A novel Betacoronavirus characterised in collared peccaries from the Rio de Janeiro Zoo (Brazil) killed by unknown disease

In an enclosure with nine collared peccaries (Pecari tajacu) from the Rio de Janeiro city Zoo, Brazil, one specimen was found dead and two others developed prostration, apathy and dehydration, resulting on its death. Necropsy of two animals pointed to pulmonary and renal damage. Histological examination revealed vasculitis in spleen from both P. tajacu, suggesting a systemic viral infection. Lungs from one specimen showed fibrinoid vasculitis, alveolar damage with hyaline membrane, and interstitial lymphocytes infiltration. Virome analysis in anal wash samples from the latter two animals revealed a new type of Betacoronavirus, lineage A, provisionally named Ptajacu-CoV.

Key words:
virome; Pecari tajacu; Betacoronavirus; zoonoses; one health

Authorship

Mirela D’arc

Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BrasilUniversidade Federal do Rio de JaneiroBrazilRio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil

Matheus Calvano Cosentino

Filipe Romero Rebello Moreira

Liliane Tavares Faria Cavalcante

Anderson Mendes Augusto

Zoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/ABrasilRio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, Brasil

Fernando Trocolli

Zoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/ABrasilRio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, Brasil

Daniel Guimarães Ubiali

Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, BrasilUniversidade Federal Rural do Rio de JaneiroBrazilSeropédica, RJ, BrazilUniversidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brasil

Carlos Eduardo Verona

Zoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/ABrasilRio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, Brasil

Marcelo Alves Soares

Instituto Nacional de Câncer, Rio de Janeiro, RJ, BrasilInstituto Nacional de CâncerBrazilRio de Janeiro, RJ, BrazilInstituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil

André Felipe Santos ⁺+ Corresponding author: afsantos.ufrj@gmail.com

https://orcid.org/0000-0003-3372-1552

+ Corresponding author: afsantos.ufrj@gmail.com

MD - Designed and performed experiments, analysed data and co-wrote the paper; MCC - performed experiments and analysed data; FRM - performed bioinformatic analyses and co-wrote the paper; LTC, AMA, FT and CEV - provided sample collect from animals and acquisition of data; DGU - performed histopathology and co-wrote the paper; MAS - conception and design of project and provided financial grants to project; AFS - conception and design of project, provided financial grants to project, supervised the experiments and co-wrote the paper.

SCIMAGO INSTITUTIONS RANKINGS

Zoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/ABrasilRio de Janeiro, RJ, BrasilZoológico do Rio de Janeiro S/A, Rio de Janeiro, RJ, Brasil

Instituto Nacional de Câncer, Rio de Janeiro, RJ, BrasilInstituto Nacional de CâncerBrazilRio de Janeiro, RJ, BrazilInstituto Nacional de Câncer, Rio de Janeiro, RJ, Brasil

Figures

Figures (1)

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Maximum likelihood phylogeny inferred under the GTR+F+I+G4 model from an open reading frame (ORF) 1AB alignment (17,592 bp, after trimming of sites with more than 10% of gaps), comprehending coronavirus sequences available on NCBI RefSeq and the novel Ptajacu-CoV. Different genera or Betacoronavirus clades are colour labelled and asterisks mark nodes inferred with low support values (SH-aLRT < 0.70). Branch lengths bigger than 0.7 have been trimmed and annotated to keep figure dimensions. Alphacoronavirus (a CoV): BtRf-AlphaCoV-YN2012 (NC_028824, bat), BtCoV-HKU2 (NC_009988, bat), AlphaCoV-DcCoV (NC_028752, camel), HCoV-229E (NC_002645, human), BtCoV-HKU8 (NC_010438, bat), BtCoV-1A (NC_010437, bat), BtNv-AlphaCoV-SC2013 (NC_028833, bat), HCoV-NL63 (NC_005831, human), BtRf-AlphaCoV-HuB2013 (NC_028814, bat), Sc-BatCoV-512 (NC_009657, bat), PEDV (NC_003436, pig), BtCoV-CDPHE15 (NC_022103, bat), LuchengRn (NC_032730, rat), MCoV-WD1127 (NC_023760, mink), SECD (NC_028806, pig) and FIP (NC_002306, cat). Gammacoronavirus (γ CoV): BWCoV-SW1 (NC_010646, beluga whale), IBV (NC_001451, chicken), TCoV (NC_010800, turkey). Deltacoronavirus (δ CoV): WiCoV-HKU20 (JQ065048, duck), BuCoV-HKU11 (FJ376619, bulbul), PorCoV-HKU15 (JQ065042, pig), MRCoV-HKU18 (JQ065046, magpie-robin). Betacoronavirus lineage A (ꞵ CoV A): HCoV-HKU1 (NC_006577, human), PRC (NC_012936, rat), MHV-A59-C12 (NC_001846, mouse), BetaCoV-HKU24 (NC_026011, rat), RbCoV-HKU14 (NC_017083, rabbit), HCoV-OC43 (NC_006213, human), PHEV-VW572 (DQ011855, pig), AntelopeCoV (EF424621, sable antelope), BCoV (NC_003045, cow), Ptajacu-CoV (MT083879, collared peccary), ECoV (NC_010327.1, horse), DcCoV (KF906251, camel). Betacoronavirus lineage B (ꞵ CoV B): 2019_nCOV (NC_045512.2, human), SARS-CoV (NC_004718, human). Betacoronavirus lineage C (ꞵ CoV C): BetaCoV-Erinaceus (NC_039207, hedgehog), BtCoV-HKU4-1 (NC_009019, bat), BtCoV-HKU5-1 (NC_009020, bat), MERS-CoV (NC_019843, human), BetaCov-England-1 (NC_038294, human). Betacoronavirus lineage D (ꞵ CoV D): BtCoV-HKU9-1 (NC_009021, bat), Ro-BatCoV (NC_030886, bat).

