COVID-19 Research and SARS-CoV-2 Surveillance

{"childPageArray":[{"createdDate":"09/2021","pageTitle":"Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/Batty-et-al-covid-19","authorName":"Batty, E.M. et al. ","publication":"bioRxiv 2020","pageDescription":"In the article, Batty, E.M. et al. present their findings from a comparison of three different library preparation methods used in the ARTIC Network protocol for SARS CoV- 2 multiplex amplicon sequencing on the Illumina® MiSeq® platform. The authors report that the ligation-based KAPA HyperPrep method resulted in higher library yield, more total reads, and equal or better overall coverage than the tagmentation-based Nextera Flex or Nextera XT workflows.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"KAPA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/dna-library-preparation/KAPA-HyperPrep-Kits"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"KAPA RNA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits"}]},{"createdDate":"09/2021","pageTitle":"Blocking of the CD80/86 axis as a therapeutic approach to prevent progression to more severe forms of COVID-19 ","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/julia-et-al-covid-19","authorName":"Julia et al.","publication":"aRxiV.org","pageDescription":"Julia et al. used KAPA RNA HyperPrep with RiboErase (HMR) Globin to investigate the transcriptional responses of SARS-CoV-2-infected patient samples to the immunomodulating drug Abatacept, and to compare this response to that of cells and blood from Rheumatoid Arthritis patients. The authors used this data to determine whether blocking the CD80/86 axis is a viable therapeutic target to prevent severe immune responses of COVID19 patients.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"KAPA RNA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits"}]},{"createdDate":"09/2021","pageTitle":"Hydroxychloroquine inhibits trained immunity \u2013 implications for COVID-19","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/rother-et-al-covid-19","authorName":"Rother et al.","publication":"medRxiV.org","pageDescription":"Rother, N. et al. constructed total RNA-seq libraries using KAPA RNA HyperPrep Kit with RiboErase (HMR) to perform transcriptome analysis of isolated monocytes of COVID-19 patients. These cells demonstrated increased expression of interferon-stimulated genes, which are likely markers of disease severity as they are associated with a poor clinical outcome. Using the Kapa HyperPrep Kit, the authors also constructed ChIP-seq libraries to investigate the effect of hydroxychloroquine on trained immunity at the functional and epigenetic level.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"ChIP-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/ChIP-Seq"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"DNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/DNA-Seq"},{"tagName":"KAPA RNA HyperPrep Kits with RiboErase","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits-with-RiboErase"}]},{"createdDate":"09/2021","pageTitle":"COVID-19 Related Genes in Sputum Cells in Asthma: Relationship to Demographic Features and Corticosteroids.","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/peters-et-al-covid-19","authorName":"Peters M. C. et al.","publication":"PubMed","pageDescription":"Peters et al. used the KAPA mRNA Hyper Prep Kit in Whole Transcriptome RNA-seq to investigate host expression levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane protease serine 2 (TMPRSS2), two proteins believed to mediate SARS \u2013CoV2 viral infection of host cells.","pageTags":[{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"}]},{"createdDate":"09/2021","pageTitle":"Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/williamson-et-al-covid-19","authorName":"Williamson et al. ","publication":"bioRxiV.org","pageDescription":"Williamson et al. use the KAPA HyperPlus Library Preparation Kit and KAPA Unique Dual-Indexed Adapters to prepare sequencing libraries from double-stranded cDNAs converted from SARS-CoV-2 viral RNA. Williamson et al. also amplified the resulting libraries using KAPA HiFi HotStart ReadyMix and quantified them with the KAPA Library Quantification Kit prior to paired-end sequencing.","pageTags":[{"tagName":"LQK","tagID":"roche-sequence:publication-reviews/additional-tags/lqk"},{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"DNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/DNA-Seq"}]},{"createdDate":"09/2021","pageTitle":"A Territory-wide study of COVID-19 cases and clusters with unknown source in Hong Kong community: A clinical, epidemiological and phylogenomic investigation. ","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/leung-et-al-covid-19","authorName":"Leung K. S. et al.","publication":"medRxiV.org","pageDescription":"Leung et al. prepared sequencing-ready libraries with the KAPA HyperPrep DNA Library Prep Kit following generation of amplicons by multiplex PCR using ARCTIC network nCoV-2019 primers; through that workflow, Leung et al. investigated the epidemiological and phylogenomic characteristics of COVID-19 cases in Hong Kong.","pageTags":[{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"DNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/DNA-Seq"}]},{"createdDate":"09/2021","pageTitle":"Patient-derived mutations impact pathogenicity of SARS-CoV-2","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/yao-et-al-covid-19","authorName":"Yao H. et al.","publication":"medRxiV.org","pageDescription":"Yao et al. performed whole viral genome sequencing using KAPA RNA-Seq library prep kit from COVID-19 patient isolates to understand whether acquired mutations of the SARS-CoV-2 genome have an impact on the pathogenicity of the virus.","pageTags":[{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"}]},{"createdDate":"09/2021","pageTitle":"Transcriptional profiling of immune and inflammatory responses in the context of SARS-CoV-2 fungal superinfection in a human airway epithelial model","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/lamballerie-et-al-covid-19","authorName":"de Lamballerie, C.N. et al. ","publication":"bioRxiV.org","pageDescription":"Following construction of poly(A)-enriched RNA-seq libraries with the KAPA mRNA HyperPrep Kit, de Lamballerie et al. compared the host transcriptional response to SARS-CoV-2 infection alone to that of SARS-CoV-2 with Aspergillus superinfection to elucidate the impact of fungal superinfections on the course and severity of viral infections in respiratory epithelial cells.