Sofie Midgley

Recombination in the Genesis and Evolution of Hepatitis B Virus Genotypes

ABSTRACT Hepatitis B virus (HBV) infection is widely distributed in both human and ape populations throughout the world and is a major cause of human morbidity and mortality. HBV variants are currently classified into the human genotypes A to H and species-associated chimpanzee and gibbon/orangutan groups. To examine the role of recombination in the evolution of HBV, large-scale data retrieval and automated phylogenetic analysis (TreeOrder scanning) were carried out on all available published complete genome sequences of HBV. We detected a total of 24 phylogenetically independent potential recombinants (different genotype combinations or distinct breakpoints), eight of which were previously undescribed. Instances of intergenotype recombination were observed in all human and ape HBV variants, including evidence for a novel gibbon/genotype C recombinant among HBV variants from Vietnam. By recording sequence positions in trees generated from sequential fragments across the genome, violations of phylogeny between trees also provided evidence for frequent intragenotype recombination between members of genotypes A, D, F/H, and gibbon variants but not in B, C, or the Asian B/C recombinant group. In many cases, favored positions for both inter- and intragenotype recombination matched positions of phylogenetic reorganization between the human and ape genotypes, such as the end of the surface gene and the core gene, where sequence relationships between genotypes changed in the TreeOrder scan. These findings provide evidence for the occurrence of past, extensive recombination events in the evolutionary history of the currently classified genotypes of HBV and potentially in changes in its global epidemiology and associations with human disease.

Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance network

EuroRotaNet, a laboratory network, was established in order to determine the diversity of co-circulating rotavirus strains in Europe over three or more rotavirus seasons from 2006/2007 and currently includes 16 countries. This report highlights the tremendous diversity of rotavirus strains co-circulating in the European population during three years of surveillance since 2006/2007 and points to the possible origins of these strains including genetic reassortment and interspecies transmission. Furthermore, the ability of the network to identify strains circulating with an incidence of ≥1% allowed the identification of possible emerging strains such as G8 and G12 since the beginning of the study; analysis of recent data indicates their increased incidence. The introduction of universal rotavirus vaccination in at least two of the participating countries, and partial vaccine coverage in some others may provide data on diversity driven by vaccine introduction and possible strain replacement in Europe.

Rotavirus Surveillance in Europe, 2005–2008: Web-Enabled Reporting and Real-Time Analysis of Genotyping and Epidemiological Data

BACKGROUND The first European rotavirus surveillance network, EuroRotaNet, comprising 16 laboratories in 15 European countries, has been established. METHODS Fecal samples from gastroenteritis cases positive for group A rotavirus antigen were collected from multiple European countries from 2005 to mid-2008 and were subjected to G and P genotyping. Epidemiological data collected included age, sex, geographical location, setting, dates of onset and sample collection, and clinical symptoms. RESULTS A total of 8879 rotavirus-positive samples were characterized: 2129 cases were from the 2005-2006 season, 4030 from the 2006-2007 season, and 2720 from the ongoing 2007-2008 season. A total of 30 different G and P type combinations of strains circulated in the region from 2005 through 2008. Of these strains, 90% had genotypes commonly associated with human infections-G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]-and 1.37% represented potential zoonotic introductions. G1P[8] remained the most prevalent genotype in Europe as a whole, but the incidence of infection with G1P[8] rotavirus strains was <50% overall, and all 3 seasons were characterized by a significant diversity of cocirculating strains. The peak incidence of rotavirus infection occurred from January through May, and 81% of case patients were aged <2.5 years. Conclusions. Data gathered through EuroRotaNet will provide valuable background information on the rotavirus strain diversity in Europe before the introduction of rotavirus vaccines, and the network will provide a robust method for surveillance during vaccine implementation.

Diversity and zoonotic potential of rotaviruses in swine and cattle across Europe

Group A rotaviruses can infect both humans and animals. Individual rotavirus strains can occasionally cross species barriers and might hereby contribute to the emergence of new genotypes in heterologous hosts. The incidence and impact of zoonotic rotavirus are not well defined, and one reason for this is a lack of data about strains circulating in suspected reservoir animal hosts. In this study we report the incidence, genetic diversity, and molecular epidemiology of rotaviruses detected in domestic cattle and swine in 6 European countries. From 2003 to 2007, 1101 and more than 2000 faecal specimens were collected from swine and cattle, both healthy and diarrhoeic, and tested for rotaviruses. Viruses from positive stools were genotyped and a subset of strains was characterized by nucleotide sequencing and phylogenetic analysis of the VP7 (G) and VP4 (P) genes. Rotaviruses were detected in 43% of bovine samples and in 14% of porcine samples. In cattle, 10 different combinations of G and P types were identified and the most common strains were G6P[11] and G6P[5]. In swine, the number of identified G-P combinations was higher (n=21), however, no single combination was predominant across Europe. Newly described genotype specificities, P[27] and P[32], were identified in swine. When compared at the nucleotide sequence level, the identified porcine rotavirus strains and contemporary human strains grouped together phylogenetically, whereas bovine rotavirus strains formed separate clades. These data demonstrate large genetic diversity of porcine and bovine rotavirus strains across Europe, and suggest that livestock herds may serve as potential reservoirs for human infections.

