Argentina/PP_006VZDC.2/2018-12-28
V. P. Martinez, U. Perez-Sautu, D. O. Alonso, N. Di Paola, C. M. Bellomo, A. A. Iglesias, R. M. Coelho, N. Periolo, E. R. Nagle, J. A. Chitty, C. B. Pratt, M. R. Wiley, J. Diaz, E. Biondo, L. Lewis, C. Anselmo, F. Pontoriero, E. Lavarra, J. H. Kuhn, M. Sanchez-Lockhart, A. Edelstein, D. Cisterna, J. Campos, M. Kaler, ..., C. Pratt

United States Army Medical Research Institute for Infectious Diseases USAMRIID, Center for Genome Sciences

Sample details

Collection date
2018-12-28
Sampling location
Argentina (Esquel, Chubut)
City
Esquel
Isolate name
Epuyen/18-19_Patient_15_12/26/18

Data use terms

Data use terms
OPEN

INSDC

INSDC accession L
INSDC accession M
INSDC accession S
NCBI release date
2020-09-30

Sampling

Sample type
Whole blood
Purpose of sampling
Outbreak

Host

Host age
7
Host age bin
10 - 19
Host gender
Male
Host origin country
Argentina
Host disease
Hantavirus Pulmonary Syndrome
Host health outcome
Survived
Exposure event
Exposure to human patient
Host role
Exposed Patient
Exposure details
Host role - Other: Nephew

Sequencing

Purpose of sequencing
Outbreak
Sequencing protocol
RNA was extracted from 400 µl of whole blood in TRIzol LS reagent using the TRIzol™ Reagent and Phasemaker™ Tubes Complete System (ThermoFisher Scientific, Waltham, MA, USA) following the manufacturer’s protocol. RNA sequencing libraries were prepared using the KAPA RNA HyperPrep kit (KAPA Biosystems, Wilmington, MA, USA) following the manufacturer’s guidelines. Unique dual-index...
Raw sequence data processing method
Trimmomatic 0.381;Cutadapt2;Prinseq-lite 0.20.43
Dehosting method
Bowtie 2.4
Consensus sequence software name
SPAdes
Consensus sequence software version
3.9.0.5

Submission details

Submission ID
MN258167.1.L/MN258200.1.M/MN258234.1.S
Version comment
https://github.com/pathoplexus/curation_reports/issues/21#issuecomment-4466642240
Date submitted
2026-05-19 01:01:59 UTC
Date released
2026-05-19 06:44:44 UTC
Earliest release date
2020-09-30

Alignment and QC

Length L
6531 (99.5%)
# of SNPs L
377
Length M
3633 (98.7%)
# of SNPs M
206
# of inserted bases M
8
Length S
1828 (97.4%)
# of SNPs S
118
# of inserted bases S
7
# of deleted bases S
2

Nucleotide mutations

Mutations called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

L

  • T47C
  • G53A
  • C74T
  • A86G
  • G89A
  • C131T
  • T143C
  • C146T
  • C147T
  • G149A
  • C155T
  • T182C
  • A200G
  • A218G
  • A296G
  • T297C
  • A302G
  • T326C

M

  • T74C
  • G114A
  • C159A
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T324C
  • G339A
  • T345C
  • A360G
  • T363C
  • T387C
  • C394T
  • C408T
  • T414C

S

  • T61C
  • G63A
  • G66A
  • G120A
  • A135G
  • C172T
  • A219G
  • T225C
  • A240G
  • T244C
  • A261G
  • T306C
  • A312G
  • G315A
  • A318G
  • T357C
  • T363C
  • T366C
Deletions

S

1443, 1573
Insertions

M

ins_3504:ATATACAT

S

ins_1482:CC, ins_1555:G, ins_1631:TTT, ins_1668:T

Amino acid substitutions

Substitutions called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

GPC

  • GPC:V8A
  • GPC:F216L
  • GPC:H294Y
  • GPC:V346I
  • GPC:T353I
  • GPC:V499I
  • GPC:I537V
  • GPC:T641I
  • GPC:T938A
  • GPC:T1023A
  • GPC:V1115I

NSs

  • NSs:Q5R
  • NSs:E33G
  • NSs:L35S
  • NSs:Q40R
  • NSs:N47S
  • NSs:I62T

RdRp

  • RdRp:T141V
  • RdRp:L277S
  • RdRp:S338A
  • RdRp:R346K
  • RdRp:N364S
  • RdRp:D780N
  • RdRp:S876A
  • RdRp:N1033D
  • RdRp:D1303E
  • RdRp:S1440N
  • RdRp:K1750R
  • RdRp:Q1965H
  • RdRp:I2109V
Deletions
N/A
Insertions
N/A

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