Replication Data for: Optimization of the SARS-CoV-2 ARTIC Network V4 whole genome sequencing protocol (doi:10.7910/DVN/VYPOOP)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
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Replication Data for: Optimization of the SARS-CoV-2 ARTIC Network V4 whole genome sequencing protocol

doi:10.7910/DVN/VYPOOP

Harvard Dataverse

2021-12-21

2

Lambisia, Arnold W.; Mohammed, Khadija S.; Makori, Timothy O.; Ndwiga, Leonard; Mburu, Maureen W.; Moraa, Edidah O.; Mwita, John; Njeri, Jane M.; Murunga, Nickson; Musyoki, Jennifer; OCholla-Oyier, Lynette Isabella; Nokes, David James; Agoti, Charles N.; Githinji, George, 2021, "Replication Data for: Optimization of the SARS-CoV-2 ARTIC Network V4 whole genome sequencing protocol", https://doi.org/10.7910/DVN/VYPOOP, Harvard Dataverse, V2, UNF:6:A4U+YD1cFEeENj2vDysMZA== [fileUNF]

Replication Data for: Optimization of the SARS-CoV-2 ARTIC Network V4 whole genome sequencing protocol

doi:10.7910/DVN/VYPOOP

Lambisia, Arnold W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mohammed, Khadija S. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Makori, Timothy O. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Ndwiga, Leonard (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mburu, Maureen W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Moraa, Edidah O. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mwita, John (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Njeri, Jane M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Musyoki, Jennifer (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

OCholla-Oyier, Lynette Isabella (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Harvard Dataverse

Lambisia, Arnold W.

Lambisia, Arnold W.

2021-12-21

https://doi.org/10.7910/DVN/VYPOOP

Medicine, Health and Life Sciences, Medicine, Health and Life Sciences, ARTIC V4, SARS-CoV-2, whole genome sequencing, amplicon drop-off, protocol

<p>This dataset is part of genomic surveillance of SARS-CoV-2 in Kenya study. This dataset contains results of an optimisation of a whole genome sequencing protocol that contains ARTIC V4 primers using samples positive for SARS-CoV-2. Aside from the samples used for optimisation, percent genome coverage and Pango lineage classifications are also included. The dataset is used to show improvement in genome recovery when using ARTIC V4 primers compared to ARTIC V3 primers. </p>

<p><strong>Data Access: </strong>Open</p> <p><strong>License: </strong><a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a></p>

<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p>

<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p>

Open Access

• Number of cases: 92

• No. of variables per record: 4

• Type of File: text/tab-separated-values

UNF:6:i6VV3zQAUK1HWqH/UGANSg==

• Number of cases: 43

• No. of variables per record: 8

• Type of File: text/tab-separated-values

UNF:6:hyObQReyM9PhwnxMp9C/Ig==

• Number of cases: 46

• No. of variables per record: 14

• Type of File: text/tab-separated-values

UNF:6:aSwSVPspa3M1uQ9Zjzv1RA==

• Serial - Serial
• V4 - V4
• V4.1 - V4.1
• Amplicon - Amplicon
• Sampleid - Sampleid
• lineage - lineage
• ambiguityscore - ambiguityscore
• scorpiocall - scorpiocall
• scorpiosupport - scorpiosupport
• scorpioconflict - scorpioconflict
• version - version
• pangolinversion - pangolinversion
• Sampleid - Sampleid
• lineagev3 - lineagev3
• lineagev4 - lineagev4
• lineagev41 - lineagev41
• cladev4 - cladev4
• totalMissingv3 - totalMissingv3
• totalMissingv4 - totalMissingv4
• totalMissingv41 - totalMissingv41
• radisgenect - radisgenect
• radirdrpgenect - radirdrpgenect
• ARTICv3 - ARTICv3
• ARTICv4 - ARTICv4
• Optimizedv4 - Optimizedv4
• diff1 - diff1

f5677240 Location:

Summary Statistics: Min. 1.0; Valid 92.0; Max. 46.0; Mean 23.5; StDev 13.34866334832118;

Variable Format: numeric

Notes: UNF:6:O4Pe2gzQftBY5Bx2Hhgufg==

f5677240 Location:

Summary Statistics: Mean 8.413043478260867; StDev 11.606319019607469; Valid 92.0; Min. 0.0; Max. 63.0

Variable Format: numeric

Notes: UNF:6:EV2LMKzYC6XaKMJQAsJYrQ==

f5677240 Location:

Summary Statistics: Min. 0.0; Valid 92.0; Mean 1354.4021739130433; Max. 3264.0; StDev 974.8004141708957

Variable Format: numeric

Notes: UNF:6:vlJ1zETmsl5o/9shkiLmHQ==

f5677240 Location:

Summary Statistics: StDev 33.68356301792341; Max. 90.0; Mean 56.5; Valid 92.0; Min. 23.0

Variable Format: numeric

Notes: UNF:6:VQl0AHA1Dis1ns1CKN7sGA==

f5677239 Location:

Variable Format: character

Notes: UNF:6:JnhwumILGD9IhnNa+QKDZw==

f5677239 Location:

