Valentijn Vergote

Circulation of HRSV in Belgium: From Multiple Genotype Circulation to Prolonged Circulation of Predominant Genotypes

Molecular surveillance of HRSV in Belgium for 15 consecutive seasons (1996–2011) revealed a shift from a regular 3-yearly cyclic pattern, into a yearly alternating periodicity where HRSV-B is replaced by HRSV-A. Phylogenetic analysis for HRSV-A demonstrated the stable circulation of GA2 and GA5, with GA2 being dominant over GA5 during 5 consecutive seasons (2006–2011). We also identified 2 new genotype specific amino acid mutations of the GA2 genotype (A122 and Q156) and 7 new GA5 genotype specific amino acid mutations (F102, I108, T111, I125, D161, S191 and L217). Several amino acid positions, all located in the second hypervariable region of HRSV-A were found to be under positive selection. Phylogenetic analysis of HRSV-B showed the circulation of GB12 and GB13, where GB13 represented 100% of the isolated strains in 4 out of 5 consecutive seasons (2007–2011). Amino acids under positive selection were all located in the aminoterminal hypervariable region of HRSV-B, except one amino acid located in the conserved region. The genotype distribution within the HRSV-B subgroup has evolved from a co-circulation of multiple genotypes to the circulation of a single predominant genotype. The Belgian GB13 strains circulating since 2006, all clustered under the BAIV branch and contained several branch specific amino acid substitutions. The demographic history of genotypes GA2, GA5 and GB13 demonstrated a decrease in the total GA2 and GA5 population size, coinciding with the global expansion of the GB13 population. The emergence of the GB13 genotype resulted in a newly established balance between the predominant genotypes.

Rapid and complete hematological response of refractory hairy cell leukemia to the BRAF inhibitor dabrafenib.

Dear Editor, Hairy cell leukemia (HCL) is a mature B-cell lymphoid cancer that can be treated successfully in the majority of patients with various agents like purine nucleoside analogues, rituximab, interferon-alpha, or splenectomy. Recently, it was reported that BRAF V600E mutations can be found in virtually all patients with HCL, suggesting that this genetic event represents a key driver of the disease. The BRAF protein is part of the RASRAF-MAPK signaling pathway, which plays a major role in regulating cell survival, proliferation, and differentiation [1]. Various case reports of successful treatment of refractory HCL with the BRAF inhibitor vemurafenib have recently been published [2–7]. Dabrafenib is a reversible BRAF inhibitor with a shorter half-life compared to vemurafenib. We report a 62-year-old male patient with refractory HCL who achieved a rapid and complete hematological response to treatment with the BRAF inhibitor dabrafenib. To our knowledge, this is the first manuscript of the use of dabrafenib in HCL. The patient was diagnosed in 2008 with HCL at the age of 57 years. The presented signs and symptoms were fatigue, splenomegaly, and pancytopenia. He was initially treated with one cycle of the purine nucleoside analogue cladribine (0.1 mg/kg for 7 days) resulting in normalization of his blood counts. After 22 months, he relapsed with worsening cytopenia and he was retreated with cladribine, but with incomplete recovery of his white blood cell count followed by progressive pancytopenia. Despite four doses of the anti-CD20 monoclonal antibody rituximab at 375 mg/m, he remained pancytopenic due to the infiltration of the bone marrow with hairy cells (Fig. 1). A BRAF V600E mutation was detected in his bone marrow by locked nucleic acid PCR followed by Sanger sequencing. Due to increasing red blood cell and platelet transfusion need and progressive splenomegaly, a splenectomy was performed but with no improvement on his blood counts. One month later, he was hospitalized with neutropenic fever due to invasive pulmonary aspergillosis. On admission, he had a neutrophil count of 100/μL and a platelet count of 13,000/μL. He received caspofungin followed by posaconazole, G-CSF, and broad-spectrum antibiotics because of persisting neutropenic fever and increasing pulmonary infiltrates. After intensive counseling, we obtained approval from the local ethics committee, and informed consent from the patient to start dabrafenib in compassionate use. Dabrafenib (Tafinlar®) was kindly provided free of charge by GlaxoSmithKline, Belgium. On October 1, 2013, dabrafenib was started at a reduced dose of 100 mg twice daily (day 0) to avoid any drug interaction with his antifungal treatment. On day 14, the dose was increased to 150 mg twice daily, the recommended dose in metastatic melanoma. His neutrophil count started to increase after 23 days of treatment. On day 30, his neutrophil count was 1.100/μl, his fever had resolved, inflammatory parameters normalized, and the patient was discharged from the hospital. Platelet count normalized on day 42, neutrophils on day 79, and hemoglobin by day 100 (Fig. 2). Antifungal treatment was discontinued after 2 months. Bone marrow aspirate and biopsy performed after 79 days of treatment with dabrafenib revealed only scarce hairy cells by morphological examination (Fig. 1), and <1 % hairy cells by flow cytometry. Dabrafenib was discontinued after 129 days. V. Vergote (*) :D. Dierickx :A. Janssens :G. Verhoef : P. Vandenberghe :M. Delforge Department of Hematology, UZ Leuven, UZGasthuisberg Herestraat 49, 3000 Leuven, Belgium e-mail: Vibeke.Vergote@gmail.com

