(B) Paired-primer approaches typically generate short amplicons flanked by upstream and downstream primers that are PCR amplified in non-overlapping pools. (C) Tiled-ClickSeq uses a single pool of …
(A) Read coverage obtained from Tiled-ClickSeq over the whole viral genome is depicted when sequencing using an Illumina MiSeq (orange) or on an Oxford Nanopore Technologies MinION device (blue). A …
(A) Read coverage obtained from Tiled-ClickSeq over the whole viral genome for 12 World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) isolates is depicted when using an Oxford …
(A) Read coverage is depicted over the 5’ UTR of the SARS-CoV-2 genome for each isolate revealing capture of this region. The 5’-most primer from the ARTICv3 protocol at nts-30–54 is illustrated. (B)…
(A) Read coverage obtained from Tiled-ClickSeq over the whole viral genome is depicted using an Illumina MiSeq when using the original primers as in Figure 2 (v1 - blue) or with an additional 326 …
The frequency of all mapped nucleotides at each genome coordinate for each WRCEVA isolate is provided.
The reference genome, nucleotide coordinate and expected reference Nucleotide is provided. Total read coverage and the numbers of each non-reference nucleotide are also shown. Finally, the mismatch/error rate at each site is provided which reveals minority variants in each isolate.
(A) A table of the most common RNA recombination events found using Tiled-ClickSeq to study ‘World Reference Center for Emerging Viruses and Arboviruses’ (WRCEVA) isolates. The recombination …
Snapshot of Tiled-ClickSeq reads from icSARS-CoV-2 delta-PRRA.
Individual reads are illustrated with short grey lines. Recombination events mapped by ViReMa are illustrated by light-blue lines. Common variants engineered into the icSARS clone are indicated by …
(A) The percent genome coverage with greater than 10 reads is plotted as a function of the measured CT value (x-axis) for each clinical sample sequenced. Each point is colour-coded according to the …
Samples are batched depending upon their measure CT value, ( < 17.5, 17.5–20, 20–25, 25–30, > 30, and unmeasured: ‘NA’) and plotted separately in a colour-coded manner.
Similarly to Figure 5B, unique RNA recombination events are plotted for 36 clinical samples as a scatterplot whereby the upstream ‘donor’ site is plotted on the y-axis and a downstream ‘acceptor’ …
BED files of RNA recombination events detected by ViReMa in the Tiled-ClickSeq data from each WRCEVA isolate and clinical sample.
A table of the most common RNA recombination events found using Tiled-ClickSeq in this study, analogues to Figure 5A. The recombination junctions are indicated on the left of the table, with their …
The read count for each unique RNA recombination event is indicated by the size of the point, while the number of samples in which this each RNA recombination event is found is indicated by the …
Sample | CT | ClickSeq reads | Virus mapped | % Viral Reads | Tiled v1 reads | Virus mapped | % Viral Reads |
---|---|---|---|---|---|---|---|
WRCEVA_00501 | 12.9 | 4,665,869 | 116,036 | 2.5% | 2,359,795 | 2,204,750 | 93.4% |
WRCEVA_00502 | 12.9 | 4,989,513 | 118,260 | 2.4% | 1,962,581 | 1,820,925 | 92.8% |
WRCEVA_00505 | 12.7 | 3,894,325 | 71,809 | 1.8% | 2,779,672 | 2,482,854 | 89.3% |
WRCEVA_00506 | 12.5 | 4,979,989 | 108,532 | 2.2% | 2,395,750 | 2,148,256 | 89.7% |
WRCEVA_00507 | 12.9 | 5,659,073 | 161,059 | 2.8% | 2,056,670 | 1,867,012 | 90.8% |
WRCEVA_00508 | 16.8 | 3,987,009 | 91,452 | 2.3% | 1,787,418 | 1,433,005 | 80.2% |
WRCEVA_00509 | 17.1 | 4,057,928 | 57,424 | 1.4% | 2,202,661 | 1,856,633 | 84.3% |
WRCEVA_00510 | 16.2 | 5,328,829 | 65,281 | 1.2% | 2,040,332 | 1,601,544 | 78.5% |
WRCEVA_00513 | 16.0 | 4,391,175 | 69,169 | 1.6% | 1,641,213 | 1,455,991 | 88.7% |
WRCEVA_00514 | 12.9 | 4,340,084 | 84,211 | 1.9% | 2,089,241 | 1,902,748 | 91.1% |
