Journal: Frontiers in microbiology

Article Title: Optimization and Clinical Validation of Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification, a Fast, Highly Sensitive and Specific COVID-19 Molecular Diagnostic Tool That Is Robust to Detect SARS-CoV-2 Variants of Concern.

doi: 10.3389/fmicb.2021.713713

Figure Lengend Snippet: FIGURE 9 | Schematic representation of SARS-CoV-2 genome indicating the amplicons for the COVID-19 molecular diagnostics by RT-LAMP. Structural representation of SARS-CoV-2 virion shows the main particle parts. LAMP primer regions are indicated as previously reported (Baek et al., 2020; Ben-Assa et al., 2020; Butler et al., 2020; Chow et al., 2020; Dudley et al., 2020; Song et al., 2021; Ganguli et al., 2020; Huang et al., 2020; Lamb et al., 2020; Lu et al., 2020; Mohon et al., 2020; Park et al., 2020; Rabe and Cepko, 2020; Thi et al., 2020; Yan et al., 2020; Yu et al., 2020; Zhang et al., 2020a,b; Anahtar et al., 2021; Bhadra et al., 2021; Bokelmann et al., 2021; González-González et al., 2021). ORF, open reading frame; RdRp, RNA-dependent RNA polymerase; NSP, nonstructural protein. Schematic representation created using Snap Gene Viewer software version 5.0.7; N1, N2, and N3_CDC correspond to the amplicons for SARS-CoV-2 detection by RT-PCR. Created with biorender.com.

Article Snippet: 2019-SARS-CoV-2 Detection Reagent Kit (Eiken Chemical, Tokyo, Japan) Turbidity or fluorescence (+ calcein) 63◦C/18–60 min 100%/100% 20–110 copies/Rx 130 PLA General Hospital, Beijing, China Yan et al., 2020 iLACO Respiratory (not detailed) NI ORF1ab NI Yes NEB #M1800 Color 65◦C/ ≥20 min 89.9%/NI 10 copies/μL (detection threshold of 60 copies/μL); equivalent to 35–37 Ct in RT-PCR 248 Shenyang province, China Yu et al., 2020 Respiratory swabs (not detailed) VTM N gene and ORF1a NI Yes NEB #M1800 + SYTO-9 Color and fluorescence 65◦C/30 min NI 4.8 copies/μL 6 Wuhan Institute of Virology, China Zhang et al., 2020a Synthetic SARS-CoV-2 RNA NA N gene; E gene and As1e gene (ORF1a) Human actin B gene Yes NEB #M1800 + SYTO-9 Color and fluorescence 65◦C/20 min 87.5% 2 copies/μL NA NA Zhang et al., 2020b NEB #M1800, WarmStart Colorimetric RT-LAMP 2 × Master Mix; NEB #E1700, WarmStart LAMP kit (DNA and RNA); RdRp, RNA-dependent RNA polymerase (harbored by ORF1ab SARS-COV-2 genome region); NI, noninformed; NA, not applied; UTM, Universal Transport medium; VTM, viral transport medium, commonly containing, Hank’s balanced salt solution at pH 7.4 containing BSA (1%), amphotericin (15 μg/mL), penicillin G (100 units/mL), and streptomycin (50 μg/mL); Prot K, proteinase K; BD UVTM, Becton–Dickinson Universal Viral Transport Media system; SPS, sample preservation solution; QuantiFluor, Promega system for dsDNA quantification using a DNA intercalating dye; Prot.

Techniques: Software, Reverse Transcription Polymerase Chain Reaction

Journal: EBioMedicine

Article Title: The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

doi: 10.1016/j.ebiom.2022.104008

Figure Lengend Snippet: SARS-CoV-2 positivity, COVID-19 hospitalizations, and variants trends November- December 2021. (a) SARS-CoV-2 daily positivity rates between November and December 2021 for both symptomatic and asymptomatic testing. (b) COVID-19 related admissions between November and December 2021. (c) SARS-CoV-2 variant distribution between November and December 2021 relative to the 7 day rolling average positives from Johns Hopkins system. (d) Percent SARS-CoV-2 variants in November and December 2021.

Article Snippet: Specimen preparation, extractions, and sequencing were performed as described previously., Library preparation for this cohort was performed using the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L).

Techniques: Variant Assay

Journal: EBioMedicine

Article Title: The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

doi: 10.1016/j.ebiom.2022.104008

Figure Lengend Snippet: SARS-CoV-2 IgG levels in upper respiratory samples of infected vaccinated patients. Boost, patients with booster dose; Vax, fully vaccinated patients who didn't receive a booster dose. Dashed lines demarcate the limit of borderline and negative ELISA results as specified per assay's package insert. Statistical analyses, one-way ANOVA. Total numbers per group are shown on top of each scatter.

Article Snippet: Specimen preparation, extractions, and sequencing were performed as described previously., Library preparation for this cohort was performed using the NEBNext® ARTIC SARS-CoV-2 Companion Kit (VarSkip Short SARS-CoV-2 # E7660-L).

Techniques: Infection, Enzyme-linked Immunosorbent Assay