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Purba AKR, Rosyid AN, Handayani S, Rachman BE, Romdhoni AC, Al Farabi MJ, Wahyuhadi J, Prananingtias R, Rahayu AN, Alkaff FF, Azmi YA, Prasetyo S, Nadjib M, Gutjahr LP, Humaidy RF. Economic Evaluation of COVID-19 Screening Tests and Surveillance Strategies in Low-Income, Middle-Income, and High-Income Countries: A Systematic Review. Med Sci Monit 2024; 30:e943863. [PMID: 38643358 PMCID: PMC11044836 DOI: 10.12659/msm.943863] [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: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Economic evaluation of the testing strategies to control transmission and monitor the severity of COVID-19 after the pandemic is essential. This study aimed to review the economic evaluation of COVID-19 tests and to construct a model with outcomes in terms of cost and test acceptability for surveillance in the post-pandemic period in low-income, middle-income, and high-income countries. MATERIAL AND METHODS We performed the systematic review following PRISMA guidelines through MEDLINE and EMBASE databases. We included the relevant studies that reported the economic evaluation of COVID-19 tests for surveillance. Also, we input current probability, sensitivity, and specificity for COVID-19 surveillance in the post-pandemic period. RESULTS A total of 104 articles met the eligibility criteria, and 8 articles were reviewed and assessed for quality. The specificity and sensitivity of COVID-19 screening tests were reported as 80% to 90% and 40% to 90%, respectively. The target population presented a mortality rate between 0.2% and 19.2% in the post-pandemic period. The implementation model of COVID-19 screening tests for surveillance with a cost mean for molecular and antigen tests was US$ 46.64 (min-max US $0.25-$105.39) and US $6.15 (min-max US $2-$10), respectively. CONCLUSIONS For the allocation budget for the COVID-19 surveillance test, it is essential to consider the incidence and mortality of the post-pandemic period in low-income, middle-income, and high-income countries. A robust method to evaluate outcomes is needed to prevent increasing COVID-19 incidents earlier.
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Affiliation(s)
- Abdul Khairul Rizki Purba
- Division of Pharmacology and Therapy, Department of Anatomy Histology and Pharmacology, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
- Department of Health Science, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Medical Education Master Program, Faculty of Medicine, Universitas Airlangga, Surabaya, West Java, Indonesia
| | - Alfian Nur Rosyid
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Samsriyaningsih Handayani
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Brian Eka Rachman
- Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Achmad Chusnu Romdhoni
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Makhyan Jibril Al Farabi
- Department of Cardiology and Vascular Medicine, Universitas Airlangga/Soetomo General Hospital, Surabaya, Eest Java, Indonesia
| | - Joni Wahyuhadi
- Department of Neurosurgery, Faculty of medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Rosita Prananingtias
- Department of Medical Record, Universitas Airlangga Hospital, Surabaya, Eest Java, Indonesia
| | - Ainun Nitsa Rahayu
- Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
| | - Firas Farisi Alkaff
- Division of Pharmacology and Therapy, Department of Anatomy, Histology, and Pharmacology, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
- Division of Nephrology, Department of Internal Medicine, University Medical Center Groningen, Groningen, The Netherlands
| | - Yufi Aulia Azmi
- Department of Urology, Faculty of Medicine, Universitas Airlangga-Dr. Soetomo General Academic Hospital, Surabaya, Eest Java, Indonesia
- Department Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sabarinah Prasetyo
- Department of Biostatistic and Population Studies, Faculty of Public Health, Universitas Indonesia, Depok, West Java, Indonesia
| | - Mardiati Nadjib
- Department of Health Administration and Health Policy, Faculty of Public Health, Universitas Indonesia, Depok, West Java, Indonesia
| | | | - Raudia Faridah Humaidy
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Eest Java, Indonesia
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2
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Curini V, Ancora M, Jurisic L, Di Lollo V, Secondini B, Mincarelli LF, Caporale M, Puglia I, Di Gialleonardo L, Mangone I, Di Domenico M, Di Pasquale A, Lorusso A, Marcacci M, Cammà C. Evaluation of next generation sequencing approaches for SARS-CoV-2. Heliyon 2023; 9:e21101. [PMID: 38027571 PMCID: PMC10643093 DOI: 10.1016/j.heliyon.2023.e21101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.
