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Hasan MS, Rahman MS, Das PK, Ul Alam AR, Islam OK, Al-Emran HM, Hossain MA, Jahid IK. Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology. MethodsX 2024; 12:102646. [PMID: 38524302 PMCID: PMC10957433 DOI: 10.1016/j.mex.2024.102646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.
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Affiliation(s)
- Md. Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Shaminur Rahman
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Prosanto Kumar Das
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - A.S.M. Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Hassan M. Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M. Anwar Hossain
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
- Genome Centre, Jashore University of Science and Technology, Jashore 7408, Bangladesh
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2
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Kwon R, Yeung CCS. Advances in next-generation sequencing and emerging technologies for hematologic malignancies. Haematologica 2024; 109:379-387. [PMID: 37584286 PMCID: PMC10828783 DOI: 10.3324/haematol.2022.282442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 08/17/2023] Open
Abstract
Innovations in molecular diagnostics have often evolved through the study of hematologic malignancies. Examples include the pioneering characterization of the Philadelphia chromosome by cytogenetics in the 1970s, the implementation of polymerase chain reaction for high-sensitivity detection and monitoring of mutations and, most recently, targeted next- generation sequencing to drive the prognostic and therapeutic assessment of leukemia. Hematologists and hematopath- ologists have continued to advance in the past decade with new innovations improving the type, amount, and quality of data generated for each molecule of nucleic acid. In this review article, we touch on these new developments and discuss their implications for diagnostics in hematopoietic malignancies. We review advances in sequencing platforms and library preparation chemistry that can lead to faster turnaround times, novel sequencing techniques, the development of mobile laboratories with implications for worldwide benefits, the current status of sample types, improvements to quality and reference materials, bioinformatic pipelines, and the integration of machine learning and artificial intelligence into mol- ecular diagnostic tools for hematologic malignancies.
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Affiliation(s)
- Regina Kwon
- Department of Laboratory Medicine and Pathology, University of Washington
| | - Cecilia C. S. Yeung
- Department of Laboratory Medicine and Pathology, University of Washington
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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3
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Gruber CEM, Tucci FG, Rueca M, Mazzotta V, Gramigna G, Vergori A, Fabeni L, Berno G, Giombini E, Butera O, Focosi D, Prandi IG, Chillemi G, Nicastri E, Vaia F, Girardi E, Antinori A, Maggi F. Treatment-Emergent Cilgavimab Resistance Was Uncommon in Vaccinated Omicron BA.4/5 Outpatients. Biomolecules 2023; 13:1538. [PMID: 37892220 PMCID: PMC10605390 DOI: 10.3390/biom13101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Mutations in the SARS-CoV-2 Spike glycoprotein can affect monoclonal antibody efficacy. Recent findings report the occurrence of resistant mutations in immunocompromised patients after tixagevimab/cilgavimab treatment. More recently, the Food and Drug Agency revoked the authorization for tixagevimab/cilgavimab, while this monoclonal antibody cocktail is currently recommended by the European Medical Agency. We retrospectively reviewed 22 immunocompetent patients at high risk for disease progression who received intramuscular tixagevimab/cilgavimab as early COVID-19 treatment and presented a prolonged high viral load. Complete SARS-CoV-2 genome sequences were obtained for a deep investigation of mutation frequencies in Spike protein before and during treatment. At seven days, only one patient showed evidence of treatment-emergent cilgavimab resistance. Quasispecies analysis revealed two different deletions on the Spike protein (S:del138-144 or S:del141-145) in combination with the resistance S:K444N mutation. The structural and dynamic impact of the two quasispecies was characterized by using molecular dynamics simulations, showing the conservation of the principal functional movements in the mutated systems and their capabilities to alter the structure and dynamics of the RBD, responsible for the interaction with the ACE2 human receptor. Our study underlines the importance of prompting an early virological investigation to prevent drug resistance or clinical failures in immunocompetent patients.
