Scientific publications

PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance
Nadon et al. 2017

PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies.

DOI:  10.2807/1560-7917.ES.2017.22.23.30544     08-06-2017          

The challenge of detecting indels in bacterial genomes from short-read sequencing data
Steglich and Nübel 2017

We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1–2321 bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size.

DOI:   10.1016/j.jbiotec.2017.02.026     20-05-2017

Outbreaks among Wild Birds and Domestic Poultry Caused by Reassorted Influenza A(H5N8) Clade 2.3.4.4 Viruses, Germany, 2016
Pohlmann et al. 2017

In November 2016, an influenza A(H5N8) outbreak caused deaths of wild birds and domestic poultry in Germany. Clade 2.3.4.4 virus was closely related to viruses detected at the Russia–Mongolia border in 2016 but had new polymerase acidic and nucleoprotein segments. These new strains may be more efficiently transmitted to and shed by birds.

DOI:  10.3201/eid2304.161949      01-04-2017

Emerging arboviral human diseases in Southern Europe
Papa 2017

Southern Europe is characterized by unique landscape and climate which attract tourists, but also arthropod vectors, some of them carrying pathogens. Among several arboviral diseases that emerged in the region during the last decade, West Nile fever accounted for high number of human cases and fatalities, while Crimean-Congo hemorrhagic fever expanded its geographic distribution, and is considered as a real threat for Europe.

DOI:   10.1002/jmv.24803      22-03-2017

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease
Joensen et al. 2017

The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples.

DOI:   10.1007/s10096-017-2947-2    11-03-2017

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis
Agoti et al. 2017

Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level.

DOI:  https://doi.org/10.1093/ve/vex006          11-03-2017

Effect of blood type on anti-α-Gal immunity and the incidence of infectious diseases
Cabezas-Cruz et al. 2017

The identification of factors affecting the susceptibility to infectious diseases is essential toward reducing their burden on the human population. The ABO blood type correlates with susceptibility to malaria and other infectious diseases. Due to the structural similarity between blood antigen B and Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal), we hypothesized that self-tolerance to antigen B affects the immune response to α-Gal, which in turn affects the susceptibility to infectious diseases caused by pathogens carrying α-Gal on their surface.

DOI:  10.1038/emm.2016.164       10-03-2017

Discordant detection of avian influenza virus subtypes in time and space between poultry and wild birds; Towards improvement of surveillance programs
Verhagen et al. 2017

Avian influenza viruses from wild birds can cause outbreaks in poultry, and occasionally infect humans upon exposure to infected poultry. Identification and characterization of viral reservoirs and transmission routes is important to develop strategies that prevent infection of poultry, and subsequently virus transmission between poultry holdings and to humans. Based on spatial, temporal and phylogenetic analyses of data generated as part of intense and large-scale influenza surveillance programs in wild birds and poultry in the Netherlands from 2006 to 2011, we demonstrate that LPAIV subtype distribution differed between wild birds and poultry, suggestive of host-range restrictions.

DOI:   10.1371/journal.pone.0173470     09-03-2017

Variegated Squirrel Bornavirus 1 in Squirrels, Germany and the Netherlands
Schlottau et al. 2017

We screened squirrels in Germany and the Netherlands for the novel zoonotic variegated squirrel bornavirus 1 (VSBV-1). The detection of VSBV-1 in 11 squirrels indicates a considerable risk for transmission to humans handling those animals. Therefore, squirrels in contact with humans should routinely be tested for VSBV-1.

DOI:   10.3201/eid2303.161061    01-03-2017

Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam
Trung et al. 2017

We investigated the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans. Detection of mcr-1–carrying bacteria in chicken samples was associated with colistin use and detection in human samples with exposure to mcr-1–positive chickens.

DOI:    10.3201/eid2303.161553    01-03-2017

A novel astrovirus associated with encephalitis and ganglionitis in domestic sheep
Pfaff et al. 2017b

In June 2013, a 4-year-old Welsh Mountain ewe and in March 2014 a 10-day-old lamb of the same breed and the same flock presented progressive neurological signs including depressed sensorium, tremor, and unusual behaviour. Neuropathological examination of the brain and spinal cord detected non-suppurative polioencephalomyelitis and dorsal root ganglionitis, characteristic of a neurotropic viral agent in both sheep. Metagenomic analysis of different tissue samples from both animals identified a novel Ovine Astrovirus (OvAstV).

DOI:  10.1111/tbed.12623   22-02-2017

A novel alphaherpesvirus associated with fatal diseases in banded Penguins
Pfaff et al. 2017a

A novel avian alphaherpesvirus, preliminarily designated sphenicid alphaherpesvirus 1 (SpAHV-1), has been independently isolated from juvenile Humboldt and African penguins (Spheniscus humboldti and Spheniscus demersus) kept in German zoos suffering from diphtheroid oropharyngitis/laryngotracheitis and necrotizing enteritis (collectively designated as penguin-diphtheria-like disease). High-throughput sequencing was used to determine the complete genome sequences of the first two SpAHV-1 isolates.

DOI:  10.1099/jgv.0.000698    20-02-2017

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats
Cabal et al. 2017

Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs).

DOI:  10.1002/mbo3.445     18-02-2017

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases
David F. Nieuwenhuijse and Marion P. G. Koopmans 2017

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses.

DOI:  10.3389/fmicb.2017.00230    15-02-2017

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
Baele et al. 2017

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses.

DOI:   10.1093/bioinformatics/btx088    13-02-2017

Genome Sequences of a Novel Vietnamese Bat Bunyavirus
Oude Munnink et al. 2016

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.