Human parechovirus infection, Denmark.

HPeV should be tested for in all young children suspected to have HPeV or enterovirus infection.

Ongoing multi-strain food-borne hepatitis A outbreak with frozen berries as suspected vehicle: four Nordic countries affected, October 2012 to April 2013.

A food-borne outbreak of hepatitis A in Denmark was notified to other countries on 1 March 2013. A case-control study identified frozen berries eaten in smoothies as potential vehicle. In the following weeks, Finland, Norway and Sweden also identified an increased number of hepatitis A patients without travel history. Most cases reported having eaten frozen berries at the time of exposure. By 17 April, 71 cases were notified in the four countries. No specific type of berry, brand or origin of berries has yet been identified. .

Genetic diversity of sapovirus infections in Danish children 2005-2007.

BACKGROUND Sapoviruses are known to cause gastroenteritis mainly in young children. OBJECTIVES To establish a collection of sapoviruses and to gain knowledge about the genetic diversity and epidemiology of sapoviruses circulating in children in Denmark. STUDY DESIGN During a 24-month period in 2005-2007 samples from 1104 children, aged 0-3 years, submitted for acute gastroenteritis diagnostics, were analysed for sapoviruses by real-time PCR. Genotyping of positive findings was carried out by sequencing part of the capsid gene, and in several cases also part of the polymerase gene. RESULTS Sapoviruses were detected in stool samples from 97 children (9%), with the highest prevalence in the 7-18 months age group. Viruses from three genogroups and seven genotypes were found. Genotype I.1 was demonstrated in half of the positive samples and was observed throughout the study period. The less common types seemed to appear during shorter periods, often in succession of each other. Positive samples were detected throughout the study period. The only months, in both years studied, with high proportions of positive samples were September, November and February. CONCLUSIONS Sapoviruses were commonly found in children with gastroenteritis in Denmark. No clear seasonal pattern could be seen. Genotype I.1 was clearly the most common genotype found, but several other genotypes circulated during shorter periods.

Clinical and virological features of enterovirus 71 infections in Denmark, 2005 to 2008.

Abstract Background: Since the late 1990s enterovirus 71 (EV71) has caused epidemics of hand, foot and mouth disease with fatal cases especially in the Asian Pacific region. The objective of this study was to describe the clinical and virological features of EV71 infections in Denmark. Methods: All enterovirus-positive samples in Denmark are submitted to the National Poliovirus Laboratory for typing, and the EV71-positive samples are characterized by sequencing and phylogenetic analysis. Clinical information was gathered for the EV71-positive patients. Results: During 2005–2008, EV71 was demonstrated in 29 patients. In 2007 EV71 was the second most common enterovirus type detected in Denmark. Twenty-one of the 29 patients were children aged ≤1 y, 24 were hospitalized, and meningitis was the most common diagnosis. Gastroenteritis and hand, foot and mouth disease were other common clinical manifestations, but no fatal cases or cases of pulmonary oedema were seen. A novel subgenotype in Europe, B5, dominated the 2007 outbreak, but co-circulated with subgenotypes C1 and C2. Conclusions: In conclusion EV71 was among the common enterovirus types in Denmark, and in 2007 a novel subgenotype, B5, was observed. EV71 was mainly diagnosed in infants, and the majority of patients were hospitalized with meningitis.

Emergence of enterovirus D68 in Denmark, June 2014 to February 2015.

From June 2014 through February 2015, respiratory samples from 130 Danish patients were screened for enterovirus D68 (EV-D68). Fourteen EV-D68 cases were detected, of which 12 presented with respiratory symptoms, and eight had known underlying disease. The median age of EV-D68 cases was three years (interquartile range: 0–30 years). Acute flaccid paralysis (AFP) was not detected although Danish EV-D68 strains showed > 98% nt identity with EV-D68-strains from AFP cases from the United States and France.

Suspected zoonotic transmission of rotavirus group A in Danish adults.

Group A rotaviruses infect humans and a variety of animals. In July 2006 a rare rotavirus strain with G8P[14] specificity was identified in the stool samples of two adult patients with diarrheoa, who lived in the same geographical area in Denmark. Nucleotide sequences of the VP7, VP4, VP6, and NSP4 genes of the identified strains were identical. Phylogenetic analyses showed that both Danish G8P[14] strains clustered with rotaviruses of animal, mainly, bovine and caprine, origin. The high genetic relatedness to animal rotaviruses and the atypical epidemiological features suggest that these human G8P[14] strains were acquired through direct zoonotic transmission events.