Variable Format: character

Notes: UNF:6:GmTQcyBwq9nnDLf4HD3Nmg==

f5677239 Location:

Summary Statistics: Max. 0.999766682221185; Valid 33.0; Min. 0.65358040201005; Mean 0.9114380714895652; StDev 0.06911672476833437

Variable Format: numeric

Notes: UNF:6:mlTqm5oXs/APqbRgcUc+lg==

f5677239 Location:

Variable Format: character

Notes: UNF:6:TD9lpNaDtF1gB8i0bZT+CA==

f5677239 Location:

Summary Statistics: Min. 0.5714; Valid 26.0; Mean 0.8758038461538462; StDev 0.09629480767214495; Max. 1.0;

Variable Format: numeric

Notes: UNF:6:8ApwQdfnatT/JeDBUpRlpg==

f5677239 Location:

Summary Statistics: Min. 0.0; Max. 0.1429; Valid 26.0; Mean 0.010515384615384612; StDev 0.03047769928728469;

Variable Format: numeric

Notes: UNF:6:U0bEmqmawYLZ0CLXVltH9A==

f5677239 Location:

Variable Format: character

Notes: UNF:6:d/in9/vBCmjcu+2zxea+Ew==

f5677239 Location:

Variable Format: character

Notes: UNF:6:P3a/eMfkeFah01jD3KYkhA==

f5677241 Location:

Variable Format: character

Notes: UNF:6:QYRHy/C278zkO8DGwED1OQ==

f5677241 Location:

Variable Format: character

Notes: UNF:6:QT8xnDr6pX+smTrIu1KSDw==

f5677241 Location:

Variable Format: character

Notes: UNF:6:w1PMYTJRA8RknNmd1KSImA==

f5677241 Location:

Variable Format: character

Notes: UNF:6:DDa11tu9+NLjMmNyFK6HMQ==

f5677241 Location:

Variable Format: character

Notes: UNF:6:HlmqO4SGRN0OHrFm0FMZEQ==

f5677241 Location:

Summary Statistics: Max. 27563.0; Min. 122.0; Valid 43.0; Mean 6676.0; StDev 8621.93420460696

Variable Format: numeric

Notes: UNF:6:eg7LBEWzRd+GxgkEZmxGoA==

f5677241 Location:

Summary Statistics: StDev 10506.39177463996; Mean 6555.5; Max. 28621.0; Min. 126.0; Valid 46.0;

Variable Format: numeric

Notes: UNF:6:siI4I/3yuKAvVGqYnlF2/g==

f5677241 Location:

Summary Statistics: Valid 46.0; Mean 2088.3043478260865; StDev 3361.3918338791696; Min. 126.0; Max. 11244.0

Variable Format: numeric

Notes: UNF:6:5g2p8o9crqxkrybDNFhR0w==

f5677241 Location:

Summary Statistics: Valid 43.0; Mean 22.090697674418603; Max. 29.92; Min. 12.57; StDev 4.047800928751807;

Variable Format: numeric

Notes: UNF:6:BPWrni5H1z4GKAs1lHBeqg==

f5677241 Location:

Summary Statistics: Min. 15.59; Max. 30.72; Valid 43.0; StDev 4.079977905831216; Mean 22.21604651162791

Variable Format: numeric

Notes: UNF:6:tykY5nk/XtF9M6NWdOxXng==

f5677241 Location:

Summary Statistics: Min. 7.82530180918302; Valid 43.0; StDev 28.83300740596916; Max. 99.5920141791793; Mean 77.67448082132228

Variable Format: numeric

Notes: UNF:6:BxYeOKM7AyoJZ274llNAbQ==

f5677241 Location:

Summary Statistics: Mean 78.07745042303446; Max. 99.5786375948901; StDev 35.134908787211856; Min. 4.28719526468916; Valid 46.0

Variable Format: numeric

Notes: UNF:6:kBU1NAgDKODlzyZ4DLOpcQ==

f5677241 Location:

Summary Statistics: Max. 99.5786375948901; Min. 62.3984215630539; Valid 46.0; StDev 11.240985298729779; Mean 93.01640521744945

Variable Format: numeric

Notes: UNF:6:JeG9Xu5Mxgy7yezNvPa5pg==

f5677241 Location:

Summary Statistics: StDev 18.938650382539308; Valid 43.0; Min. -0.0167207303614987; Max. 60.2982978296492; Mean 14.905014585920833

Variable Format: numeric

Notes: UNF:6:zIeL6yPmLyC7N7ctKup0Fw==

Label:

Description_captions.txt

text/plain

Label:

Figures_script.R

type/x-r-syntax

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LambisiaAW_SARSCoV2_ARTIC_Readme.txt

text/plain

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Supplementary Figure 1.jpg

Text:

Amplicon plots of seven sequences generated using (a) V3 primers, (b) V4 primers and (c) optimized V4 primers and classified as Alpha, Beta and Delta VOC

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Supplementary Figure 2.jpg

Text:

Amplicon plots of serially diluted positive controls amplified using (a) V4 primers and (b) optimized V4 primers and classified as B.1

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