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Del Vecchio C, Cracknell Daniels B, Brancaccio G, Brazzale AR, Lavezzo E, Ciavarella C, Onelia F, Franchin E, Manuto L, Bianca F, Cianci V, Cattelan AM, Dorigatti I, Toppo S, Crisanti A. Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants. Nat Commun 2022; 13:5870. [PMID: 36198689 PMCID: PMC9533294 DOI: 10.1038/s41467-022-33460-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/23/2022] [Accepted: 09/15/2022] [Indexed: 11/09/2022] Open
Abstract
Population testing remains central to COVID-19 control and surveillance, with countries increasingly using antigen tests rather than molecular tests. Here we describe a SARS-CoV-2 variant that escapes N antigen tests due to multiple disruptive amino-acid substitutions in the N protein. By fitting a multistrain compartmental model to genomic and epidemiological data, we show that widespread antigen testing in the Italian region of Veneto favored the undetected spread of the antigen-escape variant compared to the rest of Italy. We highlight novel limitations of widespread antigen testing in the absence of molecular testing for diagnostic or confirmatory purposes. Notably, we find that genomic surveillance systems which rely on antigen population testing to identify samples for sequencing will bias detection of escape antigen test variants. Together, these findings highlight the importance of retaining molecular testing for surveillance purposes, including in contexts where the use of antigen tests is widespread.
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Affiliation(s)
- Claudia Del Vecchio
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Bethan Cracknell Daniels
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Giuseppina Brancaccio
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | | | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Francesco Onelia
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Elisa Franchin
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Laura Manuto
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Federico Bianca
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy
| | - Vito Cianci
- ER Unit, Emergency-Urgency Department, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Anna Maria Cattelan
- Infectious and Tropical Diseases Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK.
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy. .,CRIBI Biotech Center, University of Padua, V.le G. Colombo, 3, Padua, 35131, Italy.
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padua, Via Gabelli, 63, Padua, 35121, Italy. .,Microbiology and Virology Diagnostic Unit, Padua University Hospital, Via Giustiniani 2, Padua, 35128, Italy. .,Department of Life Science, Imperial College London, South Kensington Campus, Imperial College Road, SW7 AZ, London, UK.
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Lavezzo E, Pacenti M, Manuto L, Boldrin C, Cattai M, Grazioli M, Bianca F, Sartori M, Caldart F, Castelli G, Nicoletti M, Nieddu E, Salvadoretti E, Labella B, Fava L, Vanuzzo MC, Lisi V, Antonello M, Grimaldi CI, Zulian C, Del Vecchio C, Plebani M, Padoan A, Cirillo DM, Brazzale AR, Tonon G, Toppo S, Dorigatti I, Crisanti A. Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history. Genome Med 2022; 14:61. [PMID: 35689243 PMCID: PMC9185135 DOI: 10.1186/s13073-022-01066-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The continuous emergence of SARS-CoV-2 variants of concern (VOC) with immune escape properties, such as Delta (B.1.617.2) and Omicron (B.1.1.529), questions the extent of the antibody-mediated protection against the virus. Here we investigated the long-term antibody persistence in previously infected subjects and the extent of the antibody-mediated protection against B.1, B.1.617.2 and BA.1 variants in unvaccinated subjects previously infected, vaccinated naïve and vaccinated previously infected subjects. METHODS Blood samples collected 15 months post-infection from unvaccinated (n=35) and vaccinated (n=41) previously infected subjects (Vo' cohort) were tested for the presence of antibodies against the SARS-CoV-2 spike (S) and nucleocapsid (N) antigens using the Abbott, DiaSorin, and Roche immunoassays. The serum neutralising reactivity was assessed against B.1, B.1.617.2 (Delta), and BA.1 (Omicron) SARS-CoV-2 strains through micro-neutralisation. The antibody titres were compared to those from previous timepoints, performed at 2- and 9-months post-infection on the same individuals. Two groups of naïve subjects were used as controls, one from the same cohort (unvaccinated n=29 and vaccinated n=20) and a group of vaccinated naïve healthcare workers (n=61). RESULTS We report on the results of the third serosurvey run in the Vo' cohort. With respect to the 9-month time point, antibodies against the S antigen significantly decreased (P=0.0063) among unvaccinated subjects and increased (P<0.0001) in vaccinated individuals, whereas those against the N antigen decreased in the whole cohort. When compared with control groups (naïve Vo' inhabitants and naïve healthcare workers), vaccinated subjects that were previously infected had higher antibody levels (P<0.0001) than vaccinated naïve subjects. Two doses of vaccine elicited stronger anti-S antibody response than natural infection (P<0.0001). Finally, the neutralising reactivity of sera against B.1.617.2 and BA.1 was 4-fold and 16-fold lower than the reactivity observed against the original B.1 strain. CONCLUSIONS These results confirm that vaccination induces strong antibody response in most individuals, and even stronger in previously infected subjects. Neutralising reactivity elicited by natural infection followed by vaccination is increasingly weakened by the recent emergence of VOCs. While immunity is not completely compromised, a change in vaccine development may be required going forward, to generate cross-protective pan-coronavirus immunity in the global population.
