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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Metagenomic analysis of female Aedes aegypti mosquito RNA metaviromes reveal presence of diverse insect specific viruses |
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Identification Number: |
doi:10.7910/DVN/4YV8PL |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2023-01-19 |
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Version: |
4 |
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Bibliographic Citation: |
Omuoyo, Donwilliams O.; Nyamwaya, Doris K.; Kamau, Everlyn; Nyagwange, James; Karanja, Henry K.; Gitonga, John N.; de Laurent, Zaydah; Kinyua, Johnson; Rono, Martin K.; Mwangangi, Joseph M.; Agoti, Charles N.; Warimwe, George M., 2023, "Replication Data for: Metagenomic analysis of female Aedes aegypti mosquito RNA metaviromes reveal presence of diverse insect specific viruses", https://doi.org/10.7910/DVN/4YV8PL, Harvard Dataverse, V4, UNF:6:uldxrPupDV8d6kgthu8Vrg== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Metagenomic analysis of female Aedes aegypti mosquito RNA metaviromes reveal presence of diverse insect specific viruses |
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Identification Number: |
doi:10.7910/DVN/4YV8PL |
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Authoring Entity: |
Omuoyo, Donwilliams O. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Nyamwaya, Doris K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kamau, Everlyn (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Nyagwange, James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Karanja, Henry K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Gitonga, John N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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de Laurent, Zaydah (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Kinyua, Johnson (Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology) |
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Rono, Martin K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Mwangangi, Joseph M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Warimwe, George M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Omuoyo, Donwilliams O. |
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Access Authority: |
Warimwe, George M. |
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Access Authority: |
The Data Governance Committee |
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Depositor: |
Omuoyo, Donwilliams O. |
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Date of Deposit: |
2023-01-17 |
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Holdings Information: |
https://doi.org/10.7910/DVN/4YV8PL |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Aedes aegypti, Virome, Metagenomics, Phylogenetics |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href=""></a>" submitted to Wellcome Open Research.</p> <p>Coastal Kenya has experienced repeated outbreaks of DENV and CHIKV, and cases of microcephaly have also been reported. Despite the Arboviral burden, there is lack of systematic entomological surveillance. This study collected Aedes aegypti from different sites in coastal Kenya and characterized the viruses circulating in these mosquitoes. Mosquitoes were collected using BG-Sentinel traps, and pools comprised of female Aedes aegypti only generated. The resultant mosquito pools were then screened for presence of arboviruses using RT-PCR and then sequenced using a meta genomics approach to identify other viruses circulating in them. The mosquito collection dataset highlights the geographical location names and their respective geographical position coordinates (GPS) coordinates whereas the RT-PCR dataset describes arbovirus presence or absence findings. The mosquito collection dataset was key in generating a map showing sampling sites, while the RT-PCR dataset informed the mosquito pools to prioritise for sequencing. </p> |
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Kind of Data: |
Open Access |
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Notes: |
<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> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p> |
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Other Study Description Materials |
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File Description--f6897640 |
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File: merged_mosquito_samplingdata.tab |
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Notes: |
UNF:6:uldxrPupDV8d6kgthu8Vrg== |
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List of Variables: |
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Variables |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:SOyzV/1cyHpZGXEH/NRJAg== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:OXGRS1s0cwzKD9cmrApuuA== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:lo1VBwi9ERD0VET2dpIh8Q== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:Rb1tGCHJUTpFD7hBHbDmhA== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:QkEDaluHLmcDVlb2cOg20A== |
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f6897640 Location: |
Summary Statistics: Min. 3.0; StDev 3.3813142768202016; Valid 732.0; Mean 18.98087431693989; Max. 25.0 Variable Format: numeric Notes: UNF:6:AwdenUboOfsl1ttkgTttwA== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:lBJy82UdbQZw1aCvJNMXHQ== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:sRhH5hI9rkNJbx/AMB+mww== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:rNMaIJZqi0J+8cbTvcmQ0g== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:Qec59U4+6qzwLmb3O6p5Qg== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:sL52Hri+6UkuFqaw+hDCJQ== |
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f6897640 Location: |
Summary Statistics: Mean -3.8812019057377047; Max. -3.189722; StDev 0.4595570058037262; Min. -4.66064; Valid 732.0; Variable Format: numeric Notes: UNF:6:Yhbdg37Hfk/VW1oZ5SrLRA== |
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f6897640 Location: |
Variable Format: character Notes: UNF:6:HN01S+FiBL0TRCBfAtRpXA== |
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Label: |
DOmuoyo_Mosquito_collection_ RTPCR_Data_Codebook.pdf |
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Notes: |
application/pdf |
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Label: |
DOmuoyo_Mosquito_collection_ RTPCR_Data_Readme.txt |
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Notes: |
text/plain |
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Label: |
maps.R |
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Notes: |
type/x-r-syntax |
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Label: |
merged_mosquito_samplingdata.xlsx |
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Notes: |
application/vnd.openxmlformats-officedocument.spreadsheetml.sheet |
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Label: |
Mosquito_collection_ RT-PCR_data .pdf |
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Notes: |
application/pdf |
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Label: |
PanFlavi_positive_MosquitoPools_contigs.fasta |
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Notes: |
application/octet-stream |
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Label: |
Proportion of classified and unclassified total reads across Aedes aegypti pools.pdf |
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Notes: |
application/pdf |
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Label: |
Supplementary files.zip |
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Text: |
Figures and Tables |
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Notes: |
application/zip |
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Label: |
Supplementary Table 1. Summary of RT-PCR positive samples.docx |
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Notes: |
application/vnd.openxmlformats-officedocument.wordprocessingml.document |