Spatio‐temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium

Over the last decade, the recognized host range of hantaviruses has expanded considerably with the discovery of distinct hantaviruses in shrews, moles and bats. Unfortunately, in‐depth studies of these viruses have been limited. Here we describe a comprehensive analysis of the spatial distribution, genetic diversity and evolution of Nova virus, a hantavirus that has the European mole as its natural host. Our analysis demonstrated that Nova virus has a high prevalence and widespread distribution in Belgium. While Nova virus displayed relatively high nucleotide diversity in Belgium, amino acid changes were limited. The nucleocapsid protein was subjected to strong purifying selection, reflecting the strict evolutionary constraints placed upon Nova virus by its host. Spatio‐temporal analysis using Bayesian evolutionary inference techniques demonstrated that Nova virus had efficiently spread in the European mole population in Belgium, forming two distinct clades, representing east and west of Belgium. The influence of landscape barriers, in the form of the main waterways, on the dispersal velocity of Nova virus was assessed using an analytical framework for comparing Bayesian viral phylogenies with environmental landscape data. We demonstrated that waterways did not act as an environmental resistance factor slowing down Nova virus diffusion in the mole population. With this study, we provide information about the spatial diffusion of Nova virus and contribute sequence information that can be applied in further functional studies.

Molecular characterization of hepatitis B virus (HBV) strains circulating in the northern coast of the Persian Gulf and its comparison with worldwide distribution of HBV subgenotype D1.

Iran is a large country that covers the northern coast of the Persian Gulf. Iranian residents of this coastal region interact closely with people from neighboring countries because of historical and cultural relationships, as well as economic activities. In addition, the inhabitants of this border region have experienced several wars, which have affected public health infrastructures. This study characterized for the first time, the evolution of the full‐length genome of HBV strains in asymptomatic carrier patients living in this particular region. In addition, this study was compared and complemented by a comprehensive evolutionary analysis of the worldwide geographical distribution of HBV subgenotype D1. Evolutionary analysis demonstrates that patients living in the northern coast of the Persian Gulf are mainly infected with HBV subgenotype D1, subtype ayw2. Specific mutations related to advanced liver disease were found more frequently in these strains compared to other strains isolated from asymptomatic carriers from other regions of Iran. This global comprehensive analysis showed that HBV subgenotype D1 strains have a worldwide distribution and that human mobility and immigration had a large impact on dispersal of HBV subgenotype D1, subtype ayw2 in Middle Eastern countries such as Iran, Syria, and Turkey. In addition to association of subtype ayw2 with subgenotype D1, it was demonstrated that other HBV subtypes like adw2, ayw1, and ayw3 are associated with HBV subgenotype D1 in different regions of the world. This study also revealed a remarkable distribution of subgenotype D1, subtype ayw4 although this particular subtype is associated with subgenotype D4 of HBV in European countries. J. Med. Virol. 86:745–757, 2014.

Identification of a novel species of papillomavirus in giraffe lesions using nanopore sequencing

Papillomaviridae form a large family of viruses that are known to infect a variety of vertebrates, including mammals, reptiles, birds and fish. Infections usually give rise to minor skin lesions but can in some cases lead to the development of malignant neoplasia. In this study, we identified a novel species of papillomavirus (PV), isolated from warts of four giraffes (Giraffa camelopardalis). The sequence of the L1 gene was determined and found to be identical for all isolates. Using nanopore sequencing, the full sequence of the PV genome could be determined. The coding region of the genome was found to contain seven open reading frames (ORF), encoding the early proteins E1, E2 and E5-E7 as well as the late proteins L1 and L2. In addition to these ORFs, a region located within the E2 gene is thought, based on sequence similarities to other papillomaviruses, to encode an E4 protein, although no start codon could be identified. Based on the sequence of the L1 gene, this novel PV was found to be most similar to Capreolus capreolus papillomavirus 1 (CcaPV1), with 67.96% nucleotide identity. We therefore suggest that the virus identified here is given the name Giraffa camelopardalis papillomavirus 1 (GcPV1) and is classified as a novel species within the genus Deltapapillomavirus, in line with the current guidelines for the nomenclature and classification of PVs.