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"KAPA mRNA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-mRNA-HyperPrep-Kits"}]},{"createdDate":"09/2021","pageTitle":"Expression of SARS-CoV-2 Entry Molecules ACE2 and TMPRSS2 in the Gut of Patients with IBD","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/burgueno-et-al-covid-19","authorName":"Burgueno et al.","publication":"Inflammatory Bowel Disease","pageDescription":"Burgueno et al. used the KAPA RNA HyperPrep Kit with RiboErase (HMR) and the LightCycler® 480 System to understand the expression of the viral entry molecules angiotensin I converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) in the intestine. Additionally, the authors investigated how inflammatory states in the gut of patients suffering from inflammatory bowel disease (IBD) and taking immune-modulating drugs may affect regulation of ACE2 and TMPRSS2 expression and, therefore, affect SARS-CoV-2 infection.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"LightCycler 480","tagID":"roche-sequence:product-solutions/by-category/instruments/lightcycler-480"},{"tagName":"KAPA RNA HyperPrep Kits with RiboErase","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits-with-RiboErase"}]},{"createdDate":"09/2021","pageTitle":"The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/thomson-et-al-covid-19","authorName":"Thomson, E.C. et al.","publication":"bioRxiv 2020","pageDescription":"Immune evasion mutations that maintain virulence and fitness can emerge within the SARS-CoV-2 spike protein, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics. Thomson, E.C. et al. used the ARTIC network amplicon sequencing protocol and the https://doi.org/10.1101/2020.11.04.355842 to conduct epidemiological and genome surveillance of SARS-CoV-2 and found (1) the immunodominant SARS-CoV-2 spike receptor binding motif is the most divergent region of spike protein, and (2) the N439K spike protein mutation enhances binding affinity to the hACE2 receptor. ","pageTags":[{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"},{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"DNA Library Preparation","tagID":"roche-sequence:product-solutions/by-category/library-preparation/dna-library-preparation"}]},{"createdDate":"09/2021","pageTitle":"Generation and characterization of recombinant SARS-CoV-2 expressing reporter genes. ","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/chiem-et-al-covid-19","authorName":"Chiem, K. et al.","publication":"bioRxiv 2020","pageDescription":"Chiem, K. et al. 2020 generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent (Venus or mCherry) or bioluminescent (Nluc) reporter genes. By sequencing of RNA-seq libraries constructed using KAPA RNA HyperPrep Kit, the authors showed that the reporter-expressing rSARS-CoV-2 are genetically stable in Vero E6 cells. They also used these reporter-expressing rSARS-CoV-2 to demonstrate their feasibility in the identification of neutralizing antibodies (NAbs) or antiviral drugs.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"KAPA RNA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"}]},{"createdDate":"09/2021","pageTitle":"A whole virion vaccine for COVID-19 produced via a novel inactivation method: results from animal challenge model studies.","pagePath":"/content/rochesequence/en-us/support-resources/resources/publications/Ragan-et-al-covid-19","authorName":"Ragan, I.K. et al. ","publication":"bioRxiv 2020","pageDescription":"Ragan, I.K. et al. 2020 reported on the use of a novel method (SolaVAXTM) for production of an inactivated vaccine candidate and subsequent testing in a hamster animal model for its ability to prevent infection upon challenge with SARS-CoV-2 virus. The authors used shotgun RNA sequencing with KAPA RNA HyperPrep Kit to confirm the identity of the SARS-CoV-2 isolate used in hamster challenge material and to characterize mutations that may have arisen during cell culture. The results of their study suggest that preparation of a whole virion vaccine for COVID-19 using this specific photochemical method may have utility in the preparation of one such vaccine candidate.","pageTags":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"KAPA RNA HyperPrep Kits","tagID":"roche-sequence:product-solutions/by-category/library-preparation/rna-library-preparation/KAPA-RNA-HyperPrep-Kits"},{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"}]}],"filtersJSON":[{"name":"dropdown","title":"Year","items":[{"tagName":"2020","tagID":"roche-sequence:publication-reviews/dropdown/2020"}]},{"name":"research","title":"Research","items":[{"tagName":"SARS-CoV-2","tagID":"roche-sequence:publication-reviews/research/sars-cov-2"}]},{"name":"additional-tags","title":"Applications","items":[{"tagName":"ChIP-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/ChIP-Seq"},{"tagName":"RNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/RNA-Seq"},{"tagName":"LQK","tagID":"roche-sequence:publication-reviews/additional-tags/lqk"},{"tagName":"DNA-Seq","tagID":"roche-sequence:publication-reviews/additional-tags/DNA-Seq"}]}],"showPageTags":["roche-sequence:product-solutions/by-application/research/rna-sequencing","roche-sequence:publication-reviews/research/sars-cov-2","roche-sequence:product-solutions/by-application/research/pcr"]}