, Turkey, as two illustrative case studies. The costs and economic benefits for selected risk reduction measures are estimated taking account of hazard, exposure, and vulnerability. We conclude by emphasizing the advantages and challenges of catastrophe model-based cost-benefit analyses for DRR in developing countries.
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Affiliation(s)
- E Michel-Kerjan
- Wharton School, University of Pennsylvania, Philadelphia, PA, USA.
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Rudolph AE, Standish K, Amesty S, Crawford ND, Stern RJ, Badillo WE, Boyer A, Brown D, Ranger N, Orduna JMG, Lasenburg L, Lippek S, Fuller CM. A community-based approach to linking injection drug users with needed services through pharmacies: an evaluation of a pilot intervention in New York City. AIDS Educ Prev 2010; 22:238-251. [PMID: 20528131 PMCID: PMC2883795 DOI: 10.1521/aeap.2010.22.3.238] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [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] [Indexed: 05/29/2023]
Abstract
Studies suggest that community-based approaches could help pharmacies expand their public health role, particularly pertaining to HIV prevention. Thirteen pharmacies participating in New York's Expanded Syringe Access Program, which permits nonprescription syringe sales to reduce syringe-sharing among injection drug users (IDUs), were enrolled in an intervention to link IDU syringe customers to medical/social services. Sociodemographics, injection practices, beliefs about and experiences with pharmacy use, and medical/social service utilization were compared among 29 IDUs purchasing syringes from intervention pharmacies and 66 IDUs purchasing syringes from control pharmacies using chi-square tests. Intervention IDUs reported more positive experiences in pharmacies than controls; both groups were receptive to a greater public health pharmacist role. These data provide evidence that community-based participatory research aided in the implementation of a pilot structural intervention to promote understanding of drug use and HIV prevention among pharmacy staff, and facilitated expansion of pharmacy services beyond syringe sales in marginalized drug-using communities.
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Affiliation(s)
- A E Rudolph
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, USA
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Williams M, Raghunathan P, Seibert JA, Kwan A, Lo J, Samei E, Ranger N, Fajardo L, McGruder A, Maxwell S, Maidment A, Yaffe M, Bloomquist A, Mawdsley G. TU-B-M100J-01: Optimizing Mammography Image Quality and Dose: X-Ray Spectrum and Exposure Parameter Selection. Med Phys 2007. [DOI: 10.1118/1.2761315] [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: 11/07/2022] Open
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Ranger N, Mackenzie A, Honey I, Dobbins J, Ravin C, Samei E. TU-EE-A4-06: Experimental Evaluation of Effective Detective Quantum Efficiency for Digital Radiographic Imaging Systems. Med Phys 2007. [DOI: 10.1118/1.2761409] [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: 11/07/2022] Open
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23
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Thompson CJ, Ranger N, Evans AC, Gjedde A. Validation of simultaneous PET emission and transmission scans. J Nucl Med 1991; 32:154-60. [PMID: 1988623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A technique for performing simultaneous PET emission and transmission scans is validated in a fluoro-deoxyglucose study. A point source masked into a fan beam of annihilation photons orbits the patient section under study. Coincident events are sorted into two buffers, or rejected, based on the source's position. Both static and dynamic frames of independent and simultaneous studies are compared. The noise effective count rate is reduced to 62% of the value during normal studies. However, the increase in the coefficient of variation in cortical regions is less than 6%. The RMS difference between profile contours through many brain regions is approximately 40% higher comparing two simultaneous emission/transmission scans than when the same analysis is performed on independent emission scans. This difference appears to be due to the noise patterns arising from the use of different transmission scans.
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Affiliation(s)
- C J Thompson
- Positron Imaging Laboratories, McConnell Brain Imaging Centre, Montreal Neurological Institute, Canada
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