Jonas Blomberg

Uppsala University | UU · Department of Medical Sciences

Viruses in the family Retroviridae are found in a wide variety of vertebrate hosts. Enveloped virions are 80–100 nm in diameter with an inner core containing the viral genome and replicative enzymes. Core morphology is often characteristic for viruses within the same genus. Replication involves reverse transcription and integration into host cell D...

Background: Endogenous Retroviruses (ERVs) constitute approximately 8% of every human genome and are relics of ancestral infections that affected the germ line cells. The ERV-W group contributed to primate physiology by providing an envelope protein (Syncytin-1) that has been adopted for placenta development in hominoids. Expression of Human ERV-W...

Background The genomes of all vertebrates harbor remnants of ancient retroviral infections, having affected the germ line cells during the last 100 million years. These sequences, named Endogenous Retroviruses (ERVs), have been transmitted to the offspring in a Mendelian way, being relatively stable components of the host genome even long after the...

Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also...

Tick-borne encephalitis virus (TBEV) is an important European vaccine-preventable pathogen. Discrimination of vaccine-induced antibodies from those elicited by infection is important. We studied anti-TBEV IgM/IgG responses, including avidity and neutralisation, by multiplex serology in 50 TBEV patients and 50 TBEV vaccinees. Infection induced antib...

Background About half of the human genome is constituted of transposable elements, including human endogenous retroviruses (HERV). HERV sequences represent the 8% of our genetic material, deriving from exogenous infections occurred millions of years ago in the germ line cells and being inherited by the offspring in a Mendelian fashion. HERV-K eleme...

The recent spread of Zika virus (ZIKV) in the Americas and Asia necessitates an increased preparedness for improved maternal and perinatal health and blood safety. However, serological cross-reactions, especially to Dengue virus (DENV), complicate ZIKV antibody serodiagnosis. A novel “pan-Flavi” suspension multiplex immunoassay (PFSMIA) using 25 an...

Introduction: Hantaviruses are globally distributed zoonotic pathogens. Great diversity and high antigenic cross-reactivity makes diagnosis by traditional methods cumbersome. Materials and methods: ‘Megapeptides’, 119–120-mers from the amino terminus of the nucleoprotein of 16 hantaviruses, representing the four major branches of the hantavirus phy...

Human herpesviruses have previously been implicated in the pathogenesis of Alzheimer’s disease (AD) but whether they are causal, facilitating, or confounding factors is yet to be established. A total of 50 AD subjects and 52 non-demented (ND) controls were analyzed in a multiplex assay for IgG reactivity toward herpes simplex virus (HSV), varicella...

Human endogenous retroviruses (HERVs) represent the inheritance of ancient germ-line cell infections by exogenous retroviruses and the subsequent transmission of the integrated proviruses to the descendants. ERVs have the same internal structure as exogenous retroviruses. While no replication-competent HERVs have been recognized, some retain up to...

Background Human endogenous retroviruses (HERVs) are ancient sequences integrated in the germ line cells and vertically transmitted through the offspring constituting about 8 % of our genome. In time, HERVs accumulated mutations that compromised their coding capacity. A prominent exception is HERV-W locus 7q21.2, producing a functional Env protein...

Background: Antibodies to microbes, or to autoantigens, are important markers of disease. Antibody detection (serology) can reveal both past and recent infections. There is a great need for development of rational ways of detecting and quantifying antibodies, both for humans and animals. Traditionally, serology using synthetic antigens covers line...

Multiple sclerosis (MS) is a neurological disease of unknown aetiology. Several research groups reported an increased level of human endogenous retroviruses HERV-W and HERV-H RNAs in cerebrospinal fluid, plasma and supernatants of cell cultures from MS individuals. To quantify the abundance of extracellular virion-associated HERV, RNAs in blood, pl...

Objectives: Infectious gastroenteritis is one of the most common diseases among children and has a considerable impact on health and socio-economy. Day care centres are high-risk environments for infections. The aim of this study was to investigate if asymptomatic preschool children constitute a reservoir for potential enteropathogens. Study desi...

We studied HERV expression in cell lines after hypoxia, mitogenic stimulation, and demethylation, to better understand if hypoxia may play a role in ERV activation also within the nervous system, as represented by neuroblastoma cell lines. The level of RNA of four human ERV groups (HERVs) (HERVE, I/T, H, and W), and three housekeeping genes, of dif...

