#Puumala #Hantavirus Genotypes in #Humans, #France, 2012–2016 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 1—January 2019 / Dispatch

Puumala Hantavirus Genotypes in Humans, France, 2012–2016

Jean-Marc Reynes1  , Damien Carli, Damien Thomas2, and Guillaume Castel

Author affiliations: Institut Pasteur, Lyon, France (J.-M. Reynes, D. Carli, D. Thomas); CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université Montpellier, Montpellier, France (G. Castel)



The analysis of the nucleoprotein gene of 77 Puumala hantavirus strains detected in human samples in France between 2012–2016 showed that all belonged to the Central European lineage. We observed 2 main clusters, geographically structured; one included strains with the Q64 signature and the other strains with the R64 signature.

Keywords: Hantavirus; Puumala virus; Human; France.



#Pandemics past, present, and future (Lancet Resp Med., abstract)

[Source: The Lancet Respiratory Medicine, full page: (LINK). Summary, edited.]

Pandemics past, present, and future

Talha Khan Burki

Published: November 29, 2018 / DOI: https://doi.org/10.1016/S2213-2600(18)30505-8


South London lad Albert Edward McKenzie joined the Royal Navy in April, 1915. He was sixteen years old. The Great War had been raging for seven months. The Western Front was already criss-crossed by a dense arrangement of dugouts that would barely shift over the coming years. Millions would die in defence of the waterlogged trenches; small parcels of muddy terrain were exchanged at the cost of inconceivable carnage. Behind the front, in the overcrowded British encampment at Etaples, France, a different kind of carnage might have been incubating—many experts now believe that it was here that the circulating H1N1 virus acquired the mutation it needed to allow it to transmit from human to human.



This article is available free of charge.

Copyright © 2018 Elsevier Ltd. All rights reserved.

Keywords: Pandemic Influenza; H1N1; Spanish Flu.


The #shift in #rabies #epidemiology in #France: time to adjust rabies post-exposure #risk #assessment (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

The shift in rabies epidemiology in France: time to adjust rabies post-exposure risk assessment

Perrine Parize1, Laurent Dacheux1, Florence Larrous1, Hervé Bourhy1, the French network of antirabies clinics2

Affiliations: 1 Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, National Reference Center for Rabies and WHO Collaborating Centre for Reference and Research on Rabies, Paris, France; 2 The members of the network are listed at the end of the article

Correspondence:  Perrine Parize

Citation style for this article: Parize Perrine, Dacheux Laurent, Larrous Florence, Bourhy Hervé, the French network of antirabies clinics. The shift in rabies epidemiology in France: time to adjust rabies post-exposure risk assessment. Euro Surveill. 2018;23(39):pii=1700548. https://doi.org/10.2807/1560-7917.ES.2018.23.39.1700548

Received: 02 Aug 2017;   Accepted: 11 Feb 2018



The epidemiology of rabies in France and western Europe has changed during the past 22 years. In France, rabies in non-flying terrestrial mammals was declared to be eliminated in 2001, and the risk of rabies is now limited to contact with bats, rabid animals illegally imported from rabies-enzootic countries and traveller exposure in enzootic areas. We analysed the epidemiology of rabies in France from 1995 to 2016, describing and analysing data on human rabies surveillance as well as data on post-exposure prophylaxis (PEP) collected from the network of French antirabies clinics. Over the study period, seven individuals were diagnosed with rabies in France, all of whom were infected outside mainland France. PEP data analysis revealed an expected overall decrease in PEP administration for individuals exposed in mainland France, but there was still overuse of anti-rabies drugs, given the very low epidemiological risk. On the other hand, a significant increase in PEP delivered to individuals exposed abroad was evidenced. These epidemiological trends indicate that clear guidelines should be provided to support physicians’ efforts to adjust rabies risk assessment to the evolution of the epidemiological situation.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Rabies; Human; France; Post-exposure prophylaxis.


