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Ilié M, Benzaquen J, Hofman V, Long-Mira E, Lassalle S, Boutros J, Bontoux C, Lespinet-Fabre V, Bordone O, Tanga V, Allegra M, Salah M, Fayada J, Leroy S, Vassallo M, Touitou I, Courjon J, Contenti J, Carles M, Marquette CH, Hofman P. Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens. Int J Mol Sci 2023; 24:ijms24043478. [PMID: 36834888 PMCID: PMC9964843 DOI: 10.3390/ijms24043478] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 76% of cases were identified with a low viral load (Ct ≥ 32, and ≤200 copies/µL). The NGS analysis was successful in 91% of cases, among which 57% of cases harbored the Delta variant, and 34% the Omicron BA.1.1 variant. Only 9% of cases had unreadable sequences. There was no significant difference in the viral load in patients infected with the Omicron variant compared to the Delta variant (Ct values, p = 0.0507; copy number, p = 0.252). We show that the NGS analysis of the SARS-CoV-2 genome provides reliable detection of the Delta and Omicron SARS-CoV-2 variants in low viral load samples.
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Affiliation(s)
- Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
| | - Jonathan Benzaquen
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
| | - Jacques Boutros
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Olivier Bordone
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Virginie Tanga
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Maryline Allegra
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Myriam Salah
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Julien Fayada
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Sylvie Leroy
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Matteo Vassallo
- Department of Internal Medicine and Oncology, Centre Hospitalier de Cannes, 06400 Cannes, France
| | - Irit Touitou
- Department of Infectious Diseases, Hôpital Archet 1, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, 06200 Nice, France
| | - Johan Courjon
- Department of Infectious Diseases, Hôpital Archet 1, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, 06200 Nice, France
| | - Julie Contenti
- Emergency Department, Hôpital Pasteur 2, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, 06000 Nice, France
| | - Michel Carles
- Department of Infectious Diseases, Hôpital Archet 1, Centre Hospitalier Universitaire de Nice, Université Côte d’Azur, 06200 Nice, France
| | - Charles-Hugo Marquette
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
- Department of Pulmonary Medicine and Oncology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Hospital-Related Biobank (BB-0033-00025), Centre Hospitalier Universitaire de Nice, FHU OncoAge, Université Côte d’Azur, 06000 Nice, France
- Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Université Côte d’Azur, 06107 Nice, France
- Correspondence:
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Lu R, Wang J, Li M, He J, Wang Y, Dong J, Cai W. Retrospective quantitative detection of SARS-CoV-2 by digital PCR showing high accuracy for low viral load specimens. J Infect Dev Ctries 2022; 16:10-15. [PMID: 35192516 DOI: 10.3855/jidc.15315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/12/2021] [Accepted: 08/16/2021] [Indexed: 10/31/2022] Open
Abstract
INTRODUCTION Accurate detection of severe acute respiratory syndrome coronavirus 2 is critical for diagnosis and disease status evaluation of Coronavirus disease 2019. We retrospectively evaluated the infection status and viral load of severe acute respiratory syndrome coronavirus 2 in Nantong city, China, using a quantitative digital polymerase chain reaction and reverse-transcription PCR. METHODOLOGY A total of 103 clinical specimens from 31 patients were collected and tested by digital PCR and reverse-transcription PCR. RESULTS The overall accuracy of digital PCR was 96.8%, which was higher than the overall accuracy of 87.1% for reverse-transcription PCR. 4 (3.88%) specimens for ORF1ab and 22 (21.36%) specimens for N gene were negative by reverse-transcription PCR but positive by digital PCR. 3 (2.91%, 3/103) specimens of ORF1ab were positive by reverse-transcription PCR but negative by digital PCR. The digital PCR assay exhibited higher sensitivity to measure the N gene than the ORF1ab gene (p < 0.01). CONCLUSIONS Our results showed that digital PCR assay provides more reliable detection of Coronavirus disease 2019 than reverse-transcription PCR, especially for low viral load specimens.
