Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray

Claudia Filippone,Jean-Claude Manuguerra,Antoine Gessain,Lorraine M Mcelhinney,Rainer G Ulrich,Tatjana Avšič-Županc,Sylvie Van Der Werf,Martin H Groschup,Olli Vapalahati,Misa Korva,Tarja Sironen,Valérie Caro,Frank Sauvage,Séverine Murri,Philippe Marianneau,Noël Tordo,Guillaume Castel,Myriam Ermonval

doi:10.1038/s41598-019-47508-7

Abstract

Hantaviruses are zoonotic agents transmitted from small mammals, mainly rodents, to humans, where they provoke diseases such as Hemorrhagic fever with Renal Syndrome (HFRS) and its mild form, Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS). Hantaviruses are spread worldwide and monitoring animal reservoirs is of primary importance to control the zoonotic risk. Here, we describe the development of a pan-viral resequencing microarray (PathogenID v3.0) able to explore the genetic diversity of rodent-borne hantaviruses endemic in Europe. Among about 800 sequences tiled on the microarray, 52 correspond to a tight molecular sieve of hantavirus probes covering a large genetic landscape. RNAs from infected animal tissues or from laboratory strains have been reverse transcribed, amplified, then hybridized to the microarray. A classical BLASTN analysis applied to the sequence delivered through the microarray allows to identify the hantavirus species up to the exact geographical variant present in the tested samples. Geographical variants of the most common European hantaviruses from France, Germany, Slovenia and Finland, such as Puumala virus, Dobrava virus and Tula virus, were genetically discriminated. Furthermore, we precisely characterized geographical variants still unknown when the chip was conceived, such as Seoul virus isolates, recently emerged in France and the United Kingdom.

Highlights

Hantaviruses are zoonotic agents transmitted from small mammals, mainly rodents, to humans, where they provoke diseases such as Hemorrhagic fever with Renal Syndrome (HFRS) and its mild form, Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS)
When rodent-borne orthohantaviruses are transmitted to humans through aerosolized excreta of infected rodent reservoirs, they can provoke Hemorrhagic Fever with Renal Syndrome (HFRS), its mild form Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS), mainly depending on the virus species and its genotype/strain
In Europe, cases of HFRS associated with Dobrava-Belgrade orthohantavirus (DOBV) and Seoul orthohantavirus (SEOV), and cases of NE associated with Puumala orthohantavirus (PUUV), are continuously reported in endemic areas such as the Balkans, the

Summary

Introduction

Hantaviruses are zoonotic agents transmitted from small mammals, mainly rodents, to humans, where they provoke diseases such as Hemorrhagic fever with Renal Syndrome (HFRS) and its mild form, Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS). The recent development of molecular methods without an a priori hypothesis has brought a critical benefit in the field of diagnosis and research on infectious diseases They can permit to obtain the sequence of a pathogen present in a biological sample, in absence of specific probes required for classic PCR or hybridization[15,16,17,18,19,20,21,22,23]. PathogenID is a collaborative effort of teams of Institut Pasteur that combined expertise to develop 3 generations of resequencing microarrays for the detection of different emerging pathogens, bacteria and viruses, during public health urgencies and for research studies. While PathogenID v2.0 has been validated for detection of DOBV, SEOV, HTNV, ANDV and SNV in infected Vero E6 cells, it was not for PUUV, yet the most commonly circulating orthohantavirus in Europe[20]

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Conclusion