DOI:   10.1128/genomeA.01366-16   22-12-2016

Assessing the Epidemic Potential of RNA and DNA Viruses
Woolhouse et al. 2016

Many new and emerging RNA and DNA viruses are zoonotic or have zoonotic origins in an animal reservoir that is usually mammalian and sometimes avian. Not all zoonotic viruses are transmissible (directly or by an arthropod vector) between human hosts. Virus genome sequence data provide the best evidence of transmission.

DOI:  http://dx.doi.org/10.3201/eid2212.160123          12-12-2016

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France
Polo et al. 2016

Using samples from oysters clearly implicated in human disease, we quantified norovirus levels by using digital PCR. Concentrations varied from 43 to 1,170 RNA copies/oyster. The analysis of frozen samples from the production area showed the presence of norovirus 2 weeks before consumption.

DOI:  10.3201/eid2212.160841           01-12-2016    

Dual Emergence of Usutu Virus in Common Blackbirds, Eastern France, 2015
Lecollinet et al. 2016

Usutu virus (USUV) is a mosquitoborne flavivirus amplified in an enzootic cycle involving passeriform and strigiform birds as reservoir hosts and Culex mosquitos as vectors (1). Although originating from Africa, USUV has been introduced at least twice into central and western Europe, leading to substantial bird fatalities in central Europe (particularly in Austria, Hungary, Italy, Germany, and Switzerland) since 1996.

DOI:  10.3201/eid2212.161272    01-12-2016

Severe acute respiratory infection caused by swine influenza virus in a child necessitating extracorporeal membrane oxygenation (ECMO), the Netherlands, October 2016
Fraaij et al. 2016

In October 2016, a severe infection with swine influenza A(H1N1) virus of the Eurasian avian lineage occurred in a child with a previous history of eczema in the Netherlands, following contact to pigs. The patient’s condition deteriorated rapidly and required life support through extracorporeal membrane oxygenation. After start of oseltamivir treatment and removal of mucus plugs, the patient fully recovered. Monitoring of more than 80 close unprotected contacts revealed no secondary cases.

DOI:   10.2807/1560-7917.ES.2016.21.48.30416     01-12-2016

One Health training and research activities in Western Europe
Reina Sikkema and Marion Koopmans 2016

The increase in emerging human infectious diseases that have a zoonotic origin and the increasing resistance of microorganisms to antimicrobial drugs have shown the need for collaborations between the human, animal and environmental health sectors. The One Health concept increasingly receives recognition from policy makers and researchers all over the world.

DOI: 10.3402/iee.v6.33703          29-11-2016

Epidemiological and Molecular Analysis of an Outbreak of Highly Pathogenic Avian Influenza H5N8 clade 2.3.4.4 in a German Zoo: Effective Disease Control with Minimal Culling
Globig et al. 2016

Outbreaks of highly pathogenic avian influenza A virus (HPAIV) subtype H5N8, clade 2.3.4.4, were first reported in January 2014 from South Korea. These viruses spread rapidly to Europe and the North American continent during autumn 2014 and caused, in Germany, five outbreaks in poultry holdings until February 2015. In addition, birds kept in a zoo in north-eastern Germany were affected. Only a few individual white storks (Ciconia ciconia) showed clinical symptoms and eventually died in the course of the infection, although subsequent in-depth diagnostic investigations showed that other birds kept in the same compound of the white storks were acutely positive for or had undergone asymptomatic infection with HPAIV H5N8.

DOI:   10.1111/tbed.12570      15-11-2016

Next-generation sequencing and norovirus
Matthew Cotten and Marion Koopmans 2016

Noroviruses (NoVs) are highly transmissible viruses and the most common cause of diarrhea and vomiting. While illness in most infected persons is relatively mild and self-limiting, severe complications and death may ensue in risk groups, including the extremes of age and persons with reduced immunocompetence due to a range of diseases and treatments.

DOI:  10.2217/fvl-2016-0099      11-11-2016

Novel phlebovirus detected in Haemaphysalis parva ticks in a Greek Island
Papa et al. 2016

During the last decade the number of novel tick-borne phleboviruses has increased rapidly, especially after the identification of severe fever with thrombocytopenia syndrome and Heartland viruses which can cause severe disease in humans. A novel virus, Antigone virus was recently detected in ticks collected from the mainland of Greece. The aim of the present study was to investigate the presence of tick-borne phleboviruses in an island in Greece.

DOI:  10.1016/j.ttbdis.2016.10.012   29-10-2016

Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
Knudsen et al. 2016

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs.

DOI:  10.1128/mSystems.00095-16             18-10-2016

Role for migratory wild birds in the global spread of avian influenza H5N8
The Global Consortium for H5N8 and Related Influenza Viruses

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014–2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses.

DOI:  10.1126/science.aaf8852                    14-10-2016

The evolution of Ebola virus: Insights from the 2013–2016 epidemic
Holmes et al. 2016

The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Here, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution and spread during the epidemic.

DOI:   10.1038/nature19790    12-10-2016

Unbiased whole-genome deep sequencing of human and porcine stool samples reveals circulation of multiple groups of rotaviruses and a putative zoonotic infection
Phan et al. 2016

Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases and animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is an important cause of viral gastroenteritis in humans and animals. In this study, we document the RV diversity within co-located humans and animals sampled from the Mekong delta region of Vietnam using a primer-independent, agnostic, deep sequencing approach.

DOI:   10.1093/ve/vew027     03-10-2016

Bacterial pathogens and endosymbionts in ticks
Papa et al. 2016

Ticks collected from goats in northern Greece were tested for the presence of tick-borne bacteria. Among adult ticks, 37 (57.8%) were Rhipicephalus bursa, 11 (17.2%) Dermacentor marginatus, 10 (15.6%) Ixodes ricinus, 3 (4.7%) Rhipicephalus sanguineus sensu lato and 2 (3.1%) Haemaphysalis parva; one (1.6%) Rhipicephalus spp. tick was nymph. Rickettsia monacensis, Rickettsia massilae, Anaplasma phagocytophilum and Anaplasma platys were detected in I. ricinus and Rh. bursa ticks. A variety of Coxiella-like endosymbionts were detected in all tick genera tested, forming distinct clades from Coxiella burnetii in the phylogenetic tree based on the 16S rRNA gene.