Spatio-temporal #distribution and #evolution of the A #H1N1pdm09 virus in #pigs in #France from 2009 to 2017: identification of a potential swine-specific lineage (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Spatio-temporal distribution and evolution of the A/H1N1 2009 pandemic virus in pigs in France from 2009 to 2017: identification of a potential swine-specific lineage

Amélie Chastagner, Séverine Hervé, Emilie Bonin, Stéphane Quéguiner, Edouard Hirchaud, Dinah Henritzi, Véronique Béven, Stéphane Gorin, Nicolas Barbier, Yannick Blanchard,Gaëlle Simon

DOI: 10.1128/JVI.00988-18



The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated to pig density. From these isolates, 17 whole genome sequences were obtained as well as 6 additional HA/NA sequences, in order to perform spatial and temporal analyses of the genetic diversity, and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains. Following mutation accumulation and fixation over time, phylogenetic analyses revealed for the first time the divergence of a swine-specific genogroup within the H1N1pdm lineage. The divergence is thought to have occurred around 2011, although this was only demonstrated through strains isolated in 2015-2016 in the southern half of France. To date, these H1N1pdm swine strains have not been related to any increased virulence in swine herds and have not exhibited any antigenic drift as compared to seasonal human strains. However, further monitoring is encouraged as diverging evolutionary patterns in these two species, i.e. swine and humans, may lead to the emergence of viruses with a potentially higher risk for both animal and human health.



Pigs are a ‘mixing vessel’ for influenza A viruses (IAVs) because of their ability to be infected by avian and human IAVs, and their propensity to facilitate viral genomic reassortment events. Also, as IAVs may evolve differently in swine and humans, pigs can become a reservoir for old human strains against which the human population has become immunologically naïve. Thus, viruses from the novel swine-specific H1N1pdm genogroup may continue to diverge from seasonal H1N1pdm strains and/or from other H1N1pdm viruses infecting pigs and lead to the emergence of viruses that would not be covered by human vaccines and/or swine vaccines based on antigens closely related to the original H1N1pdm virus. This discovery confirms the importance of encouraging swine IAV monitoring because H1N1pdm swine viruses could carry an increased risk for both human and swine health in the future, as a whole H1N1pdm or gene provider in subsequent reassortant viruses.

Copyright © 2018 American Society for Microbiology. All Rights Reserved.

Keywords: Seasonal Influenza; Pandemic Influenza; Swine Influenza; H1N1pdm09; Pigs; France.


#Molecular diversity and biennial #circulation of #enterovirus D68: a systematic screening study in Lyon, #France, 2010 to 2016 (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

Molecular diversity and biennial circulation of enterovirus D68: a systematic screening study in Lyon, France, 2010 to 2016

Rolf Kramer1,2,3, Marina Sabatier1,3, Thierry Wirth4,5, Maxime Pichon1,6, Bruno Lina1,6, Isabelle Schuffenecker1,6, Laurence Josset1,6

Affiliations: 1 Centre National de Référence des Enterovirus et Parechovirus, Laboratoire de Virologie, Institut des Agents Infectieux, HCL, Hôpital de la Croix-Rousse, Lyon, France; 2 European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden; 3 These authors contributed equally; 4 Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, EPHE, PSL University, Paris, France; 5 Institut Systématique Evolution Biodiversité (ISYEB), EPHE, MNHN, CNRS, Sorbonne Université, Paris, France; 6 Virpath, CIRI, Université de Lyon, INSERM U1111, CNRS 5308, ENS de Lyon, UCBL, Lyon, France

Correspondence:  Rolf Kramer

Citation style for this article: Kramer Rolf, Sabatier Marina, Wirth Thierry, Pichon Maxime, Lina Bruno, Schuffenecker Isabelle, Josset Laurence. Molecular diversity and biennial circulation of enterovirus D68: a systematic screening study in Lyon, France, 2010 to 2016. Euro Surveill. 2018;23(37):pii=1700711. https://doi.org/10.2807/1560-7917.ES.2018.23.37.1700711

Received: 20 Oct 2017;   Accepted: 06 May 2018




Understanding enterovirus D68 (EV-D68) circulation patterns as well as risk factors for severe respiratory and neurological illness is important for developing preventive strategies.


Between 2010 and 2016, 11,132 respiratory specimens from hospitalised patients in Lyon, France, were screened for EV-D68 by PCR. Phylogenetic relationships of the viral-protein-1 sequences were reconstructed using maximum-likelihood and Bayesian-Markov-Chain-Monte-Carlo approaches.


