Journal: Frontiers in Medicine

Article Title: First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

doi: 10.3389/fmed.2021.626000

Figure Lengend Snippet: Distribution of sequenced SARS-CoV-2 isolates by clades in major regions of the world, worldwide, and in Latvia. y -axis depicts cumulative complete SARS-CoV-2 genome count (with unambiguous collection date) from a particular region and has different scale within the subplots. x -axis is the same for all subplots and depicts sampling time-series from 24th of December, 2019 till 12th of September, 2020.

Article Snippet: Three SARS-CoV-2 genome-specific primer pairs and probes targeting different regions of the nucleocapsid protein (N) gene implemented in the 2019-nCoV RUO Kit (IDT) and SOLIScript® 1-step CoV Kit (Solis Biodyne) were used for the amplification ( ).

Techniques: Sampling

Journal: Frontiers in Medicine

Article Title: First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

doi: 10.3389/fmed.2021.626000

Figure Lengend Snippet: Daily numbers of positive COVID-19 cases (A) and tests performed (B) in Latvia. x -axis is the same for both tiles and represents daily time series from 28th of February, 2020 to 11th of September, 2020. The red vertical line indicates the date of the first COVID-19 case registered in Latvia. (A) Y value represents the total number of positive cases registered on a given day. Blue area shows the number of only successfully sequenced isolates, while the red area represents the positive cases not sequenced during this study. (B) Y value represents the number of tests carried out on a given date in Latvia.

Article Snippet: Three SARS-CoV-2 genome-specific primer pairs and probes targeting different regions of the nucleocapsid protein (N) gene implemented in the 2019-nCoV RUO Kit (IDT) and SOLIScript® 1-step CoV Kit (Solis Biodyne) were used for the amplification ( ).

Techniques:

Journal: Frontiers in Medicine

Article Title: First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

doi: 10.3389/fmed.2021.626000

Figure Lengend Snippet: Maximum clade credibility tree (mean node heights) estimated from the completely sequenced Latvian isolates ( n = 133) and Wuhan-Hu-1 isolate. Node labels are colored according to the GISAID major clade of particular isolate, as follows: green, GR; yellow, GH; red, G; blue, L; purple, O (other); black, Wuhan-Hu-1 reference sequence. The tree is time scaled and axis represents time in a decimal year notation (1 months is ~0.08333 of a year and 1 day is ~0.00274 of a year). Nodes are colored according to their respective posterior probabilities in gradient from blue (lowest value) to red (highest value). Dated node bars represent 95% highest posterior density intervals and are shown for the selected nodes.

Article Snippet: Three SARS-CoV-2 genome-specific primer pairs and probes targeting different regions of the nucleocapsid protein (N) gene implemented in the 2019-nCoV RUO Kit (IDT) and SOLIScript® 1-step CoV Kit (Solis Biodyne) were used for the amplification ( ).

Techniques: Sequencing

Journal: Frontiers in Medicine

Article Title: First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity

doi: 10.3389/fmed.2021.626000

Figure Lengend Snippet: Evolutionary relationships of 133 sequenced Latvian and Wuhan-Hu-1 SARS-CoV-2 isolates. The evolutionary history was inferred using the Maximum-likelihood method allowing for polytomies. The tree is rooted at Wuhan-Hu-1 reference sequence. The tree is drawn to scale; branch lengths correspond to nucleotide substitutions. The analysis involved 134 nucleotide sequences (133 Latvian SARS-CoV-2 isolates and Wuhan-Hu-1 reference sequence). There were a total of 29,903 positions in the final dataset. Node labels are colored according to the GISAID major clade of particular isolate, as follows: green, GR; yellow, GH; red, G; blue, L; purple, O (other); black, Wuhan-Hu-1 reference sequence.

Article Snippet: Three SARS-CoV-2 genome-specific primer pairs and probes targeting different regions of the nucleocapsid protein (N) gene implemented in the 2019-nCoV RUO Kit (IDT) and SOLIScript® 1-step CoV Kit (Solis Biodyne) were used for the amplification ( ).

Techniques: Sequencing

Journal: Virology Journal

Article Title: Resource-efficient internally controlled in-house real-time PCR detection of SARS-CoV-2

doi: 10.1186/s12985-021-01559-3

Figure Lengend Snippet: Principle of the RKI/ZBS1 protocol for the real-time PCR detection of SARS-CoV-2. RKI/ZBS1 SARS-CoV-2 protocol

Article Snippet: To assess the performance of further commercially available one-step RT-PCR master mixes with the RKI/ZBS1 SARS-CoV-2 protocol, 10 clinical specimens with varying viral genome load were analyzed with the AgPath-ID master mix on the Bio-Rad CFX96 cycler and compared to the SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase (Invitrogen, Carlsbad, CA, USA), the lyophilized 1-step RT-PCR Polymerase Mix (TIB MOLBIOL, Berlin, Germany), the TaqPath™ 1-Step Multiplex Master Mix (No ROX) (Applied Biosystems), two kits from Solis BioDyne (SOLIScript 1-step Multiplex Probe Kit, SOLIScript® 1-step CoV Kit; Solis BioDyne, Tartu, Estonia) and the GoTaq® Probe 1-Step RT-qPCR System (Promega, Walldorf, Germany).

Techniques: Real-time Polymerase Chain Reaction