DOI:   http://dx.doi.org/10.1016/j.ttbdis.2016.09.011      23-09-2016

Lack of virological and serological evidence for continued circulation of highly pathogenic avian influenza H5N8 virus in wild birds in the Netherlands, 14 November 2014 to 31 January 2016
Poen et al. 2016

In 2014, H5N8 clade 2.3.4.4 highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage emerged in poultry and wild birds in Asia, Europe and North America. Here, wild birds were extensively investigated in the Netherlands for HPAI H5N8 virus (real-time polymerase chain reaction targeting the matrix and H5 gene) and antibody detection (haemagglutination inhibition and virus neutralisation assays) before, during and after the first virus detection in Europe in late 2014. Between 21 February 2015 and 31 January 2016, 7,337 bird samples were tested for the virus.

DOI: 10.2807/1560-7917.ES.2016.21.38.30349          22-09-2016

Bluetongue virus serotype 27: Detection and characterization of two novel variants in Corsica, France
Schulz et al. 2016

During the compulsory vaccination program against bluetongue virus serotype 1 (BTV-1) in Corsica (France) in 2014, a BTV strain belonging to a previously uncharacterised
serotype (BTV-27) was isolated from asymptomatic goats. The present study describes the detection and molecular characterisation of two additional distinct BTV-27 variants
found in goats in Corsica in 2014 and 2015.

DOI:  10.1099/jgv.0.000557                         01-09-2016

Challenges in laboratory diagnosis of acute viral central nervous system infections in the era of emerging infectious diseases: the syndromic approach
Papa et al. 2016b

Many acute viral infections of the central nervous system (CNS) remain without etiological diagnosis. Specific treatment is available for only few of them; however, accurate diagnosis is essential for patient’s life and public Health.

DOI:   10.1080/14787210.2016.1215914        31-07-2016

Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets
van den Brand er al. 2016

Avian influenza viruses sporadically cross the species barrier to mammals, including humans, in which they may cause epidemic disease. Recently such an epidemic occurred due to the emergence of avian influenza virus of the subtype H10N7 (Seal/H10N7) in harbor seals (Phoca vitulina). This epidemic caused high mortality in seals along the north-west coast of Europe and represented a potential risk for human health. To characterize the spectrum of lesions and to identify the target cells and viral distribution, findings in 16 harbor seals spontaneously infected with Seal/H10N7 are described.

DOI: 10.1371/journal.pone.0159625              22-07-2016

Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016
Xavier et al. 2016

We identified a novel plasmid-mediated colistinresistance gene in porcine and bovine colistin-resistant Escherichia coli that did not contain mcr-1. The gene, termed mcr-2, a 1,617 bp phosphoethanolamine transferase harboured on an IncX4 plasmid, has 76.7% nucleotide identity to mcr-1. Prevalence of mcr-2 in porcine colistin-resistant E. coli (11/53) in Belgium was higher than that of mcr-1 (7/53). These data call for an immediate introduction of mcr-2 screening in ongoing molecular epidemiological surveillance of colistin-resistant Gram-negative pathogens.

DOI:  http://dx.doi.org/10.2807/1560-7917.ES.2016.21.27.30280               07-07-2016

Porcine Bocavirus Infection Associated with Encephalomyelitis in a Pig, Germany
Pfankuche et al. 2016

In 2013, a 6-week-old female piglet kept in a flatdeck cage had coughing, growth retardation, and diarrhea and was taken to a local veterinarian in Hannover, Germany; the piglet was euthanized. After necropsy at the University of Veterinary Medicine in Hannover, histologic investigation found interstitial pneumonia; a mild, multifocal, lymphohistiocytic panencephalitis that affected the cerebrum and cerebellum, including brain stem and medulla oblongata; and a mild, multifocal, lymphohistiocytic panmyelitis. Results from screening for typical neurotropic viruses (classical swine fever virus, suid herpesvirus 1, rabies virus, teschovirus, porcine enterovirus 8, 9, and 10) were negative; Mycoplasma hyorhinis was detected by multiplex PCR (Institute of Virology, University of Veterinary Medicine Hannover) within the lung and pulmonary lymph nodes. Cerebral tissue from the pig was processed for viral metagenomics by random RNA and DNA virus screening and next-generation sequencing (NGS) with the 454 sequencing platform (GS Junior; Roche, Basel, Switzerland), as described (1), and 21,359 reads were obtained. Analysis by using blastn and blastx (2) showed 10 reads had >97% nt identity with porcine bocavirus (PBoV) KU14. No other viral sequences were detected.

DOI:  http://dx.doi.org/10.3201/eid2207.152049                  01-07-2016

Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983-2015
Rasche et al. 2016

A new hepatitis E virus (HEV-7) was recently found in dromedaries and 1 human from the United Arab Emirates. We screened 2,438 dromedary samples from Pakistan, the United Arab Emirates, and 4 African countries. HEV-7 is long established, diversified and geographically widespread. Dromedaries may constitute a neglected source of zoonotic HEV infections.