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Affiliation(s)
- Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy.
| | | | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | - Marco Grazioli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Federico Bianca
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Federico Caldart
- Gastroenterology Unit, Department of Medicine, Verona B. Roma University Hospital, Verona, Italy
| | - Gioele Castelli
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Michele Nicoletti
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Eleonora Nieddu
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Elisa Salvadoretti
- Paediatrics Unit, Mother and Child Hospital, Surgery, Dentistry, Maternity and Infant Department, Verona University Hospital, Verona, Italy
| | - Beatrice Labella
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Ludovico Fava
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | | | | | - Maria Antonello
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | - Mario Plebani
- Department of Medicine, University of Padova, Padova, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padova, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padova, Italy.
- Azienda Ospedale Padova, Padova, Italy.
- Department of Life Sciences, Imperial College London, London, UK.
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Gittelman RM, Lavezzo E, Snyder TM, Zahid HJ, Carty CL, Elyanow R, Dalai S, Kirsch I, Baldo L, Manuto L, Franchin E, Del Vecchio C, Pacenti M, Boldrin C, Cattai M, Saluzzo F, Padoan A, Plebani M, Simeoni F, Bordini J, Lorè NI, Lazarević D, Cirillo DM, Ghia P, Toppo S, Carlson JM, Robins HS, Crisanti A, Tonon G. Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection. JCI Insight 2022; 7:e151849. [PMID: 35439174 PMCID: PMC9220833 DOI: 10.1172/jci.insight.151849] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/08/2021] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
T cells play a prominent role in orchestrating the immune response to viral diseases, but their role in the clinical presentation and subsequent immunity to SARS-CoV-2 infection remains poorly understood. As part of a population-based survey of the municipality of Vo', Italy, conducted after the initial SARS-CoV-2 outbreak, we sampled the T cell receptor (TCR) repertoires of the population 2 months after the initial PCR survey and followed up positive cases 9 and 15 months later. At 2 months, we found that 97.0% (98 of 101) of cases had elevated levels of TCRs associated with SARS-CoV-2. T cell frequency (depth) was increased in individuals with more severe disease. Both depth and diversity (breadth) of the TCR repertoire were positively associated with neutralizing antibody titers, driven mostly by CD4+ T cells directed against spike protein. At the later time points, detection of these TCRs remained high, with 90.7% (78 of 96) and 86.2% (25 of 29) of individuals having detectable signal at 9 and 15 months, respectively. Forty-three individuals were vaccinated by month 15 and showed a significant increase in TCRs directed against spike protein. Taken together, these results demonstrate the central role of T cells in mounting an immune defense against SARS-CoV-2 that persists out to 15 months.
