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Highly Diversified Shrew Hepatitis B Viruses Corroborate Ancient Origins and Divergent Infection Patterns of Mammalian Hepadnaviruses

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Highly Diversified Shrew Hepatitis B Viruses Corroborate Ancient Origins and Divergent Infection Patterns of Mammalian Hepadnaviruses Highly diversified shrew hepatitis B viruses corroborate ancient origins and divergent infection patterns of mammalian hepadnaviruses Andrea Raschea,b, Felix Lehmannc, Alexander Königc, Nora Goldmannc, Victor M. Cormana,b, Andres Moreira-Sotoa, Andreas Geipelc, Debby van Rield, Yulia A. Vakulenkoe, Anna-Lena Sandera, Hauke Niekampc, Ramona Kepperc,f, Mathias Schlegelg, Chantal Akoua-Koffih, Breno F. C. D. Souzai, Foday Sahrj, Ayodeji Olayemik, Vanessa Schulzeg, Rasa Petraityte-Burneikienel, Andris Kazaksm, Kira A. A. T. Lowjagan, Joachim Geyern, Thijs Kuikend, Christian Drostena,b, Alexander N. Lukasheve, Elisabeth Fichet-Calveto, Rainer G. Ulrichg, Dieter Glebec,f,1,2, and Jan Felix Drexlera,b,e,1,2 aInstitute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; bGerman Centre for Infection Research, Partner Site Charité, 10117 Berlin, Germany; cInstitute of Medical Virology, National Reference Center for Hepatitis B and D Viruses, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, 35392 Giessen, Germany; dDepartment of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; eTropical and Vector-Borne Diseases, Martsinovsky Institute of Medical Parasitology, Sechenov University, 119435 Moscow, Russia; fGerman Centre for Infection Research, Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany; gInstitute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald–Insel Riems, Germany; hCentre de Recherche pour le Développement, Alassane Ouattara University of Bouaké, BP V1801 Bouaké, Côte d’Ivoire; iInfectious Diseases Research Laboratory, Federal University of Bahia, University Hospital Prof. Edgard Santos, 40.110-060 Salvador, Brazil; jCollege of Medicine and Allied Health Sciences, University of Sierra Leone, FQQ6+3M Freetown, Sierra Leone; kNatural History Museum, Obafemi Awolowo University, GG8H+JC Ile-Ife, Nigeria; lInstitute of Biotechnology, Vilnius University Life Sciences Center Institute of Biotechnology, LT-10257 Vilnius, Lithuania; mLatvian Biomedical Research and Study Centre, University of Latvia, LV-1067 Riga, Latvia; nInstitute of Pharmacology and Toxicology, Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, 35392 Giessen, Germany; and oDepartment of Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany Edited by Ding-Shinn Chen, National Taiwan University College of Medicine, Taipei, Taiwan, and approved July 1, 2019 (received for review May 13, 2019) Shrews, insectivorous small mammals, pertain to an ancient mamma- Hepadnaviruses are ancient pathogens, likely infecting verte- MICROBIOLOGY lian order. We screened 693 European and African shrews for hepatitis brates for over 200 million years (3). Placental mammals evolved B virus (HBV) homologs to elucidate the enigmatic genealogy of HBV. ∼99 million years ago (mya) and form 2 major clades termed Shrews host HBVs at low prevalence (2.5%) across a broad geographic Laurasiatheria and Euarchontoglires (4). The known laurasiatherian and host range. The phylogenetically divergent shrew HBVs comprise HBV hosts belong to several species within the orders Chiroptera separate species termed crowned shrew HBV (CSHBV) and musk (bats) and to one species each within the orders Carnivora (cat) and shrew HBV (MSHBV), each containing distinct genotypes. Recombina- Artiodactyla (duiker). HBV hosts within the Euarchontoglires include tion events across host orders, evolutionary reconstructions, and antigenic divergence of shrew HBVs corroborated ancient origins of Significance mammalian HBVs dating back about 80 million years. Resurrected CSHBV replicated in human hepatoma cells, but human- and tupaia- derived primary hepatocytes were resistant to hepatitis D viruses Hepatitis B viruses (HBVs) have existed for millions of years. pseudotyped with CSHBV surface proteins. Functional characterization We describe divergent HBV species in shrews, which are an- of the shrew sodium taurocholate cotransporting polypeptide (Ntcp), cient insectivorous mammals. The shrew viruses corroborated CSHBV/MSHBV surface peptide binding patterns, and infection exper- ancient origins of mammalian HBV and showed mutations in iments revealed lack of Ntcp-mediated entry of shrew HBV. Contrast- genomic domains required for production of the hepatitis B e ingly, HBV entry was enabled by the shrew Ntcp. Shrew HBVs antigen, crucial for vertical transmission and chronicity of HBV universally showed mutations in their genomic preCore domains in humans. Shrew HBV infection patterns showed important impeding hepatitis B e antigen (HBeAg) production and resembling similarities with human HBV, and shrews might be susceptible those observed in HBeAg-negative human HBV. Deep sequencing and to human HBV. In contrast, shrew HBVs could neither infect in situ hybridization suggest that HBeAg-negative shrew HBVs cause human cells nor use the canonical HBV receptor molecule for intense hepatotropic monoinfections and low within-host genomic cellular entry. The discovery and characterization of shrew heterogeneity. Geographical clustering and low MSHBV/CSHBV- HBVs allow conceptualizing urgently needed new animal models specific seroprevalence suggest focal transmission and high virulence relying on engineered shrew and human HBV homologs to of shrew HBVs. HBeAg negativity is thus an ancient HBV infection elucidate HBV pathogenesis. pattern, whereas Ntcp usage for entry is not evolutionarily conserved. Author contributions: D.G. and J.F.D. designed research; A.R., F.L., A. König, N.G., V.M.C., Shrew infection models relying on CSHBV/MSHBV revertants and A.M.-S., A.G., D.v.R., Y.A.V., A.-L.S., H.N., R.K., M.S., C.A.-K., B.F.C.D.S., F.S., A.O., V.S., human HBV will allow comparative assessments of HBeAg-mediated K.A.A.T.L., E.F.-C., and R.G.U. performed research; R.P.-B., A. Kazaks, J.G., and C.D. con- HBV pathogenesis, entry, and species barriers. tributed new reagents/analytic tools; A.R., T.K., and A.N.L. analyzed data; and A.R., D.G., and J.F.D. wrote the paper. hepatitis B virus | viral evolution | zoonosis | shrew | E antigen The authors declare no conflict of interest. This article is a PNAS Direct Submission. he hepatitis B virus (HBV, genus Orthohepadnavirus)isa Published under the PNAS license. Tubiquitous pathogen that causes 887,000 deaths annually, Data deposition: Sequence data have been submitted to GenBank, https://www.ncbi.nlm. – – predominantly due to cirrhosis and hepatocellular carcinoma after nih.gov/genbank (accession nos. MK345460 MK345476 and MN170823 MN170825). 1 chronic hepatitis B (CHB) (1). Distantly related hepadnaviruses D.G. and J.F.D. contributed equally to this work. 2To whom correspondence may be addressed. Email: [email protected]. were identified recently in animals other than humans and apes de or [email protected]. (1). The newly discovered animal viruses revealed that prototypic This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. properties of HBV such as envelopment (2) and presence of an X 1073/pnas.1908072116/-/DCSupplemental. gene (3) emerged de novo during orthohepadnavirus evolution. Published online August 1, 2019. www.pnas.org/cgi/doi/10.1073/pnas.1908072116 PNAS | August 20, 2019 | vol. 116 | no. 34 | 17007–17012 Downloaded by guest on October 1, 2021 humans and several nonhuman primate species within the order (Fig. 1A) (16). To investigate shrews for HBV along their geo- Primates and 3 closely related species within the order Rodentia (ro- graphic dispersal history, we sampled 693 animals pertaining to the dents) (1, 5). Bats may play an important role for Orthohepadnavirus genera Sorex and Crocidura from Europe and Western Africa dur- evolution because they host a relatively higher genetic diversity ing 2004–2016 (SI Appendix,TableS1). Liver specimens were tested of orthohepadnaviruses than other mammals (1, 6). However, bats for HBV DNA using a broadly reactive and highly sensitive nested are not the oldest laurasiatherian order. Predating the rise of bats, the PCR assay (17). In total, 17 animals were PCR-positive, including 1 order Eulipotyphla emerged ∼80 mya (4). This order comprises small common shrew (Sorex araneus) and 12 crowned shrews (Sorex cor- insectivorous animals such as moles, hedgehogs, and shrews. After onatus) sampled in Germany during 2008–2009and4Africangiant decades at the periphery of the life sciences, diverse homologs of shrews (Crocidura olivieri) sampledinIvoryCoastin2004and1 major human viruses have been found in eulipotyphlan hosts, sug- large-headed shrew (Crocidura grandiceps) sampled in Sierra Leone gesting they may play an underestimated role in the evolution of in 2014. The detection rate in European shrews (3.7%, 95% con- – mammalian viruses (7–10). Very recently, a divergent hepadnavirus fidence interval [CI], 2.1 6.5) was not significantly higher than in – = sequence was detected in Chinese shrews (11). Shrews represent African shrews (1.4%, 95% CI, 0.5 3.2; Fisher exact, P 0.05). – about 90% of all eulipotyphlan species (12). Scarce virological data on While the overall detection rate was low at 2.5% (95% CI, 1.5 3.9), it did not differ significantly from bat HBV detection rates in nat- shrews are partly due to difficulties in sampling these solitary animals = that rapidly decay in traps due to their high metabolic rate (13). ural habitats (2.2%; Fisher exact, P 1.0) (18) and may thus be Because hepadnaviruses may coevolve with
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