Overall, 171 infections with a biennial pattern were detected, including seven, one, 55, none, 42, one and 65 cases annually during 2010–16. Children (< 16 years-old; n = 150) were mostly affected and 71% (n = 121) of the total patients were under 5 years-old. In 146 patients with medical reviews, 73% (n = 107) presented with acute respiratory distress. Among paediatric patients with medical reviews (n = 133), 55% (n=73) had an asthma/wheezing history, while among adults (n = 13), 11 had underlying diseases. In total, 45 patients had severe infections and 28 patients needed intensive care unit stays. No acute flaccid myelitis (AFM) was detected. We found genotypes A, B1, B2 B3 and D circulating, and no associations between these and clinical presentations. During the study, new genotypes continuously emerged, being replaced over time. We estimated that ancestors of currently circulating genotypes emerged in the late-1990s to 2010. Rises of the EV-D68 effective population size in Lyon coincided with infection upsurges. Phylogenetic analyses showed ongoing diversification of EV-D68 worldwide, coinciding with more infections in recent years and increases of reported AFM paediatric cases.


Reinforcement of diagnostic capacities and clinical-based surveillance of EV-D68 infections is needed in Europe to assess the EV-D68 burden.

©   This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: EV-D68; HFMD; ARDS; France.


#Serological survey of #influenza A viruses in domestic and wild #Suidae in #Corsica (France), a Mediterranean island environment (Prev Vet Med., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Prev Vet Med. 2018 Sep 1;157:94-98. doi: 10.1016/j.prevetmed.2018.06.004. Epub 2018 Jun 19.

Serological survey of influenza A viruses in domestic and wild Suidae in Corsica (France), a Mediterranean island environment.

Grech-Angelini S1, Hervé S2, Rose N3, Barbier N2, Casabianca F4, Maestrini O4, Falchi A5, Simon G2.

Author information: 1 INRA, UR045, Laboratoire de recherches sur le développement de l’élevage, Corte, France. Electronic address: grech.angelini@gtvcorse.fr. 2 ANSES, Laboratoire de Ploufragan-Plouzané, Unité Virologie Immunologie Porcines, Ploufragan, France; Université Bretagne Loire, France. 3 ANSES, Laboratoire de Ploufragan-Plouzané, Unité Epidémiologie et Bien-Etre du Porc, Ploufragan, France; Université Bretagne Loire, France. 4 INRA, UR045, Laboratoire de recherches sur le développement de l’élevage, Corte, France. 5 EA 3710, Laboratoire de virologie, Université de Corse/Inserm, Corte, France.



Corsica is a mountainous French island in the north-western Mediterranean Sea. It is a rural area, where pig farming is a major economic activity. Although no acute respiratory outbreaks due to swine influenza A viruses (swIAVs) have ever been reported in this free-ranging pig breeding system, influenza A viruses (IAVs) could be circulating within this pig population. A serological study was conducted as a first approach to domestic pigs and wild boars. Serum samples from 543 pigs raised on 91 different farms were collected during the 2013-2014 slaughtering season, and 279 sera from wild boars were obtained over four hunting seasons (between 2009 and 2014). They were first analysed by ELISA and then IAV positive and doubtful sera were subjected to haemagglutination inhibition tests using antigens representative of the four major enzootic swIAV lineages in Europe, i.e. avian-like swine H1N1 (H1avN1), pandemic-like swine H1N1 (H1N1pdm), H1N2 and H3N2. According to the ELISA results, 26.4% (CI95%: 17.7-36.7%) of herds had at least one positive animal (positive or doubtful by ELISA) and 12.4% (CI95%: 7.8-19.8%) of the pigs tested positive. Using the test characteristics (sensitivity and specificity), the true seroprevalence among Corsican pigs was estimated to be 16.4% (95% CI: 9.9-26.3). Antibodies directed against two different viral lineages were identified: H1N1pdm (in 66.2% and 45.8% of the IAV positive pigs and farms respectively) and H1avN1 (15.0% and 20.8% respectively). Evidence of exposure to viruses from two distinct lineages were detected on a single farm but in two different animals. Among the wild boars, 1.4% (CI95%: 0.4-3.6%) tested positive by ELISA and antibodies against the same two viruses were detected. Altogether, these results suggest that swIAVs from at least two different lineages are circulating among Corsican pigs, i.e. the H1N1pdm virus, probably introduced during the 2009 pandemic, and the H1avN1 virus, which is the most frequent swIAV in Europe. The low frequency of positive results observed in the Corsican wild boars hunted suggests that they would not play a major role in IAV dispersion dynamics on the island.

KEYWORDS: Corsica; Pig; Seroprevalence; Swine influenza A virus; Wild boar

PMID: 30086855 DOI: 10.1016/j.prevetmed.2018.06.004

Keywords: Swine Influenza; Influenza A; H1N1pdm09; H1N1; Pigs; France.