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Affiliation(s)
- Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Fabio Giovanni Tucci
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Giulia Gramigna
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Emanuele Nicastri
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
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4
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Tanaka H, Namkoong H, Chubachi S, Irie S, Uwamino Y, Lee H, Azekawa S, Otake S, Nakagawara K, Fukushima T, Watase M, Kusumoto T, Masaki K, Kamata H, Ishii M, Okada Y, Takano T, Imoto S, Koike R, Kimura A, Miyano S, Ogawa S, Kanai T, Sato TA, Fukunaga K. Clinical characteristics of patients with COVID-19 harboring detectable intracellular SARS-CoV-2 RNA in peripheral blood cells. Int J Infect Dis 2023; 135:41-44. [PMID: 37541421 DOI: 10.1016/j.ijid.2023.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
OBJECTIVES Although SARS-CoV-2 RNAemia has been reported to strongly impact patients with severe COVID-19, the clinical characteristics of patients with COVID-19 harboring detectable intracellular SARS-CoV-2 RNA remain unknown. METHODS We included adult patients who had developed COVID-19 between February and September 2020. Total white blood cells derived from the buffy coat of peripheral whole blood were used to detect SARS-CoV-2 RNA using the Illumina COVIDSeq test. We compared the clinical characteristics between patients with and without detected viral RNA (detected and undetected groups). RESULTS Among the 390 patients included, 17 harbored SARS-CoV-2 RNA in peripheral white blood cells. All 17 patients required oxygen support during the disease course and had higher intensive care unit admission (52.9% vs 28.9%, P = 0.035), mortality (17.7% vs 3.5%, P = 0.004), kidney dysfunction (severe, 23.5% vs 6.4%, P = 0.029), and corticosteroid treatment rates (76.5% vs 46.5%, P = 0.016) than those of patients in the undetected group. CONCLUSION We propose that patients with circulating intracellular SARS-CoV-2 RNA in the peripheral blood exhibited the most severe disease course.
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Affiliation(s)
- Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan.
| | - Shotaro Chubachi
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | - Yoshifumi Uwamino
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ho Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Azekawa
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shiro Otake
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kensuke Nakagawara
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takahiro Fukushima
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Mayuko Watase
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuya Kusumoto
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Katsunori Masaki
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hirofumi Kamata
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan; Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan; Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Tomomi Takano
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ryuji Koike
- Clinical Research Center, Tokyo Medical and Dental University Hospital of Medicine, Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Taka-Aki Sato
- iLAC Co., Ltd., Tsukuba, Ibaraki, Japan; Research and Development Center for Precision Medicine, University of Tsukuba, Ibaraki, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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5
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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Molecular Characterization of Whole-Genome SARS-CoV-2 from the First Suspected Cases of the XE Variant in the Lazio Region, Italy. Diagnostics (Basel) 2022; 12:diagnostics12092219. [PMID: 36140622 PMCID: PMC9497488 DOI: 10.3390/diagnostics12092219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022] Open
Abstract
We report two cases of SARS-CoV-2 recombinant variant XE detected in nasopharyngeal swabs (NPS) of hospitalized patients with no evident epidemiological link in Lazio, Central Italy. Whole-Genome Sequencing (WGS) performed on an Ion Torrent GSS5 platform according to Italian flash surveys showed genomes corresponding to the PANGOLIN unclassified lineage and the Nextclade XE clade. Further analyses were then carried out to investigate more deeply the genetic characteristics of these XE-like sequences. When phylogenetic trees, by using IQ-TREE, were built splitting the genome into two regions according to the putative XE recombination site, the upstream and downstream regions were seen to be clustered near BA.1 and BA.2 sequences, respectively. However, our XE-like sequences clustered separately, with a significant bootstrap, from the classified European and Italian XE strains, although the recombination site between BA.1 and BA.2 was identified at the nucleotide site 11556 by RDP4 software, consistent with the putative XE breakpoint. These findings show the risk of the introduction of novel recombinant variants of SARS-CoV-2 and the existence of XE-like strains, phylogenetically separated, that could make their exact taxonomy difficult. It follows the need for continued SARS-CoV-2 surveillance by WGS.
