Highly divergent herpesviruses in threatened river dolphins from Brazil

Abstract

River dolphins are a highly threatened polyphyletic group comprised of four odontocete families: Iniidae, Pontoporiidae, Lipotidae, and Platanistidae, the first two endemic to South America. To address the knowledge gap regarding infectious agents in this cetacean group, we surveyed the presence of herpesviruses by PCR in skin and/or blood samples of live-captured Amazon (Inia geoffrensis, n = 25) and Bolivian (Inia boliviensis, n = 22) river dolphins of the Amazon basin and in selected tissue samples of franciscanas (Pontoporia blainvillei, n = 27) stranded or bycaught in southeastern Brazil. Additionally, available franciscana tissue samples were examined by histopathology. Herpesvirus DNA was amplified in 13 Bolivian river dolphins (59.1%, 95% CI 38.5-79.6%) and 14 franciscanas (51.9%, 95% CI 33.0-70.7%). All Amazon river dolphins were herpesvirus-negative. Two different herpesviruses were found in Bolivian river dolphins: a previously known gammaherpesvirus detected in blood and/or skin samples of all positive individuals and a novel alphaherpesvirus in the skin of one animal. A new gammaherpesvirus was found in several franciscana samples-the first herpesvirus recorded in Pontoporiidae. Intranuclear inclusion bodies consistent with herpesvirus were observed in the lymph node of one franciscana. The high divergence among the obtained herpesviruses and those previously described can be explained by viral-host coevolution, and by the fact that these populations are fairly isolated.

Figure 1

Lymph node of a franciscana (Pontoporia blainvillei, case MM568). Note the presence of a basophilic intranuclear inclusion body in a macrophage (black arrow).

Figure 2

Location of the Bolivian river dolphins (Inia boliviensis), Amazon river dolphins (Inia geoffrensis) and franciscanas (Pontoporia blainvillei) tested in the study. The distribution of the species was based on the platform Botos Amazônicos for the genus Inia and on Zerbini et al. (2018) for Franciscanas. The collection sites are marked with blue.

Figure 3

(A) Maximum likelihood phylogram based on the JTT matrix-based model of the deduced amino acid DNA polymerase sequences: (i) obtained in this study (red dots), (ii) the most similar sequence form GenBank, (iii) alpha- and gammaherpesvirus sequences obtained from other cetacean species, (iv) accepted alpha- and gammaherpesvirus species recognized by the International Committee on Taxonomy of Viruses. Maximum likelihood phylogram based on the JTT matrix-based model of the deduced amino acid glycoprotein B sequences (i) obtained in this study (red dots), (ii) the most similar sequence form GenBank, (iii) gammaherpesvirus sequences obtained from other cetacean species, (iv) gammaherpesvirus species recognized by the International Committee on Taxonomy of Viruses. Human alphaherpesvirus 3 was selected as outgroup for glycoprotein B phylogram. The reliability of the tree was tested by bootstrap analysis with 1000 replicates, and those bootstrap values lower than 70 were omitted.

Figure 3

(A) Maximum likelihood phylogram based on the JTT matrix-based model of the deduced amino acid DNA polymerase sequences: (i) obtained in this study (red dots), (ii) the most similar sequence form GenBank, (iii) alpha- and gammaherpesvirus sequences obtained from other cetacean species, (iv) accepted alpha- and gammaherpesvirus species recognized by the International Committee on Taxonomy of Viruses. Maximum likelihood phylogram based on the JTT matrix-based model of the deduced amino acid glycoprotein B sequences (i) obtained in this study (red dots), (ii) the most similar sequence form GenBank, (iii) gammaherpesvirus sequences obtained from other cetacean species, (iv) gammaherpesvirus species recognized by the International Committee on Taxonomy of Viruses. Human alphaherpesvirus 3 was selected as outgroup for glycoprotein B phylogram. The reliability of the tree was tested by bootstrap analysis with 1000 replicates, and those bootstrap values lower than 70 were omitted.