#Clinical #management of respiratory syndrome in patients hospitalized for suspected #MERS-CoV #infection in the #Paris area from 2013 to 2016 (BMC Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

BMC Infect Dis. 2018 Jul 16;18(1):331. doi: 10.1186/s12879-018-3223-5.

Clinical management of respiratory syndrome in patients hospitalized for suspected Middle East respiratory syndrome coronavirus infection in the Paris area from 2013 to 2016.

Bleibtreu A1,2,3,4, Jaureguiberry S5, Houhou N6, Boutolleau D7, Guillot H5, Vallois D8, Lucet JC9,10,11, Robert J12,13, Mourvillier B10,11,14, Delemazure J15, Jaspard M5, Lescure FX8,10,11, Rioux C8, Caumes E5, Yazdanapanah Y8,10,11.

Author information: 1 APHP, Hôpital Bichat Claude Bernard, Service des Maladies Infectieuses et Tropicales, Paris Diderot University, Paris, France. alexandre.bleibtreu@aphp.fr. 2 APHP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service des Maladies Infectieuses et Tropicales, Paris, France. alexandre.bleibtreu@aphp.fr. 3 INSERM, IAME, UMR 1137, Paris, France. alexandre.bleibtreu@aphp.fr. 4 Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France. alexandre.bleibtreu@aphp.fr. 5 APHP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service des Maladies Infectieuses et Tropicales, Paris, France. 6 Virology Department, APHP-Bichat-Claude Bernard Hospital, Paris, France. 7 AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service de Virologie, et Sorbonne Universités, UPMC Univ Paris 06, CR7, CIMI, INSERM U1135, Paris, France. 8 APHP, Hôpital Bichat Claude Bernard, Service des Maladies Infectieuses et Tropicales, Paris Diderot University, Paris, France. 9 APHP, Infection control unit, Bichat Claude Bernard hospital, Paris Diderot University, Paris, France. 10 INSERM, IAME, UMR 1137, Paris, France. 11 Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France. 12 AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Bactériologie-Hygiène Hospitalière, Paris, France. 13 Faculté de Médecine P. & M. Curie Paris-6 – Site Pitié, Centre d’Immunologie et des Maladies Infectieuses (CIMI) – E13, Paris, France. 14 APHP- Hôpital Bichat Claude Bernard, Service de Réanimation médicale et Infectieuse, Paris, France. 15 Service de pneumologie et réanimation Département R3S, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, unité de Soin de Réadaptation Post Réanimation (SRPR), Paris, France.




Patients with suspected Middle East respiratory syndrome coronavirus (MERS-CoV) infection should be hospitalized in isolation wards to avoid transmission. This suspicion can also lead to medical confusion and inappropriate management of acute respiratory syndrome due to causes other than MERS-CoV.


We studied the characteristics and outcome of patients hospitalized for suspected MERS-CoV infection in the isolation wards of two referral infectious disease departments in the Paris area between January 2013 and December 2016.


Of 93 adult patients (49 male (52.6%), median age 63.4 years) hospitalized, 82 out of 93 adult patients had returned from Saudi Arabia, and 74 of them were pilgrims (Hajj). Chest X-ray findings were abnormal in 72 (77%) patients. The 93 patients were negative for MERS-CoV RT-PCR, and 70 (75.2%) patients had documented infection, 47 (50.5%) viral, 22 (23.6%) bacterial and one Plasmodium falciparum malaria. Microbiological analysis identified Rhinovirus (27.9%), Influenza virus (26.8%), Legionella pneumophila (7.5%), Streptococcus pneumoniae (7.5%), and non-MERS-coronavirus (6.4%). Antibiotics were initiated in 81 (87%) cases, with two antibiotics in 63 patients (67.7%). The median duration of hospitalization and isolation was 3 days (1-33) and 24 h (8-92), respectively. Time of isolation decreased over time (P < 0.01). Two patients (2%) died.


The management of patients with possible MERS-CoV infection requires medical facilities with trained personnel, and rapid access to virological results. Empirical treatment with neuraminidase inhibitors and an association of antibiotics effective against S. pneumoniae and L. pneumophila are the cornerstones of the management of patients hospitalized for suspected MERS-CoV infection.

KEYWORDS: Isolation ward; Legionella; Middle East respiratory syndrome coronavirus (MERS-CoV); Pilgrims; Respiratory tract infection; Saudi Arabia

PMID: 30012113 DOI: 10.1186/s12879-018-3223-5

Keywords: MERS-CoV; Quarantine Measures; France.