REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
CFAV-KPP	https://doi.org/10.1128/JVI.00705-19	ENA: LR596014
Chemicals, Peptides, and Recombinant Proteins
RNase A/T1	Thermo Scientific	Cat# EN0551
DreamTaq Green DNA Polymerase	Thermo Scientific	Cat# EP0714
DNAzol DIRECT	Molecular Research Center, Inc.	Cat# DN131
NucleoSpin DNA Insect Kit	Machery-Nagel	Cat# 740470.50
NucleoSpin Tissue Kit	Machery-Nagel	Cat# 740952.50
MEGAscript T7 in vitro transcription kit	Thermo Scientific/Ambion	Cat# AM1333
Cas9 Nuclease, S. pyogenes	New England Biolabs	Cat# M0646
TRIzol Reagent	Thermo Scientific	Cat# 15596026
M-MLV Reverse Transcriptase	Thermo Scientific	Cat# 28025013
RNaseOUT Recombinant Ribonuclease Inhibitor	Thermo Scientific	Cat# 10777019
GoTaq qPCR Master Mix	Promega	Cat# A6002;Cat# TM318
TruSeq DNA PCR-free library preparation kit	Illumina	Cat# FC-121-3001
NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1)	New England Biolabs	Cat# E7300
Universal miRNA Cloning Linker	New England Biolabs	Cat# S1315S
Critical Commercial Assays
Qubit dsDNA HS (High Sensitivity) Assay Kit	Thermo Scientific	Cat# Q32851
Agilent Small RNA Kit	Agilent	Cat# 5067-1548
Deposited Data
Outbred Thai Aedes aegypti with CFAV-EVE1 (+/?) and CFAV-EVE2 (+/?), full body, naturally infected with CFAV. sRNA.	This paper	HGW27BGXX, SRA: SAMN13244317
Outbred Thai Aedes aegypti with CFAV-EVE1 (+/?) and CFAV-EVE2 (+/?), full body, uninfected with CFAV. sRNA.	This paper	HG7CHBGXX, SRA: SAMN13244318
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, CFAV IT injected, replicate 1. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244306
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, CFAV IT injected, replicate 2. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244307
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, CFAV IT injected, replicate 3. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244308
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, mock IT injected, replicate 1. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244303
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, mock IT injected, replicate 2. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244304
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?), full body, mock IT injected, replicate 3. sRNA.	This paper	HVV5HBGXX, SRA: SAMN13244305
Isofemale line derived knockout line with CFAV-EVE1 (−/−), head, CFAV IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244315
Isofemale line derived knockout sister line with CFAV-EVE1 (+/+), head, CFAV IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244313
Isofemale line derived knockout line with CFAV-EVE1 (−/−), ovary, CFAV IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244316
Isofemale line derived knockout sister line with CFAV-EVE1 (+/+), ovary, CFAV IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244314
Isofemale line derived knockout line with CFAV-EVE1 (−/−), head, mock IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244311
Isofemale line derived knockout sister line with CFAV-EVE1 (+/+), head, mock IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244309
Isofemale line derived knockout line with CFAV-EVE1 (−/−), ovary, mock IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244312
Isofemale line derived knockout sister line with CFAV-EVE1 (+/+), ovary, mock IT injected. sRNA.	This paper	HJ5CNBGX9, SRA: SAMN13244310
Thai Aedes aegypti isofemale line with CFAV-EVE1 (+/?). WGS.	This paper	SRA: SRR01437595
SRA accessions and BLAST search output of SRA search for CFAV related sequences	This paper, https://github.com/artembaidaliuk/SRA_search_CFAV_EVE_sequences/	N/A
Experimental Models: Cell Lines
Aedes albopictus C6/36	ATCC	Cat# CRL-1660
Experimental Models: Organisms/Strains
Aedes aegypti outbred colony	https://doi.org/10.1371/journal.pgen.1006111	N/A
Aedes aegypti isofemale line	https://doi.org/10.1371/journal.pgen.1006111	Line D
	https://doi.org/10.1371/journal.pgen.1003621
Isofemale line derived knockout line with CFAV-EVE1 (−/−)	This paper	N/A
Isofemale line derived knockout sister line with CFAV-EVE1 (+/+)	This paper	N/A
Oligonucleotides
All primer sequences are listed in Table S1	[57]	N/A
Repair template sequence is listed in Table S3		N/A
Software and Algorithms
BLAST	[60]	N/A
SRA Toolkit v2.9.6	https://doi.org/10.1093/nar/gkq1019https://github.com/ncbi/sra-tools	N/A
metaSPAdes v3.11.0	https://doi.org/10.1101/gr.213959.116	N/A
R v3.5.2	http://www.r-project.org/	N/A
Trimmomatic v0.36	https://doi.org/10.1093/bioinformatics/btu170	N/A
Bowtie2 v2.3.4.3	https://doi.org/10.1038/nmeth.1923	N/A
Cutadapt v1.18	https://doi.org/10.14806/ej.17.1.200	N/A
Ray v2.3.1-mpi	https://doi.org/10.1089/cmb.2009.0238	N/A
Geneious v10.2.3	https://www.geneious.com	N/A
bedtools v2.25.0	https://doi.org/10.1093/bioinformatics/btq033	N/A
LoFreq v2.1.3.1	https://doi.org/10.1093/nar/gks918	N/A
CRISPOR	http://crispor.tefor.net/	N/A
FastQC v0.10.1	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	N/A
Bowtie1 v1.1.2	https://doi.org/10.1186/gb-2009-10-3-r25	N/A
Galaxy	https://doi.org/10.1093/nar/gky379	N/A
WebLogo 3	https://doi.org/10.1101/gr.849004	N/A
Graphpad Prism 6	https://www.graphpad.com/scientific-software/prism/	N/A
tidyverse v1.3.0 (R package)	https://doi.org/10.21105/joss.01686 [58]	N/A
viridis v0.5.1 (R package)	https://CRAN.R-project.org/package=viridis	N/A
parsedate v1.2.0 (R package)	https://CRAN.R-project.org/package=parsedate	N/A
Rsamtools v1.20.4 (R package)	https://doi.org/10.18129/B9.bioc.Rsamtools	N/A
ShortRead v1.26.0 (R package)	https://doi.org/10.18129/B9.bioc.ShortRead [59]
Other
Mississippi, Galaxy	https://mississippi.snv.jussieu.fr/	N/A
SRA_blast.sh	This paper, https://github.com/artembaidaliuk/SRA_search_CFAV_EVE_sequences/	N/A
script-SRA_prefetch_into_custom_dir.sh	This paper, https://github.com/artembaidaliuk/SRA_search_CFAV_EVE_sequences/	N/A