Special Issue "Sequencing Techniques and Genomics Technologies to Help with Diagnostics and Virus Characterization – Focus on COVID 19"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: 15 April 2021.

Special Issue Editors

Dr. Miten Jain
Website
Guest Editor
UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA
Interests: biotechology; bioinformatics; nanopore sequencing
Special Issues and Collections in MDPI journals
Dr. Hugh E. Olsen
Website
Guest Editor
UCSC Genomics Institute, University of California, Santa Cruz, CA 95064, USA
Interests: biotechnology; bioinformatics; nanopore sequencing
Prof. Dr. Ana Conesa
Website
Guest Editor
Microbiology and Cell Science, Institute for Food and Agricultural Research, Genetics Institute, University of Florida, Gainesville, FL 32611-0700, USA
Interests: bioinformatics; transcriptomics; multi-omics data integration; systems genomics; functional annotation; alternative splicing
Dr. Adam Ameur
Website
Guest Editor
Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala 75108, Sweden
Interests: next-generation sequencing; single-molecule sequencing; clinical sequencing; bioinformatics; genomics
Special Issues and Collections in MDPI journals

Special Issue Information

Dear colleagues, 

The COVID-19 pandemic has affected global health and the global economy at an unprecedented scale. This event has necessitated that we implement strong measures for the early detection of and rapid response to infectious diseases and potential pandemics in the immediate future.

This Issue will focus on technologies that have been developed for the detection and diagnosis of infectious diseases and viral agents. In particular, it will focus on the diagnosis and characterization of SARS-CoV-2 using different genomics and sequencing technologies.

Several groups, both academic and commercial, from across the world, have done groundbreaking research in regard to developing rapid, point-of-care diagnostic tests for SARS-CoV-2. Additionally, there is substantial work on tracking the genomic epidemiology of the virus using state-of-the-art sequencing platforms. There is also an ongoing focus on patient and population stratification studies as well as the search of patient SNPs associated to susceptibility.

We invite the research community from both academia and industry to submit their work on SARS-CoV-2 for this Issue. Even though the focus of the Issue is on COVID-19, we encourage colleagues to submit their work on relevant infectious diseases and genomics technologies. Per se all publications will remain open access during and after the pandemic; please ask [email protected] to be entitled a publishing fee discount.

These research findings will reveal further insights into the COVID-19 pandemic outbreak and its effects. This Issue will help define the actions and guidelines for surveillance, containment, and mitigation, for future events of such magnitude.

Dr. Miten Jain
Dr. Hugh E. Olsen
Prof. Ana Conesa
Dr. Adam Ameur
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Genomics technologies
  • Sequencing techniques
  • Metagenomics
  • Virus sequencing
  • Genetic diagnostics
  • qPCR
  • Nanopore sequencing
  • Single-molecule real-time (SMRT) sequencing
  • Next-generation sequencing (NGS)
  • Third-generation sequencing
  • Virus characterization
  • Long-read sequencing
  • Comparative genomics
  • Functional genomics
  • Diagnostic tests
  • Infectious diseases
  • Pandemic
  • SARS-CoV-2
  • COVID-19
  • Coronavirus
  • Genomic epidemiology
  • Population stratification
  • Genetic susceptibility

Published Papers (4 papers)

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Open AccessArticle
Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
Genes 2020, 11(8), 949; https://doi.org/10.3390/genes11080949 - 17 Aug 2020
Abstract
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [...] Read more.
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium. Full article
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Open AccessArticle
Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing
Genes 2020, 11(8), 929; https://doi.org/10.3390/genes11080929 - 12 Aug 2020
Abstract
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion [...] Read more.
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a SARS-CoV-2 specific primers pool from the Ion AmpliSeq SARS-CoV-2 Research Panel, was assessed in order to promote viral RNA specific reverse transcription. The aim of this study was to evaluate the effectiveness of the Ion AmpliSeq™ SARS-CoV-2 Research Panel in sequencing the entire viral genome in different samples. SARS-CoV-2 sequence data were obtained from ten viral isolates and one nasopharyngeal swab from different patients. The ten isolate samples amplified with 12 PCR cycles displayed high mean depth values compared to those of the two isolates amplified with 20 PCR cycles. High mean depth values were also obtained for the nasopharyngeal swab processed by use of a target-specific reverse transcription. The relative depth of coverage (rDoC) analysis showed that when 12 PCR cycles were used, all target regions were amplified with high sequencing coverage, while in libraries amplified at 20 cycles, a poor uniformity of amplification, with absent or low coverage of many target regions, was observed. Our results show that the Ion AmpliSeq SARS-CoV-2 Research Panel can achieve rapid and high throughput SARS-CoV-2 whole genome sequencing from 10 ng of DNA-free viral RNA from isolates and from 1 ng of DNA-free viral RNA from a nasopharyngeal swab using 12 PCR cycles for library amplification. The modified RT-PCR protocol yielded superior results on the nasopharyngeal swab compared to the reverse transcription reaction set up according to the manufacturer’s instructions. Full article
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Open AccessArticle
Rapid Direct Nucleic Acid Amplification Test without RNA Extraction for SARS-CoV-2 Using a Portable PCR Thermocycler
Genes 2020, 11(6), 664; https://doi.org/10.3390/genes11060664 - 18 Jun 2020
Cited by 5
Abstract
There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There [...] Read more.
There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There is an urgent need for rapid, simplified, and cost-effective detection methods. We have developed and analytically validated a protocol for direct rapid extraction-free PCR (DIRECT-PCR) detection of SARS-CoV-2 without the need for nucleic acid purification. As few as six RNA copies per reaction of viral nucleocapsid (N) gene from respiratory samples such as sputum and nasal exudate can be detected directly using our one-step inhibitor-resistant assay. The performance of this assay was validated on a commercially available portable PCR thermocycler. Viral lysis, reverse transcription, amplification, and detection are achieved in a single-tube homogeneous reaction within 36 min. This minimizes hands-on time, reduces turnaround-time for sample-to-result, and obviates the need for RNA purification reagents. It could enable wider use of Covid-19 testing for diagnosis, screening, and research in countries and regions where laboratory capabilities are limiting. Full article
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Open AccessBrief Report
Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract
Genes 2020, 11(6), 645; https://doi.org/10.3390/genes11060645 - 11 Jun 2020
Cited by 5
Abstract
There is increasing evidence of gastrointestinal (GI) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We surveyed the co-expression of SARS-CoV-2 entry genes ACE2 and TMPRSS2 throughout the GI tract to assess potential sites of infection. Publicly available and in-house single-cell RNA-sequencing [...] Read more.
There is increasing evidence of gastrointestinal (GI) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We surveyed the co-expression of SARS-CoV-2 entry genes ACE2 and TMPRSS2 throughout the GI tract to assess potential sites of infection. Publicly available and in-house single-cell RNA-sequencing datasets from the GI tract were queried. Enterocytes from the small intestine and colonocytes showed the highest proportions of cells co-expressing ACE2 and TMPRSS2. Therefore, the lower GI tract represents the most likely site of SARS-CoV-2 entry leading to GI infection. Full article
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