DOI:  http://dx.doi.org/10.3201/eid2207.160168                  01-07-2016

Crimean-Congo hemorrhagic fever virus lineages Europe 1 and Europe 2 in Bulgarian ticks 
Panayotova et al. 2016

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne human viral disease with fatality rate up to 30%. Two genetic lineages of CCHF virus (CCHFV) are present in Europe – lineage Europe 1 which contains pathogenic CCHFV strains, and lineage Europe 2 consisting of AP92 and AP92-like strains. In order to investigate CCHFV distribution and potential risk for humans, ticks were collected from livestock in the five districts where CCHF cases have been reported in the last five years in Bulgaria. CCHFV lineage Europe 1 was detected in 39 of 623 H. marginatum ticks (6.3%; range per village 2.7 - 15.2%), while CCHFV lineage Europe 2 was detected for the first time in Bulgaria in 49 of 415 R. sanguineus sensu lato ticks (11.8%; range 0 - 58.3%). The present study shows that both Europe 1 and Europe 2 CCHFV lineages are present in Bulgaria. The pathogenic role of the AP92-like strains remains to be elucidated.

DOI:  http://dx.doi.org/doi:10.1016/j.ttbdis.2016.05.010      01-07-2016

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases
Arias et al. 2016

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors.

DOI:  10.1093/ve/vew016                             22-06-2016

Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing 
Becker et al. 2016

We compared commercial kits for extraction of genomic DNA from the Gram-negative bacterium Klebsiella pneumoniae for subsequent Miseq sequencing. Purification of DNA was based on matrix binding (silica or anion exchange resin) or differential precipitation (salting out), respectively. The choice of extraction kit had little effect on sequencing quality and coverage across drastically different replicons, except for an apparent depletion of small plasmids (<5 kb) during precipitation-based extractions. Sequencing coverage provided copy-number estimates for small plasmids that were consistently higher than those from quantitative real-time PCR.

DOI: 10.1038/srep28063                              17-06-2016

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance
Thomsen et al. 2016

Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates.

DOI:  http://dx.doi.org/10.1371/journal.pone.0157718          21-06-2016

High Prevalence of Highly Variable Atypical Porcine Pestiviruses Found in Germany
Beer et al. 2016

Recently, a novel atypical porcine pestivirus (APPV) with significant distribution was described in the USA. Subsequent screening of the German pig sector showed a high prevalence of APPV with high variability among strains. First indication of a cell culture isolate is provided which will allow further investigations like pathogenesis studies.

DOI:  10.1111/tbed.12532                            14-06-2016

Presence of atypical porcine pestivirus (APPV) genomes in newborn piglets correlates with congenital tremor 
Postel et al. 2016

Pestiviruses are highly variable RNA viruses belonging to the continuously growing family Flaviviridae. A genetically very distinct pestivirus was recently discovered in the USA, designated atypical porcine pestivirus (APPV). Here, a screening of 369 sera from apparently healthy adult pigs demonstrated the existence of APPV in Germany with an estimated individual prevalence of 2.4% and ~10% at farm level. Additionally, APPV genomes were detected in newborn piglets affected by congenital tremor (CT), but genomes were absent in unaffected piglets. High loads of genomes were identified in glandular epithelial cells, follicular centers of lymphoid organs, the inner granular cell layer of the cerebellum, as well as in the trigeminal and spinal ganglia. Retrospective analysis of cerebellum samples from 2007 demonstrated that APPV can be found in piglets with CT of unsolved aetiology. Determination of the first European APPV complete polyprotein coding sequence revealed 88.2% nucleotide identity to the APPV sequence from the USA. APPV sequences derived from different regions in Germany demonstrated to be highly variable. Taken together, the results of this study strongly suggest that the presence of APPV genomes in newborn piglets correlates with CT, while no association with clinical disease could be observed in viremic adult pigs.

DOI: 10.1038/srep27735                              13-06-2016

The Biodefense Field
Emilio Mordini, 2016

On April 20, 2016, in Karachi, Pakistan, seven police officers were killed while escorting health workers involved in polio vaccination (Pakistan is one of three countries in the world where polio is still endemic). The Taliban claimed responsibility and promised future attacks. This news deserves to be read through the lens of a report published on October 28, 2015 by the Blue Ribbon Study Panel on Biodefense, a bipartisan commission sponsored by the Hudson Institute and the Potomac Institute for Policy Studies, two US think-tanks.

DOI: 10.1111/bioe.12269                             04-06-2016

Complete sequence of an IncFII plasmid harbouring the colistin resistance gene mcr-1 isolated from Belgian pig farms 
Xavier et al. 2016b

The monumental increase in antibiotic resistance among important bacterial pathogens, driven by inappropriate and appropriate use of ineffective drugs, is currently recognized as one of themost pressing threats to human health by the WHO.

DOI: 10.1093/jac/dkw191                             03-06-2016

Discovery and diagnosis of new viral pathogens: proposal for a generic workflow based on next-generation sequencing and new integrated data analysis approaches
Höper et al. 2016b

Diagnostic metagenomic analyses gained more impact for pathogen detection and discovery in recent years due to increasing opportunities for next-generation sequencing at simultaneously decreasing prices. However, as with all novel technologies, there is a lack of standardisation in this field. But, for day-to-day routine use in a diagnostic laboratory, standardisation is urgently required.

Euroreference, (1 June 2016), 58–62

Human norovirus transmission and evolution in a changing world 
de Graaf et al. 2016

Norovirus infections are a major cause of gastroenteritis, and outbreaks occur frequently. Several factors are currently increasing the challenge posed by norovirus infections to global health, notably the increasing number of infections in immunocompromised individuals, who are more susceptible to disease, and the globalization of the food industry, which enables large norovirus outbreaks to occur on an international scale. Furthermore, the rapid rate of the genetic and antigenic evolution of circulating noroviruses complicates the development of vaccines and therapies that are required to counter these challenges. In this Review, we describe recent advances in the study of the transmission, pathogenesis and evolution of human noroviruses, and consider the ongoing risk of norovirus outbreaks, together with the future prospects for therapeutics, in a rapidly changing world.