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Guo F, Lang Y, Long G, Liu Z, Jing G, Zhou Y, Zhang B, Yu S. Ion Torrent TM Genexus TM Integrated Sequencer and ForeNGS Analysis Software—an automatic NGS-STR workflow from DNA to profile for forensic science. Forensic Sci Int Genet 2022; 61:102753. [DOI: 10.1016/j.fsigen.2022.102753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/03/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022]
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SARS-CoV-2 Whole-Genome Sequencing by Ion S5 Technology—Challenges, Protocol Optimization and Success Rates for Different Strains. Viruses 2022; 14:v14061230. [PMID: 35746701 PMCID: PMC9227152 DOI: 10.3390/v14061230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/14/2022] [Accepted: 06/04/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic demonstrated how rapidly various molecular methods can be adapted for a Public Health Emergency. Whether a need arises for whole-genome studies (next-generation sequencing), fast and high-throughput diagnostics (reverse-transcription real-time PCR) or global immunization (construction of mRNA or viral vector vaccines), the scientific community has been able to answer all these calls. In this study, we aimed at the assessment of effectiveness of the commercially available solution for full-genome SARS-CoV-2 sequencing (AmpliSeq™ SARS-CoV-2 Research Panel and Ion AmpliSeq™ Library Kit Plus, Thermo Fisher Scientific). The study is based on 634 samples obtained from patients from Poland, with varying viral load, assigned to a number of lineages. Here, we also present the results of protocol modifications implemented to obtain high-quality genomic data. We found that a modified library preparation protocol required less viral RNA input in order to obtain the optimal library quantity. Concurrently, neither concentration of cDNA nor reamplification of libraries from low-template samples improved the results of sequencing. On the basis of the amplicon success rates, we propose one amplicon to be redesigned, namely, the r1_1.15.1421280, for which less than 50 reads were produced by 44% of samples. Additionally, we found several mutations within different SARS-CoV-2 lineages that cause the neighboring amplicons to underperform. Therefore, due to constant SARS-CoV-2 evolution, we support the idea of conducting ongoing sequence-based surveillance studies to continuously validate commercially available RT-PCR and whole-genome sequencing solutions.
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9
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Yavarian J, Nejati A, Salimi V, Shafiei Jandaghi NZ, Sadeghi K, Abedi A, Sharifi Zarchi A, Gouya MM, Mokhtari-Azad T. Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic. PLoS One 2022; 17:e0267847. [PMID: 35499994 PMCID: PMC9060343 DOI: 10.1371/journal.pone.0267847] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/14/2022] [Indexed: 12/23/2022] Open
Abstract
Purpose Whole genome sequencing of SARS-CoV2 is important to find useful information about the viral lineages, variants of interests and variants of concern. As there are not enough data about the circulating SARS-CoV2 variants in Iran, we sequenced 54 SARS-CoV2 genomes during the 5 waves of pandemic in Iran. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq platform. The sequencing data were analyzed and compared with reference sequences. Results During the 1st wave, V and L clades were detected. The second wave was recognized by G, GH and GR clades. Circulating clades during the 3rd wave were GH and GR. In the fourth wave GRY (alpha variant), GK (delta variant) and one GH clade (beta variant) were detected. All viruses in the fifth wave were in clade GK (delta variant). There were different mutations in all parts of the genomes but Spike-D614G, NSP12-P323L, N-R203K and N-G204R were the most frequent mutants in these studied viruses. Conclusions These findings display the significance of SARS-CoV2 monitoring to help on time detection of possible variants for pandemic control and vaccination plans.
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Affiliation(s)
- Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Nejati
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kaveh Sadeghi
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Adel Abedi
- Mathematics Department, Shahid Beheshti University, Tehran, Iran
| | - Ali Sharifi Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | | | - Talat Mokhtari-Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- * E-mail:
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10
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Yermanos A, Hong KL, Agrafiotis A, Han J, Nadeau S, Valenzuela C, Azizoglu A, Ehling R, Gao B, Spahr M, Neumeier D, Chang CH, Dounas A, Petrillo E, Nissen I, Burcklen E, Feldkamp M, Beisel C, Oxenius A, Savic M, Stadler T, Rudolf F, Reddy ST. DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. BMC Genomics 2022; 23:289. [PMID: 35410128 PMCID: PMC8995413 DOI: 10.1186/s12864-022-08403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. RESULTS Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. CONCLUSIONS DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity. DeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2. Image was created using Biorender.com .
