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. 2013 Apr;158(4):729-34.
doi: 10.1007/s00705-012-1562-x. Epub 2012 Dec 5.

Coronavirus genotype diversity and prevalence of infection in wild carnivores in the Serengeti National Park, Tanzania

Katja V Goller  1 , Jörns Fickel, Heribert Hofer, Sandra Beier, Marion L East
Affiliations

Coronavirus genotype diversity and prevalence of infection in wild carnivores in the Serengeti National Park, Tanzania

Katja V Goller et al. Arch Virol. 2013 Apr.

Abstract

Knowledge of coronaviruses in wild carnivores is limited. This report describes coronavirus genetic diversity, species specificity and infection prevalence in three wild African carnivores. Coronavirus RNA was recovered from fresh feces from spotted hyena and silver-backed jackal, but not bat-eared fox. Analysis of sequences of membrane (M) and spike (S) gene fragments revealed strains in the genus Alphacoronavirus, including three distinct strains in hyenas and one distinct strain in a jackal. Coronavirus RNA prevalence was higher in feces from younger (17 %) than older (3 %) hyenas, highlighting the importance of young animals for coronavirus transmission in wild carnivores.

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Figures

Fig. 1
Fig. 1
Phylogenetic relationship between coronavirus strains from spotted hyenas (Hyena), a silver-backed jackal (Jackal) and other published alphacoronavirus strains (canine, feline and porcine coronaviruses), plus betacoronavirus strains (bovine, canine and equine) based on a 369-nt fragment of the M gene. The unrooted neighbor joining (NJ) tree was constructed using the Tamura Nei model as implemented in Mega 5.0 [18]. Numbers at nodes represent bootstrap values for NJ, maximum-likelihood (ML) and maximum-parsimony (MP) trees in the order NJ/ML/MP. The scale bar indicates the estimated number of nt substitutions per site. Identical sequences from spotted hyenas in 2006 and 2007 were grouped as CoV Hyenas 06/07. Accession numbers of sequences generated in this study are as follows: CoV Hyena 36/04 (HQ339898), CoV Hyena 42/04 (HQ339900), CoV Hyena 91/07 (HQ339910), CoV Hyena 110/07 (HQ339911) and CoV Hyena Jackal/07 (HQ339912); ‘CoV Hyenas 06/07’: CoV Hyena 64/06 (HQ339901), CoV Hyena 33/07 (HQ339902), CoV Hyena 34/07 (HQ339903), CoV Hyena 35/07 (HQ339904), CoV Hyena 36/07 (HQ339905), CoV Hyena 37/07 (HQ339906), CoV Hyena 44/07 (HQ339907), CoV Hyena 62/07 (HQ339908), CoV Hyena 82/07 (HQ339909). The accession numbers of published coronavirus sequences used in this study are as follows: canine CoVs type I: CCoV 23/03 (AY548235), CCoV 259/01 (AF502583, only M gene sequence available); canine CoVs type II: CCoV 430/07 (EU924790), CCoV 341/05 (EU856361), CCoV CB/05 (DQ112226), CCoV 119/08 (EU924791), CCoV 174/06 (EU856362); feline CoVs type I: FIPV Black (AB086903), FCoV/NTU2/R/2003 (DQ160294), FIPV UCD1 (AB088222); feline CoVs type II: FIPV 79-1146 (DQ010921), FECV 79-1683 (Y13921, only M gene sequence available) and porcine CoVs: TGEV virulent Purdue (DQ811789), TGEV PUR46-MAD (AJ271965) and TGEV Miller M60 (DQ811786); betacoronavirus strains: canine respiratory CoV K37 (GQ918142), equine CoV NC99 (AY316300), bovine CoV DB2 (DQ811784)
Fig. 2
Fig. 2
Phylogenetic relationship between coronavirus strains from spotted hyenas (Hyena), a silver-backed jackal (Jackal), other published alphacoronavirus strains, plus betacoronavirus strains (canine, bovine and equine), based on a 624-nt portion of the S gene. Identical sequences obtained from spotted hyena in 2007 were grouped as CoV Hyenas 07. The unrooted neighbor joining (NJ) tree was constructed using the Tamura Nei model as implemented in Mega 5.0 [18]. Numbers at nodes represent bootstrap values for (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) trees in the order NJ/ML/MP. Scale bar indicates the estimated number of nt substitutions per site. Accession numbers of sequences generated in this study are as follows: CoV Hyena 36/04 (HQ339884), CoV Hyena 42/04 (HQ339885), CoV Hyena 64/06 (HQ339886) and CoV Jackal/07 (HQ339897); ‘CoV Hyenas 07’: CoV Hyena 33/07 (HQ339887), CoV Hyena 34/07 (HQ339888), CoV Hyena 35/07 (HQ339889), CoV Hyena 36/07 (HQ339890), CoV Hyena 37/07 (HQ339891), CoV Hyena 44/07 (HQ339892), CoV Hyena 62/07 (HQ339893), CoV Hyena 82/07 (HQ339894), CoV Hyena 91/07 (HQ339895), CoV Hyena 110/07 (HQ339896). The accession numbers of published sequences from alphacoronaviruses used in this study are as follows: canine CoVs type I: CCoV 23/03 (AY548235), CCoV Elmo/02 (AY307020, only S gene sequence available); canine CoVs type II: CCoV 430/07 (EU924790), CCoV 341/05 (EU856361), CCoV CB/05 (DQ112226), CCoV 119/08 (EU924791), CCoV 174/06 (EU856362); feline CoVs type I: FIPV Black (AB086903), FCoV/NTU2/R/2003 (DQ160294), FIPV UCD1 (AB088222), FIPV KU-2 (D32044); feline CoV type II: FIPV 79-1146 (DQ010921), and porcine coronaviruses: TGEV virulent Purdue (DQ811789), TGEV PUR46-MAD (AJ271965) and TGEV Miller M60 (DQ811786); betacoronavirus strains: canine respiratory CoV K37 (GQ918142), equine CoV NC99 (AY316300), bovine CoV DB2 (DQ811784)
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