DOI: 10.1038/nrmicro.2016.48                                           23-05-2016

Detection of Hepatitis E Virus in Sewage After an Outbreak on a French Island 
Miura et al. 2016

A hepatitis E outbreak, which occurred on a small isolated island, provided an opportunity to evaluate the association between the number of hepatitis E cases in the community and the concentration of virus detected in sewage.

DOI: 10.1007/s12560-016-9241-9                  10-05-2016

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes
Bielejec et al. 2016

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST ( http://beast.bio.ed.ac.uk , last accessed 9 May 2016). The integration of JavaScript D3 libraries ( www.d3.org , last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.

DOI:  10.1093/molbev/msw082   23-04-2016

Using genomics data to reconstruct transmission trees during disease outbreaks
Hall et al. 2016a

Genetic sequence data from pathogens present a novel means to investigate the spread of infectious disease between infected hosts or infected premises, complementing traditional contact-tracing approaches, and much recent work has gone into developing methods for this purpose. The objective is to recover the epidemic transmission tree, which identifies who infected whom. This paper reviews the various approaches that have been taken.

DOI:  http://dx.doi.org/10.20506/rst.35.1.2433                                          01-04-2016

Metagenomic approaches to identifying infectious agents
Höper et al. 2016a

Since the advent of next-generation sequencing (NGS) technologies, the untargeted screening of samples from outbreaks for pathogen identification using metagenomics has become technically and economically feasible. However, various aspects need to be considered in order to exploit the full potential of NGS for virus discovery. Here, the authors summarise those aspects of the main steps that have a significant impact, from sample selection through sample handling and processing, as well as sequencing and finally data analysis, with a special emphasis on existing pitfalls.

DOI:  http://dx.doi.org/10.20506/rst.35.1.2419                                          01-04-2016

Sharing data for global infectious disease surveillance and outbreak detection 
Aarestrup and Koopmans 2016

Rapid global sharing and comparison of epidemiological and genomic data on infectious diseases would enable more rapid and efficient global outbreak control and tracking of diseases. Several barriers for global sharing exist but, in our opinion, the presumed magnitude of the problems appears larger than they are, and solutions can be found. 

DOI:  http://dx.doi.org/10.1016/j.tim.2016.01.009                01-04-2016

Deletion Variants of Middle East Respiratory Syndrome Coronavirus from Humans, Jordan, 2015 
Lamers et al. 2016

We characterized Middle East respiratory syndrome coronaviruses from a hospital outbreak in Jordan in 2015. The viruses from Jordan were highly similar to isolates from Riyadh, Saudi Arabia, except for deletions in open reading frames 4a and 3. Transmissibility and pathogenicity of this strain remains to be determined.

DOI: http://dx.doi.org/10.3201/eid2204.152065                                        01-04-2016

Comparative Proteomics Identifies Host Immune System Proteins Affected by Infection with Mycobacterium bovis 
Lopez et al. 2016

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly impact human and animal health worldwide. The mycobacterial life cycle is complex, and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Eurasian wild boar (Sus scrofa) are natural reservoir hosts for MTBC and a model for mycobacterial infection and tuberculosis (TB). In the wild boar TB model, mycobacterial infection affects the expression of innate and adaptive immune response genes in mandibular lymph nodes and oropharyngeal tonsils, and biomarkers have been proposed as correlates with resistance to natural infection. However, the mechanisms used bymycobacteria tomanipulate host immune response are not fully characterized. Our hypothesis is that the immune system proteins under-represented in infected animals, when compared to uninfected controls, are used by mycobacteria to guarantee pathogen infection and transmission.

DOI: 10.1371/journal.pntd.0004541              30-03-2016

The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study
Hall et al. 2016b

The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This raises questions about how a set of sequences should be selected for analysis, particularly if the data are used to infer more than just the phylogenetic tree itself.

DOI:  10.1093/ve/vew003                             02-03-2016

Genetic Detection of Hantaviruses in Rodents, Albania 
Papa et al. 2016a

In order to have a first insight into the epidemiology of hantaviruses in Albania, 263 small mammals (248 rodents, 15 insectivores) were captured in 352 locations in 29 districts and tested for hantavirus infection. Dobrava– Belgrade virus (DOBV) was detected in 10 of 148 (6.7%) Apodemus flavicollis rodents. DOBV-positive A. flavicollis were detected in six districts (Diber, Korce, Kolonje, Librazhd, Pogradec, and Vlore). The obtained nucleotide sequences were highly similar to each other and to DOBV sequences from northwestern Greece. Understanding the epidemiology of hantaviruses and identifying the endemic foci enables the public health strategies to minimize the risk of human infection.

DOI: 10.1002/jmv.24486                              08-02-2016

Dissemination of the mcr-1 colistin resistance gene
Arcilla et al. 2016

Plasmid-mediated transferable colistin resistance encoded by the mcr-1 gene was described in Escherichia coli and Klebsiella pneumoniae isolates from pigs and chicken at a prevalence of around 20%, and in clinical isolates from human beings at a prevalence of around 1% in China.1 The prevalence of the mcr-1 gene in Enterobacteriaceae in other countries and in the
community is unknown. 

DOI:  http://dx.doi.org/10.1016/S1473-3099(15)00540-X      01-02-2016

Consolidating and exploring antibiotic resistance gene data resources
Xavier et al. 2016

The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multi-drug-resistant (MDR) bacterial pathogens. With the advent of next generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency and accuracy of information vary considerably across different databases. In this article, we sought to explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions. 