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland. .,Institute of Microbiology, ETH Zurich, Zurich, Switzerland. .,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cecilia Valenzuela
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Asli Azizoglu
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Roy Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael Spahr
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ching-Hsiang Chang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Dounas
- Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Mirjam Feldkamp
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Miodrag Savic
- Department of Health, Economics and Health Directorate Canton Basel-Landschaft, Liestal, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. .,Botnar Research Centre for Child Health, Basel, Switzerland.
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Sheffield BS, Beharry A, Diep J, Perdrizet K, Iafolla MAJ, Raskin W, Dudani S, Brett MA, Starova B, Olsen B, Cheema PK. Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care. Curr Oncol 2022; 29:1326-1334. [PMID: 35323313 PMCID: PMC8947443 DOI: 10.3390/curroncol29030113] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2-5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care.
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Affiliation(s)
- Brandon S. Sheffield
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Andrea Beharry
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Joanne Diep
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Kirstin Perdrizet
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada; (K.P.); (M.A.J.I.); (W.R.); (S.D.); (P.K.C.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Marco A. J. Iafolla
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada; (K.P.); (M.A.J.I.); (W.R.); (S.D.); (P.K.C.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - William Raskin
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada; (K.P.); (M.A.J.I.); (W.R.); (S.D.); (P.K.C.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Shaan Dudani
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada; (K.P.); (M.A.J.I.); (W.R.); (S.D.); (P.K.C.)
| | - Mary Anne Brett
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Blerta Starova
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Brian Olsen
- Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada; (A.B.); (J.D.); (M.A.B.); (B.S.); (B.O.)
| | - Parneet K. Cheema
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada; (K.P.); (M.A.J.I.); (W.R.); (S.D.); (P.K.C.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
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12
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Scapaticci M, Bartolini A, Vitone F, Cerreta V, Vignoli M, Gnudi E, Frazzoni A, Sitta B, Capitani S, Lopriore A, Donadio M, Chiarastella S, Bioli M, Mancini R. Detection of a characteristic melting profile of a SARS-CoV-2 Kappa variant in Italy using the SARS-CoV-2 Variants ELITe MGB® Kit. J Virol Methods 2022; 301:114458. [PMID: 35026304 PMCID: PMC8758410 DOI: 10.1016/j.jviromet.2022.114458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 11/13/2022]
Abstract
Background Although more than a year has passed since the start of the pandemic, SARS-CoV-2 infection still represents a major challenge for public health all over the world due to viral genome capability of gaining rapid mutations. Whole-genome sequencing (WGS) is the gold standard for variant identification, but it is time consuming and relatively expensive. For this reason, assays targeting multiple regions of the SARS-CoV-2 genome may be useful for a rapid traceability of either known or new variants, anyway, not all the manufacturers are able to sustain the rapid development of variants. Objective We tested forty nasopharyngeal swabs, resulted positive for the presence of SARS-CoV-2 RNA at low cycle threshold (CT < 25), with SARS-CoV-2 Variants ELITe MGB® Kit, which was designed to identify Nigerian variant, possible UK variant and South African or Brazilian variant. Results During the analysis, we noted an atypical melting curve, different from the other variants recognizable by the kit. The subsequent WGS reported this variant as Kappa, so we assess the possibility of "suspecting" the presence of a Kappa variant using SARS-CoV-2 Variants ELITe MGB® Kit. Conclusions Rapid variant screening followed by WGS offers the opportunity to study mutation dynamics and quickly identify possible variants of interest (VOI) and/or variants of concern (VOC), which is crucial in virus spreading control. Furthermore, an accurate analysis of the melting peak could be useful to suspect the presence of new variants.
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Affiliation(s)
| | | | | | | | - Monica Vignoli
- LUM, AUSL Bologna, Largo Nigrisoli 2, 40133, Bologna, Italy
| | - Elena Gnudi
- LUM, AUSL Bologna, Largo Nigrisoli 2, 40133, Bologna, Italy
| | | | - Barbara Sitta
- LUM, AUSL Bologna, Largo Nigrisoli 2, 40133, Bologna, Italy
| | | | | | | | | | - Marina Bioli
- LUM, AUSL Bologna, Largo Nigrisoli 2, 40133, Bologna, Italy
| | - Rita Mancini
- LUM, AUSL Bologna, Largo Nigrisoli 2, 40133, Bologna, Italy
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