Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia

  1. Kim R Blasdell
  2. Veasna Duong
  3. Marc Eloit
  4. Fabrice Chretien
  5. Sowath Ly
  6. Vibol Hul
  7. Vincent Deubel
  8. Serge Morand
  9. Philippe Buchy  Is a corresponding author
  1. Institut Pasteur in Cambodia, Cambodia
  2. Australian Animal Health Laboratory, Australia
  3. Institut Pasteur, France
  4. CNRS, IRD, Université Montpellier, France
  5. GlaxoSmithKline Vaccines R&D, Singapore
5 figures, 4 tables and 1 additional file

Figures

Maximum likelihood phylogenetic tree of novel arenavirus isolates and other representative arenaviruses for a, the complete ORF of the L gene with sequences from rodents only, b, partial L sequences including sequences from rodents and patients.

Cambodian strains detected in rodent (triangle), human (square) and Thai strains detected in rodent (circle) are in bold. Clade A, B and C are three evolutionary lineages of New World arenaviruses within the Tacaribe complex. A/Rec denotes the recombinant clade including the three Northern American viruses. The virus names are in abbreviation according to Radoshitzky et al. (2015).

https://doi.org/10.7554/eLife.13135.006
Maximum likelihood phylogenetic tree of novel arenavirus isolates and other representative arenaviruses for a, the complete ORF of GPC gene and b, complete ORF of NP gene.

Cambodian strains (triangle) and Thai strains (circle) detected in rodents are in bold. Clade A, B and C are three evolutionary lineages of New World arenaviruses within the Tacaribe complex. A/Rec denotes the recombinant clade including Northern American viruses. The virus names are in abbreviation according to Radoshitzky et al. (2015).

https://doi.org/10.7554/eLife.13135.007
Electron microscope images of the Cardamones variant of Wēnzhōu virus in the rat lung tissues, a (scale: 200 nm) & b (scale: 2 µm).

Histopathological examination of the lungs revealed only severe diffuse pneumonia, with lesions associated with acute exudative inflammation characterised by foci of consolidation surrounded by extremely rare aerated parenchyma, c, vascular congestion, acute bronchiolitis and diffuse leukocytic infiltration with lymphocytes, polymorphonuclear and macrophages (suppurative exudate in the lumen and parietal inflammation), c and d. Reticulin staining demonstrated the severe destruction of lung parenchyma, e. Chromogenic immunohistochemistry identified inflammatory foci with numerous positive cells, f, primarily inflammatory cells including macrophages, but in the more preserved parenchyma and aerated parenchyma some epithelial (pneumocytes), g, and alveolar macrophages, h, were also clearly stained.

https://doi.org/10.7554/eLife.13135.008
Representation map of the percentage (%) of patients who tested positive by anti-arenavirus IgG ELISA and of 6 patients who tested positive by L gene RT-PCR in the villages from Kampong Cham province.

Village names: AC=Andoung Chea, AK=Ampil Kraom, AL=Ampil Leu, AS=Andoung Svay, BH=Banteay Thma, BT=Boeng Tras, CH=Chachak, CM=Chong Thnal Muoy, CP=Chong Thnal Pir, KD=Kdei Boeng, KH=Kakaoh, KK=Kouk Kream, KP=Krasang Pul, KR=Krala, MM=Memay, OD=Ou Da, PP=Prey Phdau, RK=Roung Kou, RM=Romeas, SS=Srae Siem, SY=Sya, TA=Tuol Ampil and TV=Tuol Vihear.

https://doi.org/10.7554/eLife.13135.010
Positions of primers used in diagnostic PCR assays.

The positions of the primers used for qRT-PCR are included in their names and these positions are based on the sequence of the L gene of Cardamones variant of Wēnzhōu virus. The positions of the primers used in the nested RT-PCR originate from the article of Vieth et al. (Vieth et al., 2007).

https://doi.org/10.7554/eLife.13135.012

Tables

Table 1

Nucleotide and amino acid sequence identities (%) between Cambodian and Thai isolates and selected other arenaviruses.