DOI: 10.1128/JCM.02717-15                        27-01-2016

Spatiotemporal analysis of the genetic diversity of seal influenza A(H10N7) virus, Northwestern Europe 
Bodewes et al. 2016

Influenza A viruses are major pathogens for humans, domestic animals and wildlife that cross the species barrier occasionally. In spring 2014, increased mortality of harbor seals (Phoca vitulina) was reported in Sweden and Denmark, associated with infection with an influenza A(H10N7) virus. Within a few months, this virus spread to seals of the coastal waters of Germany and the Netherlands, causing the death of thousands of animals. Genetic analysis of the hemagglutinin (HA) and neuraminidase (NA) genes of this seal influenza A(H10N7) virus revealed that it was most closely related to various avian influenza A(H10N7) viruses. The collection of samples from infected seals during the course of the outbreak provided an unique opportunity to follow the adaptation of this avian virus to its new seal host. Sequence data was obtained from samples collected from 41 different seals from four different countries between April 2014 and January 2015 using Sanger sequencing and next-generation sequencing to describe the molecular epidemiology of the seal influenza A(H10N7) virus. The majority of sequence variation occurred in the HA gene, and some mutations corresponded with amino acid changes not found in H10 viruses isolated from Eurasian birds. Also, sequence variation in the HA gene was greater at the beginning than at the end of the epidemic, when a number of the mutations observed earlier had been fixed. These results imply that when an avian influenza virus jumps the species barrier from birds to seals, amino acid changes in the HA may occur rapidly and are important for virus adaptation to its new mammalian host. 

DOI: 10.1128/JVI.03046-15                          27-01-2016

Immunolabelling of non-phosphorylated neurofilament indicates damage of spinal cord axons in TSE-infected goats 
Nadeem et al. 2016

TRANSMISSIBLE spongiform encephalopathies (TSEs) including bovine spongiform encephalopathy (BSE) are devastating neurodegenerative disorders caused by conversion of the normal cellular prion protein (PrPC) into an abnormal isoform (PrPSc; Prusiner, 1982, Chesebro, 2003). Following the discovery of goat BSE cases in the UK and France (Eloit and others 2005, Jeffrey and others 2006, Spiropoulos and others 2011) small ruminants were considered to pose a BSE infection risk/source for cattle, and human beings in particular.

DOI: 10.1136/vr.103425                               21-01-2016

Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam 
Malhotra et al. 2016b

In The Lancet Infectious Diseases, Yi-Yun Liu and colleagues1 reported, for the first time, plasmid-mediated colistin resistance in Escherichia coli isolated from animals, food, and patients in China. We screened 24 extendedspectrum β-lactamase (ESBL, blaCTX-M) harbouring E coli isolated during 2014–15 from rectal swabs taken from chickens on two farms (n=11) in
the Van Lam district of the Hung Yen province, and from a pig farm (seven) and a pig slaughterhouse (four) located in the Hoai Duc region of the Hanoi province, Vietnam.

DOI: http://dx.doi.org/10.1016/S1473-3099(16)00014-1       08-01-2016

Colistin resistance gene mcr-1 harboured on a multidrug resistant plasmid 
Malhotra et al. 2016a

In The Lancet Infectious Diseases, Yi-Yun Liu and colleagues reported, for the fi rst time, plasmid-mediated colistin resistance in Escherichia coli isolated from animals, food, and patients in China.1 These data bring to the fore an as yet unknown facet of colistin resistance and yet again show the effect of antibiotic use in animal farming on human health.2,3

DOI:  http://dx.doi.org/10.1016/S1473-3099(16)00012-8      08-01-2016

Emergence of a Clonal Lineage of Multidrug-Resistant ESBL-Producing Salmonella Infantis Transmitted from Broilers and Broiler Meat to Humans in Italy between 2011 and 2014 
Franco et al. 2015

We report the spread of a clone of multidrug-resistant (MDR), ESBL-producing (bla CTX-M-1) Salmonella enterica subsp. enterica serovar Infantis, in the Italian broiler chicken industry and along the food-chain. This was first detected in Italy in 2011 and led to human infection in Italy in 2013–2014.A set (n = 49) of extended-spectrum cephalosporin (ESC)-resistant (R) isolates of S. Infantis (2011–2014) from humans, food-producing animals and meat thereof, were studied along with a selected set of earlier and more recent ESC-susceptible (ESC-S) isolates (n = 42, 2001–2014). They were characterized by macrorestriction-PFGE analysis and genetic environment of ESC-resistance. Isolates representative of PFGE-patterns and origin were submitted to Whole Genome Sequencing. The emerging ESC-R clone, detected mainly from broiler chickens, broiler meat and humans, showed a minimum pattern of clinical resistance to cefotaxime, tetracycline, sulfonamides, and trimethoprim, beside ciprofloxacin microbiological resistance (MIC 0.25 mg/L). All isolates of this clone harbored a conjugative megaplasmid (~ 280–320 Kb), similar to that described in ESC-susceptible S. Infantis in Israel (pESI-like) in 2014. This megaplasmid carried the ESBL gene bla CTX-M-1, and additional genes [tet(A), sul1, dfrA1 and dfrA14] mediating cefotaxime, tetracycline, sulfonamide, and trimethoprim resistance. It also contained genes conferring enhanced colonization capability, virulence (fimbriae, yersiniabactin), resistance and fitness (qacE1, mer) in the intensive-farming environment. This emerging clone of S. Infantis has been causing infections in humans, most likely through the broiler industry. Since S. Infantis is among major serovars causing human infections in Europe and is an emerging non-typhoidal Salmonella globally, further spread of this lineage in primary productions deserves quick and thorough risk-management strategies.