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Affiliation(s)
- Valentina Curini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Lucija Jurisic
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | | | - Ilaria Puglia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | | | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Adriano Di Pasquale
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Teramo, Italy
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3
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Oyola S. Characterization of SARS-CoV-2 genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population. RESEARCH SQUARE 2023:rs.3.rs-3457875. [PMID: 37961584 PMCID: PMC10635312 DOI: 10.21203/rs.3.rs-3457875/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Vaccination is a key control measure of COVID-19 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing herd immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2, largely through vaccine-induced immune pressure. Here we investigated the recombination events and single nucleotide polymorphisms (SNPs) on SARS-CoV-2 genome in non-vaccinated and vaccinated patients in the Kenyan population. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within-wave and inter-wave recombination events from the beginning of the pandemic (June 2020) to (October 2022) in Kenya. An in-depth analysis of (SNPs) on the S, ORf1a/b, and N genes identified previously unreported mutations. We detected a minority variant in non-vaccinated patients in Kenya, that contained immune escape mutation S255F of the spike gene and showing a differential recombination pattern within the non-vaccinated patients. Detailed analysis of recombination between waves suggested an association between increased population immunity and declining risk of emergence of variants of concern. Overall, this work identified unique mutations in SARS-CoV-2 which could have significant implications for virus evolution, virulence, and immune escape.
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4
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Lim HGM, Fann YC, Lee YCG. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2. Brief Bioinform 2023; 24:bbad280. [PMID: 37738400 PMCID: PMC10516370 DOI: 10.1093/bib/bbad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 09/24/2023] Open
Abstract
Implementing a specific cloud resource to analyze extensive genomic data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a challenge when resources are limited. To overcome this, we repurposed a cloud platform initially designed for use in research on cancer genomics (https://cgc.sbgenomics.com) to enable its use in research on SARS-CoV-2 to build Cloud Workflow for Viral and Variant Identification (COWID). COWID is a workflow based on the Common Workflow Language that realizes the full potential of sequencing technology for use in reliable SARS-CoV-2 identification and leverages cloud computing to achieve efficient parallelization. COWID outperformed other contemporary methods for identification by offering scalable identification and reliable variant findings with no false-positive results. COWID typically processed each sample of raw sequencing data within 5 min at a cost of only US$0.01. The COWID source code is publicly available (https://github.com/hendrick0403/COWID) and can be accessed on any computer with Internet access. COWID is designed to be user-friendly; it can be implemented without prior programming knowledge. Therefore, COWID is a time-efficient tool that can be used during a pandemic.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
- Department of Medical Research, Tzu Chi Hospital Indonesia, Pantai Indah Kapuk, Greater Jakarta, Indonesia 14470
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA 20892
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan 11031
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5
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Carbo EC, Mourik K, Boers SA, Munnink BO, Nieuwenhuijse D, Jonges M, Welkers MRA, Matamoros S, van Harinxma Thoe Slooten J, Kraakman MEM, Karelioti E, van der Meer D, Veldkamp KE, Kroes ACM, Sidorov I, de Vries JJC. A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2. Eur J Clin Microbiol Infect Dis 2023; 42:701-713. [PMID: 37017810 PMCID: PMC10075175 DOI: 10.1007/s10096-023-04590-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastien Matamoros
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Joost van Harinxma Thoe Slooten
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margriet E M Kraakman
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Karin Ellen Veldkamp
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
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6
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Tzou PL, Tao K, Sahoo MK, Kosakovsky Pond SL, Pinsky BA, Shafer RW. Sierra SARS-CoV-2 sequence and antiviral resistance analysis program. J Clin Virol 2022; 157:105323. [PMID: 36334368 PMCID: PMC9595491 DOI: 10.1016/j.jcv.2022.105323] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/11/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Although most laboratories are capable of employing established protocols to perform full-genome SARS-CoV-2 sequencing, many are unable to assess sequence quality, select appropriate mutation-detection thresholds, or report on the potential clinical significance of mutations in the targets of antiviral therapy METHODS: We describe the technical aspects and benchmark the performance of Sierra SARS-CoV-2, a program designed to perform these functions on user-submitted FASTQ and FASTA sequence files and lists of Spike mutations. Sierra SARS-CoV-2 indicates which sequences contain an unexpectedly large number of unusual mutations and which mutations are associated with reduced susceptibility to clinical stage mAbs, the RdRP inhibitor remdesivir, or the Mpro inhibitor nirmatrelvir RESULTS: To assess the performance of Sierra SARS-CoV-2 on FASTQ files, we applied it to 600 representative FASTQ sequences and compared the results to the COVID-19 EDGE program. To assess its performance on FASTA files, we applied it to nearly one million representative FASTA sequences and compared the results to the GISAID mutation annotation. To assess its performance on mutations lists, we applied it to 13,578 distinct Spike RBD mutation patterns and showed that exactly or partially matching annotations were available for 88% of patterns CONCLUSION: Sierra SARS-CoV-2 leverages previously published data to improve the quality control of submitted viral genomic data and to provide functional annotation on the impact of mutations in the targets of antiviral SARS-CoV-2 therapy. The program can be found at https://covdb.stanford.edu/sierra/sars2/ and its source code at https://github.com/hivdb/sierra-sars2.
