sars-cov-2 surrogate virus neutralization test kit (svnt, genscript, l00847)  (GenScript corporation)

Journal: Nature Communications

Article Title: Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

doi: 10.1038/s41467-023-40706-y

Figure Lengend Snippet: Counties classified as urban are colored gray and rural counties are white. The size of circles plotted over the county centroids indicate the number of samples collected and the color scale indicates SARS-CoV-2 estimated prevalence in each county by rRT-PCR ( a ) and seroprevalence by surrogate virus neutralization ( b ). Counties that are outlined in bold borders indicate counties from which we obtained SARS-CoV-2 genomic sequences (Table ). Counties marked with an asterisk indicate counties from which samples were collected from culled WTD as a part of population management programs (Table ). Map created with ArcMap (ESRI) using base layers and data from Esri, Garmin, OpenStreetMap, GIS user community, Infogroup and the US Census Bureau.

Article Snippet: Sixty microliters of each eluted sample was directly (without further dilution) analyzed using the GenScript SARS-COV-2 Surrogate Virus Neutralization Test (sVNT, L00847-A) in accordance with the manufacturer’s instructions .

Techniques: Quantitative RT-PCR, Virus, Neutralization, Genomic Sequencing

Journal: Nature Communications

Article Title: Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

doi: 10.1038/s41467-023-40706-y

Figure Lengend Snippet: a MCC tree inferred for 786 B.1.1.7 viruses collected from humans and WTD. Branches shaded by host species and location. The two Ohio WTD clusters are labeled. b AY.25 subtree (entire delta MCC tree shown in Fig. , n = 1094 delta viruses). Ohio WTD virus transmission clusters are shaded similarly to Fig. , with the addition of black branches indicating Ohio WTD singleton detections from this study and dark gray branches indicating non-Ohio WTD singletons. c The number of bi-weekly COVID-19 cases in humans in Ohio from January 2021 to February 2022, shaded by the proportion of human SARS-CoV-2 sequences from Ohio that belong to one of four Pango lineages (or ‘other’). Red box delineates the B.1.1.7 wave in humans. Below, green bars show the estimated number of human-to-deer transmission events of B.1.1.7 viruses, per 20-week increments, based on “Markov jump” counts inferred on the alpha MCC tree ( n = 786 B.1.1.7 viruses). Green circles indicate the collection dates of 9 B.1.1.7 viruses in Ohio WTD. d Similar to c , but inferred on the delta MCC tree ( n = 1094). e The detection lag (months) is the time difference between a human-to-deer transmission event (estimated) and the first observed sequence from a WTD transmission cluster, shown for 14 delta and 2 alpha WTD transmission clusters, inferred from the MCC trees. Red lines represent the two time points of the two nodes defining the branch on the phylogenetic tree on which the human-to-deer transition occurred; thick black bar represents the mean time of the branch. f Estimated number of human-to-deer transmission events in Ohio and North America and long-distance deer-to-deer transmission events that span Ohio counties, inferred from the MCC trees. Data for North America does not include Ohio.

Article Snippet: Sixty microliters of each eluted sample was directly (without further dilution) analyzed using the GenScript SARS-COV-2 Surrogate Virus Neutralization Test (sVNT, L00847-A) in accordance with the manufacturer’s instructions .

Techniques: Labeling, Virus, Transmission Assay, Sequencing

Journal: Nature Communications

Article Title: Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

doi: 10.1038/s41467-023-40706-y

Figure Lengend Snippet: Each shape represents a county in Ohio where SARS-CoV-2 virus was identified in WTD for this study (triangle = alpha variant; circle = delta variant). Large circles indicate WTD transmission clusters, as identified on the phylogenetic tree (black = clusters restricted to one county; shaded = clusters identified in more than one county). Large circles shaded the same color belong to the same transmission cluster. Small black circles indicate singleton WTD viruses. PANGO lineage provided for all clusters. Human population density is shown in the background (red = high; green = low) and major cities are labeled. Ohio population map [created by JimIrwin, from Wikimedia Commons] was used with modification under CC BY-SA 3.0 license.

Article Snippet: Sixty microliters of each eluted sample was directly (without further dilution) analyzed using the GenScript SARS-COV-2 Surrogate Virus Neutralization Test (sVNT, L00847-A) in accordance with the manufacturer’s instructions .

Techniques: Virus, Variant Assay, Transmission Assay, Labeling, Modification

Journal: Nature Communications

Article Title: Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

doi: 10.1038/s41467-023-40706-y

Figure Lengend Snippet: a The posterior distributions of evolutionary rates (substitutions per site per year) for five partitions of the SARS-CoV-2 genome (ORF1a, ORF1b, ORF3–ORF8 plus envelope (E) and membrane (M), spike (S), and nucleocapsid (N)) are presented for human (pink) and WTD (blue) for the delta variant (Fig. ). Alpha results (similar) are provided in Fig. . b Mutations in spike protein that were found in delta WTD clusters (orange), L18F is shown in red, alpha WTD clusters (green), and T29I found in both alpha and delta WTD clusters (yellow). Characteristic mutations for delta lineages (mutations present in human and WTD viruses belonging to delta compared to Wuhan reference genome) are shown in dark orange, while characteristic mutations for alpha lineages are shown in dark green. All recurrent mutations from WTD clusters are documented in Supplementary Data . The log deviation (random-effect) from HKY model relative rates is presented for c alpha, humans, d alpha, WTD, e alpha, WTD-to-human ratio, f delta, humans, g delta, WTD, and h delta, WTD-to-human ratio, inferred independently for alpha ( n = 786) and delta ( n = 1094). Box midlines indicate the median, the box limits show the upper and lower quartiles, and the whiskers extend to 1.5 times the interquartile range. Asterisks indicate transversions. WTD-to-human ratios that significantly differ from zero are highlighted.

Article Snippet: Sixty microliters of each eluted sample was directly (without further dilution) analyzed using the GenScript SARS-COV-2 Surrogate Virus Neutralization Test (sVNT, L00847-A) in accordance with the manufacturer’s instructions .

Techniques: Membrane, Variant Assay