A Novel Hantavirus of the European Mole, Bruges Virus, Is Involved in Frequent Nova Virus Coinfections

Abstract Hantaviruses are zoonotic viruses with a complex evolutionary history of virus–host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus–host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hantavirus harbored by the European mole (Talpa europaea), which is the well-known host of Nova virus. Phylogenetic analyses of all three genomic segments showed tree topology inconsistencies, suggesting that Bruges virus has emerged from cross-species transmission and ancient reassortment events. A high number of coinfections with Bruges and Nova viruses was detected, but no evidence was found for reassortment between these two hantaviruses. These findings highlight the complexity of hantavirus evolution and the importance of further investigation of hantavirus–reservoir relationships.

A lethal disease model for New World hantaviruses using immunosuppressed Syrian hamsters

Background Hantavirus, the hemorrhagic causative agent of two clinical diseases, is found worldwide with variation in severity, incidence and mortality. The most lethal hantaviruses are found on the American continent where the most prevalent viruses like Andes virus and Sin Nombre virus are known to cause hantavirus pulmonary syndrome. New World hantavirus infection of immunocompetent hamsters results in an asymptomatic infection except for Andes virus and Maporal virus; the only hantaviruses causing a lethal disease in immunocompetent Syrian hamsters mimicking hantavirus pulmonary syndrome in humans. Methodology/Principal findings Hamsters, immunosuppressed with dexamethasone and cyclophosphamide, were infected intramuscularly with different New World hantavirus strains (Bayou virus, Black Creek Canal virus, Caño Delgadito virus, Choclo virus, Laguna Negra virus, and Maporal virus). In the present study, we show that immunosuppression of hamsters followed by infection with a New World hantavirus results in an acute disease that precisely mimics both hantavirus disease in humans and Andes virus infection of hamsters. Conclusions/ Significance Infected hamsters showed specific clinical signs of disease and moreover, histological analysis of lung tissue showed signs of pulmonary edema and inflammation within alveolar septa. In this study, we were able to infect immunosuppressed hamsters with different New World hantaviruses reaching a lethal outcome with signs of disease mimicking human disease.

Complete Genome Sequence of Nova Virus, a Hantavirus Circulating in the European Mole in Belgium

ABSTRACT The complete genome sequence of Nova virus, a divergent hantavirus, originating from the kidney tissue of a European mole (Talpa europaea) from Belgium was determined. The 3 genomic segments have a total length of 11,979 nucleotides, and nucleotide identities to other Nova viruses are between 80 and 89%.

Expanding the Arterivirus Host Spectrum: Olivier’s Shrew Virus 1, A Novel Arterivirus Discovered in African Giant Shrews

The family Arteriviridae harbors a rapidly expanding group of viruses known to infect a divergent group of mammals, including horses, pigs, possums, primates, and rodents. Hosts infected with arteriviruses present with a wide variety of (sub) clinical symptoms, depending on the virus causing the infection and the host being infected. In this study, we determined the complete genome sequences of three variants of a previously unknown virus found in Olivier’s shrews (Crocidura olivieri guineensis) sampled in Guinea. On the nucleotide level, the three genomes of this new virus, named Olivier’s shrew virus 1 (OSV-1), are 88–89% similar. The genome organization of OSV-1 is characteristic of all known arteriviruses, yet phylogenetic analysis groups OSV-1 separately from all currently established arterivirus lineages. Therefore, we postulate that OSV-1 represents a member of a novel arterivirus genus. The virus described here represents the first discovery of an arterivirus in members of the order Eulipotyphla, thereby greatly expanding the known host spectrum of arteriviruses.

Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins

BackgroundIn the past decade, many new paramyxoviruses that do not belong to any of the seven established genera in the family Paramyxoviridae have been discovered. Amongst them are J-virus (JPV), Beilong virus (BeiPV) and Tailam virus (TlmPV), three paramyxovirus species found in rodents. Based on their similarities, it has been suggested that these viruses should compose a new genus, tentatively called ‘Jeilongvirus’.ResultsHere we present the complete genomes of three newly discovered paramyxoviruses, one found in a bank vole (Myodes glareolus) from Slovenia and two in a single, co-infected Rungwe brush-furred rat (Lophuromys machangui) from Mozambique, that represent three new, separate species within the putative genus ‘Jeilongvirus’. The genome organization of these viruses is similar to other paramyxoviruses, but like JPV, BeiPV and TlmPV, they possess an additional open reading frame, encoding a transmembrane protein, that is located between the F and G genes. As is the case for all Jeilongviruses, the G genes of the viruses described here are unusually large, and their encoded proteins are characterized by a remarkable amino acid composition pattern that is not seen in other paramyxoviruses, but resembles certain motifs found in Orthopneumovirus G proteins.ConclusionsThe phylogenetic clustering of JPV, BeiPV and TlmPV with the viruses described here, as well as their shared features that set them apart from other paramyxoviruses, provide additional support for the recognition of the genus ‘Jeilongvirus’.