Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Development of primer-probe sets to rapidly distinguish single nucleotide polymorphisms in SARS-CoV-2 lineages

doi: 10.3389/fcimb.2023.1283328

Figure Lengend Snippet: SARS-CoV-2 strains previously circulating in South Africa and schematic of the SARS-CoV-2 genome with qPCR assay targeting the S -gene. (A) Representative VOC between March 2020 and August 2023 (retrieved from https://www.covariantsorg ). (B) Genomic architecture of SARS-CoV-2 virus. Regions in the gene encoding the spike protein highlighted to show domain structure (not drawn to scale). Regions in the S -gene with characterized SNPs at amino acid positions indicated. Amino acids occurring in the spike protein of the Wuhan-Hu-1 strain are highlighted in yellow. Three VOC classified according to PANGO lineage and clade (α, β and O sub-lineages) with corresponding mutations in the spike protein are shown in red and black blocks. Green blocks indicate no change. The table indicates the SNPs targeted for qPCR assay development (red blocks). The genome was adapted from (12, 40). Nucleic acid mutation profiles: D405N (GAT→AAT); G446S (GGT→AGT); E484K (GAA→AAA); L981F (CTT→TTT). § Mutations are also present in newer sub-variants of Omicron, that emerged after BA.5, as highlighted in the main text.

Article Snippet: Other approaches for genomics surveillance, including the commercially available Seegene Allplex SARS-Cov_2 Variants I (E484K, N501Y and ΔH69/V70) and II (L452R, W152C, K417T, and K417N) assays, have opted to sequence the entire S-gene to identify VOC ( ).

Techniques: Virus, Mutagenesis

Journal: Tropical Medicine and Infectious Disease

Article Title: The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review

doi: 10.3390/tropicalmed8120514

Figure Lengend Snippet: Overview of articles on diagnostic testing for SARS-CoV-2 in South Africa.

Article Snippet: Umunnakwe et al., 2022 [ ] , Allplex TM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (Seoul, South Korea) , Illumina MiSeq (Illumina Inc., San Diego, CA, USA), PacBio Sequel IIe (Pacific Biosciences Inc., Menlo Park, CA, USA) or Genexus Ion Torrent (Thermo Scientific, Waltham, MA, USA) platforms. , 187 , Not reported , K417N (Beta), K417T (Gamma). L452R (Delta), W152C (Epsilon) , Not reported , No cross reactivity.

Techniques: Diagnostic Assay, Sampling, Western Blot

Journal: Tropical Medicine and Infectious Disease

Article Title: The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review

doi: 10.3390/tropicalmed8120514

Figure Lengend Snippet: Performance characteristics of the diagnostic tests for SARS-CoV-2.

Article Snippet: Umunnakwe et al., 2022 [ ] , Allplex TM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (Seoul, South Korea) , Illumina MiSeq (Illumina Inc., San Diego, CA, USA), PacBio Sequel IIe (Pacific Biosciences Inc., Menlo Park, CA, USA) or Genexus Ion Torrent (Thermo Scientific, Waltham, MA, USA) platforms. , 187 , Not reported , K417N (Beta), K417T (Gamma). L452R (Delta), W152C (Epsilon) , Not reported , No cross reactivity.

Techniques: Diagnostic Assay, Multiplex Assay, Real-time Polymerase Chain Reaction, Genotyping Assay, Sample Prep, Lateral Flow Assay, Enzyme-linked Immunosorbent Assay, Recombinant, Clinical Proteomics

Journal: Tropical Medicine and Infectious Disease

Article Title: The Performance of Diagnostic Tests for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the South African Population: A Scoping Review

doi: 10.3390/tropicalmed8120514

Figure Lengend Snippet: Analytical assessment of antigen- and antibody-based diagnostic tests for SARS-CoV-2.

Article Snippet: Umunnakwe et al., 2022 [ ] , Allplex TM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (Seoul, South Korea) , Illumina MiSeq (Illumina Inc., San Diego, CA, USA), PacBio Sequel IIe (Pacific Biosciences Inc., Menlo Park, CA, USA) or Genexus Ion Torrent (Thermo Scientific, Waltham, MA, USA) platforms. , 187 , Not reported , K417N (Beta), K417T (Gamma). L452R (Delta), W152C (Epsilon) , Not reported , No cross reactivity.

Techniques: Diagnostic Assay, Multiplex Assay, Real-time Polymerase Chain Reaction, Genotyping Assay, Sample Prep, Nucleic Acid Purification, Lateral Flow Assay, Variant Assay, Enzyme-linked Immunosorbent Assay, Recombinant, Clinical Proteomics