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Affiliation(s)
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | | | | | | | - Sudeb Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padua, Italy
| | | | - Monia Pacenti
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Caterina Boldrin
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Margherita Cattai
- Azienda Ospedale Padova, Microbiology and Virology Unit, Padua, Italy
| | - Francesca Saluzzo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padua, Italy
| | - Mario Plebani
- Department of Medicine, University of Padova, Padua, Italy
| | | | - Jessica Bordini
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Nicola I. Lorè
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Daniela M. Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy
- CRIBI Biotech Center, University of Padova, Padua, Italy
| | | | | | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padua, Italy
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giovanni Tonon
- Center for Omics Sciences and
- Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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4
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Dorigatti I, Lavezzo E, Manuto L, Ciavarella C, Pacenti M, Boldrin C, Cattai M, Saluzzo F, Franchin E, Del Vecchio C, Caldart F, Castelli G, Nicoletti M, Nieddu E, Salvadoretti E, Labella B, Fava L, Guglielmo S, Fascina M, Grazioli M, Alvisi G, Vanuzzo MC, Zupo T, Calandrin R, Lisi V, Rossi L, Castagliuolo I, Merigliano S, Unwin HJT, Plebani M, Padoan A, Brazzale AR, Toppo S, Ferguson NM, Donnelly CA, Crisanti A. SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo'. Nat Commun 2021; 12:4383. [PMID: 34282139 PMCID: PMC8289856 DOI: 10.1038/s41467-021-24622-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
In February and March 2020, two mass swab testing campaigns were conducted in Vo', Italy. In May 2020, we tested 86% of the Vo' population with three immuno-assays detecting antibodies against the spike and nucleocapsid antigens, a neutralisation assay and Polymerase Chain Reaction (PCR). Subjects testing positive to PCR in February/March or a serological assay in May were tested again in November. Here we report on the results of the analysis of the May and November surveys. We estimate a seroprevalence of 3.5% (95% Credible Interval (CrI): 2.8-4.3%) in May. In November, 98.8% (95% Confidence Interval (CI): 93.7-100.0%) of sera which tested positive in May still reacted against at least one antigen; 18.6% (95% CI: 11.0-28.5%) showed an increase of antibody or neutralisation reactivity from May. Analysis of the serostatus of the members of 1,118 households indicates a 26.0% (95% CrI: 17.2-36.9%) Susceptible-Infectious Transmission Probability. Contact tracing had limited impact on epidemic suppression.
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Affiliation(s)
- Ilaria Dorigatti
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK.
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy.
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Constanze Ciavarella
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | | | | | | | - Francesca Saluzzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elisa Franchin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Federico Caldart
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gioele Castelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Michele Nicoletti
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Eleonora Nieddu
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Beatrice Labella
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ludovico Fava
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Simone Guglielmo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Marco Grazioli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | | | | | | | - Stefano Merigliano
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Mario Plebani
- Department of Medicine, University of Padova, Padova, Italy
| | - Andrea Padoan
- Department of Medicine, University of Padova, Padova, Italy
| | | | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
- CRIBI Biotech Centre, University of Padova, Padova, Italy
| | - Neil M Ferguson
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Andrea Crisanti
- Department of Molecular Medicine, University of Padova, Padova, Italy.
- Azienda Ospedale Padova, Padova, Italy.
- Department of Life Science Imperial College London, Exhibition Road, London, UK.
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5
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Chatzidimitriou E, Bisaccia P, Corrà F, Bonato M, Irato P, Manuto L, Toppo S, Bakiu R, Santovito G. Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature. Antioxidants (Basel) 2020; 9:antiox9040325. [PMID: 32316382 PMCID: PMC7222407 DOI: 10.3390/antiox9040325] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/29/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
In the present study, we describe the purification and molecular characterization of Cu,Zn superoxide dismutase (SOD) from Chionodraco hamatus, an Antarctic teleost widely distributed in many areas of the Ross Sea that plays a pivotal role in the Antarctic food chain. The primary sequence was obtained using biochemical and molecular biology approaches and compared with Cu,Zn SODs from other organisms. Multiple sequence alignment using the amino acid sequence revealed that Cu,Zn SOD showed considerable sequence similarity with its orthologues from various vertebrate species, but also some specific substitutions directly linked to cold adaptation. Phylogenetic analyses presented the monophyletic status of Antartic Teleostei among the Perciformes, confirming the erratic differentiation of these proteins and concurring with the theory of the "unclock-like" behavior of Cu,Zn SOD evolution. Expression of C. hamatus Cu,Zn SOD at both the mRNA and protein levels were analyzed in various tissues, highlighting the regulation of gene expression related to environmental stress conditions and also animal physiology. The data presented are the first on the antioxidant enzymes of a fish belonging to the Channichthyidae family and represent an important starting point in understanding the antioxidant systems of these organisms that are subject to constant risk of oxidative stress.
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Affiliation(s)
- Evangelia Chatzidimitriou
- Institute of Natural Resource Sciences, ZHAW Zurich University of Applied Sciences, 8820 Wädenswil, Switzerland;
| | - Paola Bisaccia
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Francesca Corrà
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Marco Bonato
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Paola Irato
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
| | - Laura Manuto
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (L.M.); (S.T.)
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, 35131 Padova, Italy; (L.M.); (S.T.)
- CRIBI Biotech Centre, University of Padova, 35131 Padova, Italy
| | - Rigers Bakiu
- Department of Aquaculture and Fisheries, Agricultural University of Tirana, 1000 Tiranë, Albania;
| | - Gianfranco Santovito
- Department of Biology, University of Padova, 35131 Padova, Italy; (P.B.); (F.C.); (M.B.); (P.I.)
- Correspondence:
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