WRCEVA_00515 | 15.7 | 5,416853 | 102,179 | 1.9% | 2,205,166 | 1,915,129 | 86.8% |
WRCEVA_00516 | 17.4 | 4,290,929 | 61,017 | 1.4% | 1,988,939 | 1,715,448 | 86.2% |
Sample | Nt | Nuc | ReadDepth | A | U | G | C | VariantRate | Location | Result |
---|---|---|---|---|---|---|---|---|---|---|
WRCEVA_000501 | 12,049 | C | 2,116 | 0 | 95 | 1 | 2020 | 4.5% | ORF1ab | N3928K |
WRCEVA_000502 | 10,207 | C | 2,240 | 0 | 118 | 0 | 2,122 | 5.3% | - | - |
WRCEVA_000502 | 16,050 | U | 3,853 | 0 | 3,322 | 0 | 531 | 13.8% | - | - |
WRCEVA_000502 | 17,489 | A | 4,597 | 4,433 | 162 | 1 | 1 | 3.6% | ORF1ab | E5742V |
WRCEVA_000502 | 21,526 | A | 8,749 | 6,508 | 0 | 2,240 | 1 | 25.6% | ORF1ab | I7088V |
WRCEVA_000503 | 14,220 | C | 1,638 | 1 | 463 | 0 | 1,174 | 28.3% | - | - |
WRCEVA_000504 | 1,556 | A | 2,828 | 2,499 | 0 | 328 | 1 | 11.6% | ORF1ab | I431V |
WRCEVA_000504 | 27,925 | C | 2,857 | 0 | 134 | 0 | 2,723 | 4.7% | ORF8 | T11I |
WRCEVA_000507 | 19,515 | A | 2,393 | 2,295 | 1 | 97 | 0 | 4.1% | - | - |
WRCEVA_000508 | 9,756 | G | 1,376 | 28 | 0 | 1,348 | 0 | 2.1% | ORF1ab | R3164H |
WRCEVA_000508 | 26,056 | G | 2092 | 0 | 86 | 2006 | 0 | 4.1% | ORF3a | D222Y |
WRCEVA_000508 | 27,556 | G | 2066 | 128 | 0 | 1938 | 0 | 6.2% | ORF7a | A55T |
WRCEVA_000509 | 11,956 | C | 1962 | 0 | 199 | 0 | 1,763 | 10.1% | - | - |
WRCEVA_000509 | 17,245 | C | 4,062 | 2 | 470 | 0 | 3,590 | 11.6% | ORF1ab | R5661C |
WRCEVA_000509 | 18,005 | U | 5,408 | 1 | 4,949 | 458 | 0 | 8.5% | ORF1ab | L5915R |
WRCEVA_000509 | 25,569 | U | 3,448 | 4 | 3,326 | 113 | 5 | 3.5% | - | - |
WRCEVA_000509 | 27,919 | U | 839 | 0 | 809 | 0 | 30 | 3.6% | ORF8 | I9T |
WRCEVA_000509 | 28,767 | C | 2011 | 0 | 109 | 0 | 1902 | 5.4% | N | T165I |
WRCEVA_000511 | 3,003 | U | 2,880 | 79 | 2,787 | 1 | 13 | 2.7% | ORF1ab | V913E |
WRCEVA_000511 | 10,738 | U | 4,580 | 0 | 4,440 | 0 | 140 | 3.1% | - | - |
WRCEVA_000511 | 25,892 | U | 133 | 0 | 130 | 0 | 3 | 2.3% | ORF3a | I167T |
WRCEVA_000511 | 28,001 | G | 1,414 | 1 | 29 | 1,384 | 0 | 2.1% | - | - |
WRCEVA_000513 | 27,046 | C | 5,539 | 0 | 138 | 0 | 5,401 | 2.5% | M | T175M |
WRCEVA_000514 | 11,603 | A | 5,405 | 5,075 | 0 | 330 | 0 | 6.1% | ORF1ab | M3780V |
WRCEVA_000514 | 26,526 | G | 525 | 0 | 20 | 505 | 0 | 3.8% | M | A2S |
Sample | MicroInDel | Nucs | VariantRate | Location | Result | |
---|---|---|---|---|---|---|
WRCEVA_000502 | Δ519^523 | UGGUU | 2.2% | ORF1AB | Frameshift | |
WRCEVA_000504 | Δ29686^29,693 | CAGUGUGU | 3.5% | 3’UTR | - | |
WRCEVA_000505 | Δ519^523 | UGGUU | 2.9% | ORF1AB | Frameshift | |
WRCEVA_000506 | Δ519^523 | UGGUU | 3.8% | ORF1AB | Frameshift | |
WRCEVA_000509 | Δ1237^1,239 | UCA | 2.9% | ORF1AB | ΔH325 | |
WRCEVA_000510 | Δ686^694 | AAGUCAUUU | 5.1% | ORF1ab | ΔLSF141-143 | |
WRCEVA_000511 | Δ519^523 | UGGUU | 3.7% | ORF1AB | Frameshift | |
WRCEVA_000511 | Δ10811^10,813 | CUU | 3.1% | ORF1AB | ΔL3516 | |
WRCEVA_000512 | Δ29750^29,759 | GAUCGAGUG | 10.0% | 3’UTR | - |
Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
---|---|---|---|---|
Chemical compound, drug | AzNTPs | BaseClick |
| |
Sequence-based reagent | 5’-hexynyl-functionalized i5 oligo | IDT |
| |
Sequence-based reagent | TCSv3 | This Paper | PCR Primers | Source data 1 |
Software, algorithm | Bash and python3 text files | This Paper | .txt and.py files | Source data 2 |
Annotations and sequences of tiled-primers used in this manuscript are provided in BED format.
Batch scripts provided all computational tools and parameters used and python3 scripts used in this study are provided.
A summary of all Single-Nucleotide Variants (SNVs) detected for all samples sequenced in this study are provided.
Each unique sample/isolate is listed, together with the SNVs relative to the WA-1 (NC_045512.2) strain in different NGS library preparation methods and sequencing platforms. The accession number for each reconstructed genome deposited in GenBank is also indicated.