Maximum likelihood phylogeny inferred under the GTR+F+I+G4 model from an open reading frame (ORF) 1AB alignment (17,592 bp, after trimming of sites with more than 10% of gaps), comprehending coronavirus sequences available on NCBI RefSeq and the novel Ptajacu-CoV. Different genera or Betacoronavirus clades are colour labelled and asterisks mark nodes inferred with low support values (SH-aLRT < 0.70). Branch lengths bigger than 0.7 have been trimmed and annotated to keep figure dimensions. Alphacoronavirus (a CoV): BtRf-AlphaCoV-YN2012 (NC_028824, bat), BtCoV-HKU2 (NC_009988, bat), AlphaCoV-DcCoV (NC_028752, camel), HCoV-229E (NC_002645, human), BtCoV-HKU8 (NC_010438, bat), BtCoV-1A (NC_010437, bat), BtNv-AlphaCoV-SC2013 (NC_028833, bat), HCoV-NL63 (NC_005831, human), BtRf-AlphaCoV-HuB2013 (NC_028814, bat), Sc-BatCoV-512 (NC_009657, bat), PEDV (NC_003436, pig), BtCoV-CDPHE15 (NC_022103, bat), LuchengRn (NC_032730, rat), MCoV-WD1127 (NC_023760, mink), SECD (NC_028806, pig) and FIP (NC_002306, cat). Gammacoronavirus (γ CoV): BWCoV-SW1 (NC_010646, beluga whale), IBV (NC_001451, chicken), TCoV (NC_010800, turkey). Deltacoronavirus (δ CoV): WiCoV-HKU20 (JQ065048, duck), BuCoV-HKU11 (FJ376619, bulbul), PorCoV-HKU15 (JQ065042, pig), MRCoV-HKU18 (JQ065046, magpie-robin). Betacoronavirus lineage A (ꞵ CoV A): HCoV-HKU1 (NC_006577, human), PRC (NC_012936, rat), MHV-A59-C12 (NC_001846, mouse), BetaCoV-HKU24 (NC_026011, rat), RbCoV-HKU14 (NC_017083, rabbit), HCoV-OC43 (NC_006213, human), PHEV-VW572 (DQ011855, pig), AntelopeCoV (EF424621, sable antelope), BCoV (NC_003045, cow), Ptajacu-CoV (MT083879, collared peccary), ECoV (NC_010327.1, horse), DcCoV (KF906251, camel). Betacoronavirus lineage B (ꞵ CoV B): 2019_nCOV (NC_045512.2, human), SARS-CoV (NC_004718, human). Betacoronavirus lineage C (ꞵ CoV C): BetaCoV-Erinaceus (NC_039207, hedgehog), BtCoV-HKU4-1 (NC_009019, bat), BtCoV-HKU5-1 (NC_009020, bat), MERS-CoV (NC_019843, human), BetaCov-England-1 (NC_038294, human). Betacoronavirus lineage D (ꞵ CoV D): BtCoV-HKU9-1 (NC_009021, bat), Ro-BatCoV (NC_030886, bat).

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Instituto Oswaldo Cruz, Ministério da Saúde Av. Brasil, 4365 - Pavilhão Mourisco, Manguinhos, 21040-900 Rio de Janeiro RJ Brazil, Tel.: (55 21) 2562-1222, Fax: (55 21) 2562 1220 - Rio de Janeiro - RJ - Brazil
E-mail: memorias@fiocruz.br

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A novel Betacoronavirus characterised in collared peccaries from the Rio de Janeiro Zoo (Brazil) killed by unknown disease

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[1] + Corresponding author: afsantos.ufrj@gmail.com