https://doi.org/10.7554/eLife.13135.003
IsolatesSegment or ORFnt/ aaCambodian isolatesThai isolatesWēnzhōuLassaIppyMopeiaLCMVJunínLunaMorogoro
Cambodian isolatesL segmentnt98.969.2-69.487.5-88.655.8-56.457.7-57.860.856.950.2-50.461.1-61.460.9-61.0
L ORFnt99.367.3-67.588.0-89.059.7-60.660.4-60.559.2-59.455.650.6-50.959.6-60.959.6
aa99.669.2-69.492.2-94.855.5-56-457.7-57.856.6-57.148.537.9-38.055.8-55.955.6
Z ORFnt99.573.4-74.5837.-87.966.8-67.463.662.557.6-58.254.9-55.469.0-70.164.7-65.2
Aa98.879.289.4-93.970.1-75.370.164.959.440.363.6-64.961.0
S segmentnt99.571.7-72.187.5-89.861.7-68.166.6-66.866.6-67.061.6-61.854.6-54.867.6-68.266.7-66.9
NP ORFnt99.373.1-74.486.6-90.067.1-68.268.3-68.467.6-67.962.9-63.255.1-55.669.0-70.368.7
aa99.882.9-84.287.3-96.572.2-73.874.4-74.673.5-73.864.051.9-52.573.3-74.074.0-74.6
GPCnt99.769.1-70.088.6-89.767.3-68.664.7-65.765.3-65.761.2-61.453.4-53.666.3-66.649.9-65.2
aa99.879.5-81.195.5-96.474.2-76.269.5-71.371.5-72.857.2-57.548.2-43.072.6-74.473.1-74.4
Thai virusL segmentnt68-68.194.666.6-67.560.7-61.861.3-61.561.1-61.457.150.2-50.560.7-61.461.4-61.5
L ORFnt67.3-67.595.167.9-68.859.6-59.959.9-60.461.6-62.155.7-56.249.9-50.860.4-61.659.9-60.2
aa69.2-69.496.769.6-70.755.7-56.456.556.6-57.149.0-49.437.1-37.555.9-56.356.5-56.7
Z ORFnt73.4-74.595.469.4-75.065.2-66.864.1-65.869.0-69.658.7-59.254.3-56.065.8-72.866.3-66.8
aa79.298.573.1-74.667.5-71.468.870.158.442.9-44.270.1-71.466.2
S segmentnt71.7-72.194.471.0-72.265.8-67.366.1-66.866.2-6761.7-62.653.9-55.065.2-68.166.1-67.9
NP ORFnt73.1-74.494.672.2-74.165.2-67.866.6-67.366.9-67.762.4-63.254.1-54.466.1-68.067.3-68.9
aa82.9-84.298.178.3-87.273.3-74.672.0-72.973.8-74.464.2-64.649.9-51.072.0-73.574-75.5
GPCnt69.1-7094.169.2-69.966.0-67.665.0-66.166.4-6761.5-62.653.9-56.065.8-69.266.1-67.5
aa79.5-81.197.580.1-81.173.5-75.771.5-72.471.0-74.259.7-61.043.0-43.974.2-74.873.1-75.9
  1. Note where (L & S gene): Cambodian = KC669690, KC669691& KC669694, KC669696; Thai = KC669692, KC669693 & KC669697, KC669698; Wenhzhou = KM386661, KM051421, KJ909795, KM051420 and KM386660, KM051423, KJ909794, and KM051422; Lassa = GU481076 & GU481077; Ippy = DQ328877 & DQ328878; Mopeia = DQ328874 & DQ328875; LCMV = AY847350 & AY847351; Junín = D10072 & AY216507; ORF = Open reading frame; NP = Nucleoprotein; GPC = Glycoprotein; nt = Nucleotide; aa = Amino acid; LCMV =: Lymphocytic Choriomeningitis Virus

Table 2

Summary of PASC analysis.

https://doi.org/10.7554/eLife.13135.004
Sample IDCountry of originPASC: S segmentPASC: L segment
Sequence identity (%)Closest virusSequence identity (%)Closest virus
C0617Cambodia88.80Wēnzhōu virus86.27Wēnzhōu virus
C0649Cambodia88.51Wēnzhōu virus85.98Wēnzhōu virus
R4937Thailand70.63Wēnzhōu virus62.71Wēnzhōu virus
R5074Thailand70.29Wēnzhōu virus63.08Wēnzhōu virus
Table 3

Details of patient samples tested.