DOI: 10.1371/journal.pone.0144802              30-12-2015

Seroprevalence of Antibodies against Seal Influenza A(H10N7) Virus in Harbor Seals and Gray Seals from the Netherlands 
Bodewes et al. 2015

In the spring and summer 2014, an outbreak of seal influenza A(H10N7) virus infection occurred among harbor seals (Phoca vitulina) off the coasts of Sweden and Denmark. This virus subsequently spread to harbor seals off the coasts of Germany and the Netherlands. While thousands of seals were reported dead in Sweden, Denmark and Germany, only a limited number of seals were found dead in the Netherlands. To determine the extent of exposure of seals in the Netherlands to influenza A/H10N7 virus, we measured specific antibody titers in serum samples from live-captured seals and seals admitted for rehabilitation in the Netherlands by use of a hemagglutination inhibition assay and an ELISA. In harbor seals in 2015, antibodies against seal influenza A(H10N7) virus were detected in 41% (32 out of 78) pups, 10% (5 out of 52) weaners, and 58% (7 out of 12) subadults or adults. In gray seals (Halichoerus grypus) in 2015, specific antibodies were not found in the pups (n = 26), but in 26% (5 out of 19) of the older animals. These findings indicate that, despite apparent low mortality, infection with seal influenza A(H10N7) virus was geographically widespread and also occurred in grey seals.

DOI: 10.1371/journal.pone.0144899              14-12-2015

Neurotropic virus infections as the cause of immediate and delayed neuropathology 
Ludlow et al. 2015

A wide range of viruses from different virus families in different geographical areas, may cause immediate or delayed neuropathological changes and neurological manifestations in humans and animals. Infection by neurotropic viruses as well as the resulting immune response can irreversibly disrupt the complex structural and functional architecture of the central nervous system, frequently leaving the patient or affected animal with a poor or fatal prognosis. Mechanisms that govern neuropathogenesis and immunopathogenesis of viral infections are highlighted, using examples of wellstudied virus infections that are associated with these alterations in different populations throughout the world. A better understanding of the molecular, epidemiological and biological characteristics of these infections and in particular of mechanisms that underlie their clinical manifestations may be expected to provide tools for the development of more effective intervention strategies and treatment regimens.

DOI: 10.1007/s00401-015-1511-3                  10-12-2015

Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015
Hasman et al. 2015

The plasmid-mediated colistin resistance gene, mcr-1, was detected in an Escherichia coli isolate from a Danish patient with bloodstream infection and in five E. coli isolates from imported chicken meat. One isolate from chicken meat belonged to the epidemic spreading sequence type ST131. In addition to IncN2, an incX4 replicon was found to be linked to mcr-1. This report follows a recent detection of mcr-1 in E. coli from animals, food and humans in China. 

DOI:  http://dx.doi.org/10.2807/1560-7917.ES.2015.20.49.30085               10-12-2015

Comparative Genomics of Field Isolates of Mycobacterium bovis and M. caprae Provides Evidence for Possible Correlates with Bacterial Viability and Virulence 
de la Fuente et al. 2015b

Mycobacteria of the Mycobacterium tuberculosis complex (MTBC) greatly affect humans and animals worldwide. The life cycle of mycobacteria is complex and the mechanisms resulting in pathogen infection and survival in host cells are not fully understood. Recently, comparative genomics analyses have provided new insights into the evolution and adaptation of the MTBC to survive inside the host. However, most of this information has been obtained using M. tuberculosis but not other members of the MTBC such as M. bovis and M. caprae. In this study, the genome of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different lesion score, prevalence and host distribution phenotypes were sequenced. Genomesequence information was used for whole-genome and protein targeted comparative genomics analysis with the aim of finding correlates with phenotypic variation with potential implications for tuberculosis (TB) disease risk assessment and control.

DOI:10.1371/journal.pntd.0004232               19-11-2015

Biocuration of functional annotation at the European nucleotide archive 
Gibson et al. 2015

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed.

DOI: 10.1093/nar/gkv1311                           09-11-2015

Evolutionary origins of hepatitis A virus in small mammals 
Drexler et al. 2015

Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl- terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3Dpol sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of epatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.

DOI:  http://www.pnas.org/content/112/49/15190                02-11-2015

Molecular Epidemiology of Crimean–Congo Hemorrhagic Fever in Bulgaria—An Update
Papa et al. 2015

Crimean–Congo hemorrhagic fever (CCHF) is endemic in Bulgaria. During 2013–2014, 11 confirmed CCHF cases have been reported in the country (seven in 2013 and four in 2014). The present study provides the CCHF molecular epidemiology in Bulgaria based on all currently available S, M, and L RNA segment nucleotide sequences spanning the years 1978–2014. A relatively low genetic difference (0–6%, the maximum seen in the M RNA segment) was seen among the CCHFV sequences suggesting that a slow evolving CCHFV strain belonging to “Europe 1” clade is present in Bulgaria. Although the virus emerged in new foci during the recent years, it is more active in the established endemic foci which seem to offer the most suitable ecosystem and environment. Understanding the CCHF epidemiology and virus evolution is the basis for public health programs and vaccine design.

DOI: 10.1002/jmv.24400                              15-10-2015

Genotypic anomaly in Ebola virus strains circulating in magazine wharf area, Freetown, Sierra Leone, 2015 
Smits et al. 2015 

The Magazine Wharf area, Freetown, Sierra Leone, was a focus of ongoing Ebola virus transmission from late June 2015. Viral genomes linked to this area contain a series of 13 T to C substitutions in a 150 base pair intergenic region downstream of viral protein 40 open reading frame, similar to the Ebolavirus/H.sapienswt/ SLE/2014/Makona-J0169 strain (J0169) detected in the same town in November 2014. This suggests that recently circulating viruses from Freetown descend from a J0169-like virus. 