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Affiliation(s)
- Renfei Lu
- Clinical Laboratory, the Nantong Third Hospital Affiliated to Nantong University, Nantong, P. R. China
| | - Jian Wang
- Clinical Laboratory, the Nantong Third Hospital Affiliated to Nantong University, Nantong, P. R. China
| | - Min Li
- Clinical Laboratory, the Nantong Third Hospital Affiliated to Nantong University, Nantong, P. R. China
| | - Jing He
- Department of Research and Development, RainSure Scientific Co, Ltd., Suzhou, P.R. China
| | - Yaqi Wang
- Department of Research and Development, RainSure Scientific Co, Ltd., Suzhou, P.R. China
| | - Jia Dong
- Department of Research and Development, RainSure Scientific Co, Ltd., Suzhou, P.R. China
| | - Weihua Cai
- Infectious Diseases Division, the Nantong Third Hospital Affiliated to Nantong University, Nantong, P. R. China.
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Erken R, Loukachov VV, de Niet A, Jansen L, Stelma F, Helder JT, Peters MW, Zaaijer HL, Kootstra NA, Willemse SB, Reesink HW. A Prospective Five-Year Follow-up After peg-Interferon Plus Nucleotide Analogue Treatment or no Treatment in HBeAg Negative Chronic Hepatitis B Patients. J Clin Exp Hepatol 2022; 12:735-44. [PMID: 35677522 DOI: 10.1016/j.jceh.2021.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Currently available treatment options for chronic hepatitis B (CHB) are not recommended for HBeAg-negative patients with a low viral load. These patients may however benefit from treatment by achieving a functional cure, defined by HBsAg-loss and undetectable HBV DNA. This study evaluated the long-term effect of combination treatment with peg-interferon-alpha-2a (peg-IFN) and adefovir or tenofovir compared to no treatment in these patients. METHODS HBeAg-negative CHB patients with HBV-DNA levels < 20,000 IU/mL (n = 151) were previously randomised 1:1:1 for peg-IFN 180 μg/week plus either adefovir 10 mg/day or tenofovir 245 mg/day, or no treatment and treated for 48 weeks in an open-label study. In this prospective long-term follow-up study, patients were monitored yearly up to five years after end of treatment (week 308). The primary outcome was sustained HBsAg-loss and secondary outcome the dynamics of HBsAg and HBV-DNA levels over time. RESULTS Of the 131 followed patients, the HBsAg-status was known for 118 patients after five-year follow-up. HBsAg-loss occurred similarly (P = 0.703) in all arms: 8/43 (18.6%) peg-IFN + adefovir, 4/34 (11.7%) peg-IFN + tenofovir, and 6/41 (14.6%) among the untreated patients. The time to HBsAg-loss did not differ between groups (P = 0.641). Low baseline HBsAg levels and genotype A were independently associated with HBsAg-loss irrespective of allocation. HBsAg and HBV-DNA levels declined similarly during follow-up in all patient groups. CONCLUSIONS This prospective randomised controlled study showed that HBsAg-loss overtime was not influenced by treatment with a combination of nucleotide analogue and Peg-IFN. Low baseline HBsAg levels can predict HBsAg-loss irrespective of treatment allocation.