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Affiliation(s)
- Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Benjamin A Pinsky
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
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7
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Shishir TA, Jannat T, Naser IB. Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh. Front Genet 2022; 13:966939. [PMID: 36226176 PMCID: PMC9548531 DOI: 10.3389/fgene.2022.966939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
The highly pathogenic virus SARS-CoV-2 has shattered the healthcare system of the world causing the COVID-19 pandemic since first detected in Wuhan, China. Therefore, scrutinizing the genome structure and tracing the transmission of the virus has gained enormous interest in designing appropriate intervention strategies to control the pandemic. In this report, we examined 4,622 sequences from Bangladesh and found that they belonged to thirty-five major PANGO lineages, while Delta alone accounted for 39%, and 78% were from just four primary lineages. Our research has also shown Dhaka to be the hub of viral transmission and observed the virus spreading back and forth across the country at different times by building a transmission network. The analysis resulted in 7,659 unique mutations, with an average of 24.61 missense mutations per sequence. Moreover, our analysis of genetic diversity and mutation patterns revealed that eight genes were under negative selection pressure to purify deleterious mutations, while three genes were under positive selection pressure. Together with an ongoing genomic surveillance program, these data will contribute to a better understanding of SARS-CoV-2, as well as its evolution pattern and pandemic characteristics in Bangladesh.
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Affiliation(s)
- Tushar Ahmed Shishir
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
- Rangamati General Hospital, Chattogram, Bangladesh
| | - Taslimun Jannat
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Iftekhar Bin Naser
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
- *Correspondence: Iftekhar Bin Naser,
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8
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Receptor-Binding-Motif-Targeted Sanger Sequencing: a Quick and Cost-Effective Strategy for Molecular Surveillance of SARS-CoV-2 Variants. Microbiol Spectr 2022; 10:e0066522. [PMID: 35638906 PMCID: PMC9241651 DOI: 10.1128/spectrum.00665-22] [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] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) is the gold standard for characterizing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and identification of new variants. However, the cost involved and time needed for WGS prevent routine, rapid clinical use. This study aimed to develop a quick and cost-effective surveillance strategy for SARS-CoV-2 variants in saliva and nasal swab samples by spike protein receptor-binding-motif (RBM)-targeted Sanger sequencing. Saliva and nasal swabs prescreened for the presence of the nucleocapsid (N) gene of SARS-CoV-2 were subjected to RBM-specific single-amplicon generation and Sanger sequencing. Sequences were aligned by CLC Sequence Viewer 8, and variants were identified based upon specific mutation signature. Based on this strategy, the present study identified Alpha, Beta/Gamma, Delta, and Omicron variants in a quick and cost-effective manner. IMPORTANCE The coronavirus disease 2019 (COVID-19) pandemic resulted in 427 million infections and 5.9 million deaths globally as of 21 February 2022. SARS-CoV-2, the causative agent of the COVID-19 pandemic, frequently mutates and has developed into variants of major public health concerns. Following the Alpha variant (B.1.1.7) infection wave, the Delta variant (B.1.617.2) became prevalent, and now the recently identified Omicron (B.1.1.529) variant is spreading rapidly and forming BA.1, BA.1.1, BA.2, BA.3, BA.4, and BA.5 lineages of concern. Prompt identification of mutational changes in SARS-CoV-2 variants is challenging but critical to managing the disease spread and vaccine/therapeutic modifications. Considering the cost involved and resource limitation of WGS globally, an RBM-targeted Sanger sequencing strategy is adopted in this study for quick molecular surveillance of SARS-CoV-2 variants.