https://doi.org/10.7554/eLife.13135.009
GroupClinical signsSample type (number of samples)Collection datesCollection locationsMean age in years (range)95% CI (years)Sex ratioTest usedNumber (proportion) of positive
1Dengue-like/ influenza-like illnessAcute and convalescent sera (n=510 including 98 acute, 214 convalescent and 198 paired sera)2005-2010Kampong Cham, various11.0
(4 months to 70 years)
10.0-12.00.44IgG ELISA89 (17.4%)
- Acute sera: 33 (33.7%)
- Convalescence sera: 25 (11.7%)
- Paired sera: 31 (15.7%) with evidence of seroconversion in 7 pairs (3.5%)
2Healthy individuals (community dengue seroprevalence study)Sera (n=529)2009Kampong Cham10.0 (1 month-20 years)9.59-10.420.50IgG ELISA70 (13.23%)
3Meningo-encephalitisCerebrospinal fluid (n=200£)2013-2014Various6.5 (3 months-15 years)5.95-7.060.40Real Time RT-PCR0 (0%)
4Dengue-like febrile illnessSera collected during febrile stage (n=253*)2009, 2011-2013Various8.2
(1 to 38 years)
7.6-8.80.48Semi-nested RT-PCR0 (0%)
5aInfluenza-like illness (negative for four common respiratory viruses)Nasopharyngeal swabs (n=328)2007-2012Various13.2
(1 month to 83 years)
12.0-14.40.51Semi-nested RT-PCR4 (1.2%)
5bInfluenza-like illness (positive for four common respiratory viruses)Nasopharyngeal swabs (n=392#)0 (0%)
6Acute lower respiratory infectionNasopharyngeal swabs (n=279$)2008-2009Various2.7
(7 months to 63 years)
2.1-3.40.41Semi-nested RT-PCR2 (0.7%)
7Healthy individuals (H5N1 contacts) – negative controlNasopharyngeal swabs (n=266§)2005-2011Various29.3
(1 to 79 years)
27.1-31.50.45Semi-nested RT-PCR0 (0%)
8Healthy anti-rabies vaccination volunteers – negative controlNasopharyngeal swabs (n=238¥)2013Institute Pasteur Cambodia (Phnom Penh)26.7
(9 months to 83 years)
24.5-28.80.56Semi-nested RT-PCR0 (0%)
  1. CI = Confidence Interval

  2. £ 3 no information on age; * 8 no information on age and sex; # 2 no information on age and sex; $ 1 no information on age; § 5 no information on age and sex; 51 no information on sex; ¥ 5 no information on age and sex

Table 4

Clinical details of human arenavirus infections.

https://doi.org/10.7554/eLife.13135.011
Case no.Test usedSexAgeHospitalisedFeverCoughRhinorrheaNausea/ vomitingSevere headacheMuscle painOther symptomsCo-infection
1Screening nested RT-PCRFemale3 yearsNoYesYesYesHuman para-influenza virus 1
2Screening nested RT-PCRMale9 yearsNoYesYesYesYesYes
3Screening nested RT-PCRMale31 yearsNoYesYesYesYesYes
4Screening nested RT-PCRFemale45 yearsNoYesYesYesYesYesYes
5Screening nested RT-PCRFemale8 monthsYesYesYesDyspnea, wheezing, moderate anaemia (93g/L)Unspecified Rhinovirus
6Screening nested RT-PCRMale3 monthsYesYesYesDyspnea, wheezing, hypoglycaemia (28mmol/L)Unspecified Rhinovirus
S1ELISAMale3 yearsNoYesYesYes
S2ELISAMale9 yearsNoYesYesYesYesYes
S3-7ELISANoYes

Additional files

Supplementary file 1

(A) Details of primers used for diagnostic RT-PCRs and genome sequencing. (B) Animals tested for arenavirus RNA by species and site, with number of positives shown in bold. (C) Details of rodent samples positive for arenavirus infection by screening RT-PCR .(D) Details of animals used for Cambodian virus infections. (E) Detailed IgG ELISA results for 7 patients with seroconversion. (F) Comparison between IFA and IgG ELISA results in human sera. (G) Arenavirus infections in patients with ILI symptoms who tested negative for 4 common respiratory viruses versus patients with ILI symptoms who tested positive and control group of healthy individuals. (H) Statistic analysis by age between respiratory illness group and healthy control group. (I) Multiple alignment of the sequences of the amplicons obtained by PCR for 3 patients. (J) Results of IgG ELISA in experimentally-infected rodents.

https://doi.org/10.7554/eLife.13135.013

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  1. Kim R Blasdell
  2. Veasna Duong
  3. Marc Eloit
  4. Fabrice Chretien
  5. Sowath Ly
  6. Vibol Hul
  7. Vincent Deubel
  8. Serge Morand
  9. Philippe Buchy
(2016)
Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia
eLife 5:e13135.
https://doi.org/10.7554/eLife.13135