REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-E (5D4)	Hybridoma from ATCC	5D4-11 (ATCC® HB-49™), RRID: CVCL_J928; Henchal et al. (1982)
anti-NS3 (E1D8)	Hybridoma generated in Harris Laboratory	E1D8, Balsitis et al. (2009)
Bacterial and Virus Strains
E. coli TOP10 competent cells	Invitrogen	C4040-10
Biological Samples
PBMC and plasma samples	This paper: Table S1	N/A
Chemicals, Peptides, and Recombinant Proteins
Kanamycin Sulfate	Life Technologies	11815-024
Chloramphenicol >=98% (TLC)	Sigma-Aldrich	C0378-25G
Critical Commercial Assays
RNeasy Mini kit	Qiagen	Cat No./ID: 74104
QIAamp Viral RNA Mini Kit	Qiagen	Cat No./ID: 52904
QIAquick Gel Extraction Kit	Qiagen	Cat No./ID: 28704
Nextera XT DNA Sample Preparation Kit	Illumina	FC-131-1096
SuperScript III One-Step RT-PCR System	Invitrogen	12574-035
mMessage mMachine T7 Kit	Life Technology	AM1344M
MinElute Gel Extraction Kit (50) (70bp to 4kb)	Qiagen	Qia 28604
Deposited Data
Fastq files for all these samples have been deposited into	NCBI's Sequence Read Archive	BioProject ID PRJNA394021
Experimental Models: Cell Lines
Baby hamster kidney cells (BHK-21 clone 15)	Gift from B. Childs (Center for Vector-born Diseases, University of California, Davis, CA)	N/A
C6/36 cells, 37°C in 5% CO2.	Gift from Dr. Ralph Baric, University of North Carolina, Chapel Hill	N/A
U937-DC-SIGN cells	Gift of Dr. Aravinda de Silva, University of North Carolina, Chapel Hill	N/A
Oligonucleotides
Sequences of primers used for amplifying the DENV-3 genome	Table S4 of this paper	N/A
DV3Ewt_r: CGACCTTAATGAGTATTGTCCCAT	This paper	N/A
DV3E∗_r: CGACCTTAATGAGTATTGTCCCAa	This paper	N/A
PP49_DENV3_32_F (GACTCGGAAGCTTGCTTAAC)	This paper	N/A
primers (5’- GACTCGGAAGCTTGCTTAAC-3’ and 5’-TATTGACAGGCTCCTCCTTCTTAG-3’) designed to capture the prM100,101 and E315 hotspot loci	This paper	N/A
Sequencing primer for prM100,101: 5’-TCAATATGCTGAAACGCGTG-3’	This paper	N/A
Sequencing primer for E315: 5’-CGGACAGGTTTGGATTTCAATG-3’	This paper	N/A
Recombinant DNA
plasmid A-D	Gift of Dr. Ralph Baric	Messer et al., 2012
plasmid A Nicaraguan WT	This paper	N/A
plasmid A Nicaraguan prM100,101	This paper	N/A
plasmid A Nicaraguan E315	This paper	N/A
Software and Algorithms
Bowtie2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools	Li et al., 2009	http://samtools.sourceforge.net/
ShoRAH	Zagordi et al., 2011	http://www.cbg.ethz.ch/software/shorah