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Key Words
- ADV, Adefovir dipivoxil
- ALT, Alanine aminotransferase
- CHB, Chronic hepatitis B
- EOT, End of treatment
- GZ, Grey zone
- HBeAg, Hepatitis B e antigen
- HBsAg, Hepatitis B surface antigen
- HCC, Hepatocellular Carcinoma
- HNCH, HBeAg-negative chronic infection
- NA, Nucleot(s)ide analogue
- ROC, Receiver operating characteristic
- TAF, Tenofovir alafenamide fumarateor
- TDF, Tenofovir disoproxil fumarate
- ULN, Upper limit of normal
- UMC, University Medical Centers
- combination therapy
- functional cure
- hepatitis B virus
- inactive carrier
- low viral load
- peg-IFN, Pegylated-interferon
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Abstract
A method for detecting HBV DNA in peripheral blood at low viral load using real-time PCR was developed and its significance in identifying HBsAg-negative viral hepatitis B was evaluated. When developing the method, blood plasma samples and liver tissue biopsy material were used from 128 patients living in St. Petersburg, in various regions of the Russian Federation, as well as in the Central Asia countries. We also used blood plasma samples from 96 pregnant women and 37 hemodialysis center patients living in Northwestern Federal District, 199 foreign citizens undergoing medical examination to obtain work permits at the Directorate for Migration in the Northwestern Federal District, 397 conditionally healthy people living in the Socialist Republic of Vietnam. HBV was detected by nested PCR. Analytical sensitivity was tested using the stepwise dilution method. According to the method developed by us, at the first stage, the HBV DNA is amplified using at the first stage oligonucleotides flanking the genome region 2932-3182 ... 1-1846 nt., and at the second stage two oligonucleotides pairs to the genome virus regions (gene S and gene X) and corresponding oligonucleotide fluorescently labeled probes complementary to the amplified fragments regions carrying fluorophores at the 5'-end, and non-fluorescent quenchers at the 3'-end. The channel corresponding to the FAM fluorophore detects the HBV DNA S-region amplification product, and the channel corresponding to the ROX fluorophore detects the HBV DNA X-region amplification product. The method sensitivity for DNA extraction from plasma with a 100 μl volume was 10 IU/ml. Obtaining a threshold cycle Ct for only one FAM or ROX fluorophore may indicate the HBV DNA presence in a sample at a load of less than 10 IU / ml, HBV detection in this case is possible with a repeated PCR study of the corresponding sample with HBV DNA extraction from an increased plasma volume (200-1000 μl). The developed method makes it possible to identify various HBV genovariants, both characteristic and rare in the Russian Federation, circulating in other world regions. The method can be used to detect HBV in risk groups, in the population, as well as in screening blood donors in order to ensure the blood transfusions safety.
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Affiliation(s)
| | - A V Semenov
- Saint-Petersburg Pasteur Institute.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov.,North-West State Medical University n.a. I.I. Mechnikov
| | | | - Areg A Totolian
- Saint-Petersburg Pasteur Institute.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov
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Ostankova YV, Semenov AV, Totolian AA. [Hepatitis B virus identification in a blood plasma at a low viral load.]. Klin Lab Diagn 2019; 64:635-640. [PMID: 31742959 DOI: 10.18821/0869-2084-2019-64-10-635-640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 10/04/2019] [Accepted: 10/10/2019] [Indexed: 02/06/2023]
Abstract
To analyze the method for detecting HBV DNA in peripheral blood at low viral load and evaluate its significance in identifying HBsAg-negative viral hepatitis B. In this work, samples of blood and liver tissue biopsy material were used from 128 patients living in the Russian Federation and the Republic of Uzbekistan without CHB and with CHB confirmed detection of circle covalently closed HBV DNA in hepatocytes. Plasma viral load was measured using the «AmpliSens® HBV-Monitor-FL» kit. HBV at low viral load was detected by nested PCR. Analytical sensitivity was checked by step dilution. According to our method, at the first stage, an asymmetric PCR is carried out using extended oligonucleotide primers with different melting points, complementary to the hepatitis B different genotypes genomes greatest similarity region. To increase the sensitivity, a second PCR is performed using the first reaction amplification product and internal primers. The sensitivity of the method for DNA extraction from 100 μl of plasma was 5 IU / ml, specificity 100%. Since, in spite of the HBV genotypes characteristic geographical distribution, the detection of "alien" genovariants for certain territories is becoming more frequent, we tested the method in geographically remote but active international relations with the Russian Federation regions with a high frequency of hepatotropic viruses. The developed method for detecting HBV DNA in blood plasma at low viral load based on PCR technology allows the various HBV gene variants identification and genotyping, both characteristic and rare in the Russian Federation, circulating in other world regions. The method can be used to detect HBV in risk groups, in a population, as well as when screening blood donors in order to ensure the blood transfusions safety.
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Affiliation(s)
- Y V Ostankova
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia
| | - A V Semenov
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov, 197022, Saint Petersburg, Russia.,North-West State Medical University n.a. I.I. Mechnikov, 191015, Saint Petersburg, Russia
| | - A A Totolian
- Saint-Petersburg Pasteur Institute, 197191, Saint Petersburg, Russia.,Saint-Petersburg State Medical University n.a. acad. I.P. Pavlov, 197022, Saint Petersburg, Russia
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