Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System

Hourdel, Véronique; Kwasiborski, Aurélia; Balière, Charlotte; Matheus, Séverine; Batéjat, Christophe; Manuguerra, Jean-Claude; Vanhomwegen, Jessica; Caro, Valérie

doi:10.3389/fmicb.2020.571328

Cited by 50 publications

(62 citation statements)

References 19 publications

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“…As already mentioned, amplicon-based and metagenomic approaches based on the sequence-independent single primer amplification (SISPA) method are able to detect mutations occurring in the sequence of SARS-CoV-2 and potentially associated with vaccine inefficacy or resistance to antiviral therapies ( 110 , 111 ). Examples of this type of sequencing technique are the MinION and IDbyDNA platforms produced by Oxford Nanopore Technologies and Illumina, respectively ( 112 ). As regards the IDbyDNA platform, it ensures the collection of >13 million reads of which >8 million are unique reads with an average length of ~75 bp and an in-depth coverage.…”

Section: Alternative Methods For the Effective Diagnosis Of Covid-mentioning

confidence: 99%

Current and innovative methods for the diagnosis of COVID‑19 infection (Review)

et al. 2021

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The Coronavirus Disease 2019 (COVID-19) pandemic has forced the scientific community to rapidly develop highly reliable diagnostic methods in order to effectively and accurately diagnose this pathology, thus limiting the spread of infection. Although the structural and molecular characteristics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were initially unknown, various diagnostic strategies useful for making a correct diagnosis of COVID-19 have been rapidly developed by private research laboratories and biomedical companies. At present, rapid antigen or antibody tests, immunoenzymatic serological tests and molecular tests based on RT-PCR are the most widely used and validated techniques worldwide. Apart from these conventional methods, other techniques, including isothermal nucleic acid amplification techniques, clusters of regularly inter-spaced short palindromic repeats/Cas (CRISPR/Cas)-based approaches or digital PCR methods are currently used in research contexts or are awaiting approval for diagnostic use by competent authorities. In order to provide guidance for the correct use of COVID-19 diagnostic tests, the present review describes the diagnostic strategies available which may be used for the diagnosis of COVID-19 infection in both clinical and research settings. In particular, the technical and instrumental characteristics of the diagnostic methods used are described herein. In addition, updated and detailed information about the type of sample, the modality and the timing of use of specific tests are also discussed.

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Section: Alternative Methods For the Effective Diagnosis Of Covid-mentioning

confidence: 99%

Current and innovative methods for the diagnosis of COVID‑19 infection (Review)

et al. 2021

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“…In the past twenty years, several diseases caused by coronavirus have posed significant global health challenges-including Severe Acute Respiratory Syndrome (SARS, 2002), Middle East Respiratory Syndrome (MERS, 2012), as well as the current pandemic of COVID-19 [1,2]. COVID-19 is caused by a single-stranded, positive-sense RNA virus (SARS-CoV-2) which belongs to the Coronaviridae family [2].…”

Section: Introductionmentioning

confidence: 99%

“…Environmental surveillance (ES) offers a complementary and more feasible approach to clinical disease surveillance. This approach provides unbiased information on a population level and detects viral shedding by symptomatic and asymptomatic patients [1,16], thus providing a snapshot of the outbreak over an entire sewage catchment area and an early indication of clinical cases in the area [17]. Because not all symptomatic patients get tested due to reluctance or lack of access to tests, clinical samples are not a sensitive indicator of the occurrence of cases in a given area [18,19].…”

Section: Introductionmentioning

confidence: 99%

“…Portable and reliable sequencing tools such as MinION can play a crucial role in conducting genomic surveillance in a developing country like Nepal where access to high throughput DNA sequencing machines is limited. The pocket-sized and field-deployable, the next-generation sequencer has enabled real-time outbreak surveillance of several recent outbreaks of Zika, Ebola, and Lassa viruses [1]. Obtaining whole or partial genome sequences of the virus during outbreak is critical in understanding viral evolution and disease epidemiology, and can help design accurate diagnostic tests for rapidly evolving RNA viruses such as SARS-CoV-2 [25].…”

Section: Introductionmentioning

confidence: 99%

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Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples

Napit

Manandhar

Chaudhary

et al. 2021

Preprint

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Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized, and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.

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“…NGS can also provide quantitative data on the concentration of organisms in a sample by counting the sequence reads [21]. iSeq100, a recently released instrument, is capable of processing a targeted NGS library with accuracy comparable to that of MiSeq, the most widely used instrument in microbiome studies [22,23]. iSeq100 also features shortened sequencing work ow preparation time and a total sequencing run time of under 24 hours, as it allows the sequencing of a lower read count than the MiSeq [22].…”

Section: Introductionmentioning

confidence: 99%

iSeq100 for metagenomic pathogen screening in ticks

Kim

Mahdi

et al. 2021

Preprint

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Background: Ticks are blood sucking ectoparasites that play a pivotal role in the transmission of various pathogens to humans and animals. In Korea, Haemaphysalis longicornis is the predominant tick species and is recognized as the vector of pathogens causing various diseases such as babesiosis, borreliosis, rickettsiosis, and severe fever with thrombocytopenia syndrome. Methods: In this study, we developed a method to screen bacterial pathogens in H. longicornis using targeted high-throughput sequencing of the 16S rRNA V4 region using the state-of-the-art sequencing instrument, iSeq 100, and compared the findings with those of conventional PCR with specific primers. Results: Rickettsia spp. were detected in 18 out of 39 samples using iSeq 100 but in only 14 samples using conventional PCR. In the phylogenetic analysis using gltA and ompA sequences of the detected Rickettsia, the highest sequence similarity was found with Candidatus Rickettsia jingxinensis isolate Xian-Hl-79, Ca. R. jingxinensis isolate F18, and Ca. R. longicornii isolate ROK-HL727. In the microbiome study, Coxiella AB001519, a known tick symbiont, was detected in all 39 tick samples. The Actinomycetospora chiangmaiensis group was more abundant in Rickettsia spp.-positive samples than in Rickettsia spp.-negative samples. Conclusions: Thus, we demonstrated that iSeq100 can rapidly and economically screen potential pathogens in ticks and can be applied to large-scale pathogen screening in arthropods for vector-borne disease control programs.

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Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System

Cited by 50 publications

References 19 publications

Current and innovative methods for the diagnosis of COVID‑19 infection (Review)

Current and innovative methods for the diagnosis of COVID‑19 infection (Review)

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples

iSeq100 for metagenomic pathogen screening in ticks

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