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9
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Warneford-Thomson R, Shah PP, Lundgren P, Lerner J, Morgan J, Davila A, Abella BS, Zaret K, Schug J, Jain R, Thaiss CA, Bonasio R. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. eLife 2022; 11:69949. [PMID: 35532013 PMCID: PMC9084890 DOI: 10.7554/elife.69949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/24/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5–10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.
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Affiliation(s)
- Robert Warneford-Thomson
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Parisha P Shah
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Patrick Lundgren
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Lerner
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jason Morgan
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Antonio Davila
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,University of Pennsylvania School of Nursing, Philadelphia, United States
| | - Benjamin S Abella
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Kenneth Zaret
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Schug
- Next-Generation Sequencing Core, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Rajan Jain
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Christoph A Thaiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
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10
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Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y, Schultz J, McDevitt J, LaPorta J, Kwon E, Buyske S, Garbolino D, Biloholowski G, Pastuszak A, Storella M, Bhalla A, Charlier-Rodriguez F, Hager R, Grimwood R, Nahas SA. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 2022; 22:404. [PMID: 35468749 PMCID: PMC9035976 DOI: 10.1186/s12879-022-07374-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. METHODS RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. RESULTS An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. CONCLUSION These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Chirayu Goswami
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Michael Sheldon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Christian Bixby
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | | | - Yihe Wang
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jonathan Schultz
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jessica McDevitt
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - James LaPorta
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Elaine Kwon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Rutgers University, 559 Hill Center, 110 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | - Dana Garbolino
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Alex Pastuszak
- Vault Health, 115 Broadway Suite 1800, 18th Floor, Dobbs Ferry, NY, 10522, USA
| | - Mary Storella
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Amit Bhalla
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Russ Hager
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Robin Grimwood
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Shareef A Nahas
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA.
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11
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Lim HGM, Hsiao SH, Fann YC, Lee YCG. Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. Genes (Basel) 2022. [PMID: 35456492 DOI: 10.3390/genes1304068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Several variants of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging all over the world. Variant surveillance from genome sequencing has become crucial to determine if mutations in these variants are rendering the virus more infectious, potent, or resistant to existing vaccines and therapeutics. Meanwhile, analyzing many raw sequencing data repeatedly with currently available code-based bioinformatics tools is tremendously challenging to be implemented in this unprecedented pandemic time due to the fact of limited experts and computational resources. Therefore, in order to hasten variant surveillance efforts, we developed an installation-free cloud workflow for robust mutation profiling of SARS-CoV-2 variants from multiple Illumina sequencing data. Herein, 55 raw sequencing data representing four early SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) from an open-access database were used to test our workflow performance. As a result, our workflow could automatically identify mutated sites of the variants along with reliable annotation of the protein-coding genes at cost-effective and timely manner for all by harnessing parallel cloud computing in one execution under resource-limitation settings. In addition, our workflow can also generate a consensus genome sequence which can be shared with others in public data repositories to support global variant surveillance efforts.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Shih-Hsin Hsiao
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Yang C Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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12
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Lim HGM, Hsiao SH, Fann YC, Lee YCG. Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw Illumina Sequencing Data with Cloud Workflow. Genes (Basel) 2022; 13:genes13040686. [PMID: 35456492 PMCID: PMC9028989 DOI: 10.3390/genes13040686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Several variants of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging all over the world. Variant surveillance from genome sequencing has become crucial to determine if mutations in these variants are rendering the virus more infectious, potent, or resistant to existing vaccines and therapeutics. Meanwhile, analyzing many raw sequencing data repeatedly with currently available code-based bioinformatics tools is tremendously challenging to be implemented in this unprecedented pandemic time due to the fact of limited experts and computational resources. Therefore, in order to hasten variant surveillance efforts, we developed an installation-free cloud workflow for robust mutation profiling of SARS-CoV-2 variants from multiple Illumina sequencing data. Herein, 55 raw sequencing data representing four early SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) from an open-access database were used to test our workflow performance. As a result, our workflow could automatically identify mutated sites of the variants along with reliable annotation of the protein-coding genes at cost-effective and timely manner for all by harnessing parallel cloud computing in one execution under resource-limitation settings. In addition, our workflow can also generate a consensus genome sequence which can be shared with others in public data repositories to support global variant surveillance efforts.