DOI: http://dx.doi.org/10.2807/1560-7917.ES.2015.20.40.30035                08-10-2015

Recovering full-length viral genomes from metagenomes 
Smits et al. 2-2015

Infectious disease metagenomics is driven by the question: “what is causing the disease?” in contrast to classical metagenome studies which are guided by “what is out there?” In case of a novel virus, a first step to eventually establishing etiology can be to recover a full-length viral genome from a metagenomic sample. However, retrieval of a full-length genome of a divergent virus is technically challenging and can be time-consuming and costly. Here we discuss different assembly and fragment linkage strategies such as iterative assembly, motif searches, k-mer frequency profiling, coverage profile binning, and other strategies used to recover genomes of potential viral pathogens in a timely and cost-effective manner.

DOI: 10.3389/fmicb.2015.01069                   01-10-2015

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management
Woolhouse et al. 2015

The current Ebola virus disease outbreak in West Africa has revealed serious shortcomings in national and international capacity to detect, monitor, and respond to infectious disease outbreaks as they occur. Recent advances in diagnostics, risk mapping, mathematical modeling, pathogen genome sequencing, phylogenetics, and phylogeography have the potential to improve substantially the quantity and quality of information available to guide the public health response to outbreaks of all kinds.

DOI:  10.1126/scitranslmed.aab0191            30-09-2015

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Petersen et al. 2015

Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions.

DOI:  10.1038/srep11444                             10-07-2015

Emergence of a novel GII.17 norovirus – End of the GII.4 era? 
de Graaf et al. 2015

In the winter of 2014/15 a novel GII.P17-GII.17 norovirus strain (GII.17 Kawasaki 2014) emerged, as a major cause of gastroenteritis outbreaks in China and Japan. Since their emergence these novel GII.P17-GII.17 viruses have replaced the previously dominant GII.4 genotype Sydney 2012 variant in some areas in Asia but were only detected in a limited number of cases on other continents. This perspective provides an overview of the available information on GII.17 viruses in order to gain insight in the viral and host characteristics of this norovirus genotype.

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=21178             02-07-2015

Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009–2013 
Bexton et al. 2015

A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated. 

DOI:  http://dx.doi.org/10.3201/eid2107.150228                  01-07-2015

Complete Genome Sequences of Field Isolates of Mycobacterium bovis and Mycobacterium caprae 
de la Fuente et al. 2015a

Here we report the complete genome sequences of field isolates of Mycobacterium bovis and the related mycobacterial species, Mycobacterium caprae. The genomes of three M. bovis (MB1, MB3, MB4) and one M. caprae (MB2) field isolates with different virulence, prevalence, and host distribution phenotypes were sequenced.

DOI: 10.1128/genomeA.00247-15                 25-06-2015

Low Virulence and Lack of Airborne Transmission of the Dutch Highly Pathogenic Avian Influenza Virus H5N8 in Ferrets 
Richard et al. 2015

Highly pathogenic avian influenza (HPAI) H5N8 viruses that emerged in poultry in East Asia spread to Europe and North America by late 2014. Here we show that the European HPAI H5N8 viruses differ from the Korean and Japanese HPAI H5N8 viruses by several amino acids and that a Dutch HPAI H5N8 virus had low virulence and was not transmitted via the airborne route in ferrets. The virus did not cross-react with sera raised against pre-pandemic H5 vaccine strains. This data is useful for public health risk assessments.

DOI: 10.1371/journal.pone.0129827              19-06-2015

Complete Genome Sequence of a Porcine Epidemic Diarrhea S Gene Indel Strain Isolated in France in December 2014
Grassland et al. 2015

We report the first and only case of a porcine epidemic diarrhea (PED) outbreak occurring in December 2014 in northern France, and we show using the full-length genome sequence of the French PED virus (PEDV) isolate that it was a PEDV indel strain close to German PEDV strains recently isolated.

DOI: 10.1128/genomeA.00535-15                 04-06-2015

Influenza A(H5N8) Virus Similar to Strain in Korea Causing Highly Pathogenic Avian Influenza in Germany
Harder et al. 2015

Highly pathogenic avian influenza (H5N8) virus, like the recently described H5N8 strain from Korea, was detected in November 2014 in farmed turkeys and in a healthy common teal (Anas crecca) in northeastern Germany. Infected wild birds possibly introduced this virus.

DOI:  http://dx.doi.org/10.3201/eid2105.141897                  01-05-2015

Wild bird surveillance around outbreaks of highly pathogenic avian influenza A(H5N8) virus in the Netherlands, 2014, within the context of global flyways
Verhagen et al. 2015

Highly pathogenic avian influenza (HPAI) A(H5N8) viruses that emerged in poultry in east Asia since 2010 spread to Europe and North America by late 2014. Despite detections in migrating birds, the role of free-living wild birds in the global dispersal of H5N8 virus is unclear. Here, wild bird sampling activities in response to the H5N8 virus outbreaks in poultry in the Netherlands are summarised along with a review on ring recoveries. 

DOI: http://dx.doi.org/10.2807/1560-7917.ES2015.20.12.21069                 26-03-2015

One health, multiple challenges: The inter-species transmission of influenza A virus
Short et al. 2015

Influenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Influenza
A viruses are unique in many ways. Firstly, they are unique in the diversity of host species that they infect.
This includes waterfowl (the original reservoir), terrestrial and aquatic poultry, swine, humans, horses, dog, cats,
whales, seals and several other mammalian species. Secondly, they are unique in their capacity to evolve and
adapt, following crossing the species barrier, in order to replicate and spread to other individuals within the
new species. Finally, they are unique in the frequency of inter-species transmission events that occur. Indeed,
the consequences of novel influenza virus strain in an immunologically naïve population can be devastating.

DOI: 10.1016/j.onehlt.2015.03.001          26-03-2015

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