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Affiliation(s)
- Hendrick Gao-Min Lim
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Shih-Hsin Hsiao
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Yang C. Fann
- IT and Bioinformatics Program, Division of Intramural, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yuan-Chii Gladys Lee
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Correspondence:
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13
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VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data. Microbiol Spectr 2022; 10:e0256421. [PMID: 35234489 PMCID: PMC8941893 DOI: 10.1128/spectrum.02564-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for detecting and investigating viral pathogens; however, analysis and management of the enormous amounts of data generated from these technologies remains a challenge. Here, we present VPipe (the Viral NGS Analysis Pipeline and Data Management System), an automated bioinformatics pipeline optimized for whole-genome assembly of viral sequences and identification of diverse species. VPipe automates the data quality control, assembly, and contig identification steps typically performed when analyzing NGS data. Users access the pipeline through a secure web-based portal, which provides an easy-to-use interface with advanced search capabilities for reviewing results. In addition, VPipe provides a centralized system for storing and analyzing NGS data, eliminating common bottlenecks in bioinformatics analyses for public health laboratories with limited on-site computational infrastructure. The performance of VPipe was validated through the analysis of publicly available NGS data sets for viral pathogens, generating high-quality assemblies for 12 data sets. VPipe also generated assemblies with greater contiguity than similar pipelines for 41 human respiratory syncytial virus isolates and 23 SARS-CoV-2 specimens. IMPORTANCE Computational infrastructure and bioinformatics analysis are bottlenecks in the application of NGS to viral pathogens. As of September 2021, VPipe has been used by the U.S. Centers for Disease Control and Prevention (CDC) and 12 state public health laboratories to characterize >17,500 and 1,500 clinical specimens and isolates, respectively. VPipe automates genome assembly for a wide range of viruses, including high-consequence pathogens such as SARS-CoV-2. Such automated functionality expedites public health responses to viral outbreaks and pathogen surveillance.
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14
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Rosenthal SH, Gerasimova A, Ruiz-Vega R, Livingston K, Kagan RM, Liu Y, Anderson B, Owen R, Bernstein L, Smolgovsky A, Xu D, Chen R, Grupe A, Tanpaiboon P, Lacbawan F. Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory. Sci Rep 2022; 12:2054. [PMID: 35136154 PMCID: PMC8826425 DOI: 10.1038/s41598-022-06091-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
Monitoring new mutations in SARS-CoV-2 provides crucial information for identifying diagnostic and therapeutic targets and important insights to achieve a more effective COVID-19 control strategy. Next generation sequencing (NGS) technologies have been widely used for whole genome sequencing (WGS) of SARS-CoV-2. While various NGS methods have been reported, one chief limitation has been the complexity of the workflow, limiting the scalability. Here, we overcome this limitation by designing a laboratory workflow optimized for high-throughput studies. The workflow utilizes modified ARTIC network v3 primers for SARS-CoV-2 whole genome amplification. NGS libraries were prepared by a 2-step PCR method, similar to a previously reported tailed PCR method, with further optimizations to improve amplicon balance, to minimize amplicon dropout for viral genomes harboring primer-binding site mutation(s), and to integrate robotic liquid handlers. Validation studies demonstrated that the optimized workflow can process up to 2688 samples in a single sequencing run without compromising sensitivity and accuracy and with fewer amplicon dropout events compared to the standard ARTIC protocol. We additionally report results for over 65,000 SARS-CoV-2 whole genome sequences from clinical specimens collected in the United States between January and September of 2021, as part of an ongoing national genomics surveillance effort.
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Affiliation(s)
| | | | | | | | - Ron M Kagan
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA.
| | - Yan Liu
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Ben Anderson
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Renius Owen
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | | | | | - Dong Xu
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Rebecca Chen
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Andrew Grupe
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
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15
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Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting. Diagnostics (Basel) 2021; 11:diagnostics11101788. [PMID: 34679489 PMCID: PMC8534650 DOI: 10.3390/diagnostics11101788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/28/2022] Open
Abstract
SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the past 18 months, numerous SARS-CoV-2 variants have emerged. Many of these variants are suggested to be more transmissible as well as less responsive to neutralization by vaccine-induced antibodies. Viral whole-genome sequencing is the current standard for tracking these variants. However, whole-genome sequencing is costly and the technology and expertise are limited to larger reference laboratories. Here, we present the feasibility of a fast, inexpensive methodology using snapback primer-based high-resolution melting to test for >20 high-consequence SARS-CoV-2 spike mutations. This assay can distinguish between multiple variant lineages and be completed in roughly 2 h for less than $10 per sample.
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