Background: Human parvovirus B19 (B19V), cytomegalovirus (CMV) and Toxoplasma gondii (T. gondii) may cause intrauterine infections with potentially severe consequences to the fetus. Current serodiagnosis of these infections is based on detection of antibodies most often by EIA and individually for each pathogen. We developed singleplex and multipl...

The high sequence variation of RNA viruses necessitates use of degenerate primers and probes or multiple primers and probes in molecular diagnostic assays. We showed previously that PCR amplification in two rounds, first with long target-specific primers and then with short generic primers, followed by detection using long probes, can tolerate sequ...

Exposure to Ljungan virus (LV) is implicated in the risk of autoimmune (type 1) diabetes but possible contribution by other parechoviruses is not ruled out. The aim was to compare children diagnosed with type 1 diabetes in 2005-2011 (n = 69) with healthy controls (n = 294), all from the Jämtland County in Sweden, using an exploratory suspension mul...

Rotavirus infections are one of the most common reasons for hospitalizations due to gastrointestinal diseases. Rotavirus is often diagnosed by latex agglutination assay, chromatography immunoassay, or by electron microscopy, which are all quite insensitive. Reverse transcription polymerase chain reaction, on the other hand, is very sensitive to var...

About 8% of the human genome is composed by Endogenous Retrovirus sequences (HERVs) that after an ancestral infection have been integrated in the germ line cells and vertically transmitted through the offspring. The HERVW group belongs to class I Gammaretroviruses and one provirus, named locus ERVWE1, has a full length sequence producing a function...

About 8% of our genome is composed by Endogenous Retrovirus sequences (HERVs), integrated in germ line cells and vertically transmitted through the offspring. The HERVW group belongs to class I Gammaretroviruses and one provirus, locus ERVWE1, has a full length sequence producing a functional env protein, Syncytin-1, coopted during evolution for th...

Epidemiology and transmission patterns of hepatitis C virus (HCV) are important subjects as we enter a new era of treatment with directly acting antivirals (DAAs). The highest prevalence of HCV in developed countries is found among intravenous drug users (IDUs), where unsafe needle sharing practices provide the main route of infection. Efforts to p...

Myalgic encephalomyelitis (ME, also called Chronic Fatigue Syndrome), a common disease with chronic fatigability, cognitive dysfunction and myalgia of unknown etiology, often starts with an infection. The chaperonin human heat shock protein 60 (HSP60) occurs in mitochondria and in bacteria, is highly conserved, antigenic and a major autoantigen. Th...

Background: Long terminal repeats (LTRs, consisting of U3-R-U5 portions) are important elements of retroviruses and related retrotransposons. They are difficult to analyse due to their variability.The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible. Results: Hidden Markov models (H...

Long weblogo of Sire. Long weblogo for a Viterbi alignment of the Sire training set. Conventions as in Figure 1. Figure S2. Long weblogo of Gamma. Long weblogo for a Viterbi alignment of the Gamma training set. Conventions as in Figure 1. Figure S3. Long weblogo of class III retroviruses. Long weblogo for a Viterbi alignment of the training set of...

Constituents of the internal coding sequence clusters for Metaviridae and Pseudoviridae as generated by the CLANS software. Table S2. Constituents of the training set for the LTR HMMs presented in this paper, and the previous paper (Benachenhou et al. [21]).

The multiplexing qualities of padlock probes and Luminex™ technology combined with the well-established quantitative feature of qPCR were the base for a ten-plex fungal detection protocol that quantitatively reveals ten different fungal species in a single experiment. Padlock probes are oligonucleotides designed to form circular DNA when hybridizin...

By combining the multiplexing qualities of padlock probes and Luminex™ (Luminex Corporation, Austin, Texas, USA) technology, together with the well-established quantitative feature of qPCR, a ten-plex fungal detection protocol that quantitatively reveals ten different fungal species in a single experiment has been devised. Padlock probes are oligon...

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from...

The 27 most intact avian ERVs and their relationships to avian and nonavian retroviruses described earlier. Among the 1,863 avian proviruses, 27 had fewer than three stops or frameshifts in the gag and pol genes and fewer than two stops or frameshifts in their pro genes. The 27 included 2 alpha (of which 1 in the turkey genome was rather alphabeta-...

Genome charts of representatives of the avian ERV clades produced by ReTe. The presence of a GPY/F motif, the number of zinc fingers, the presence of a dUTPase, and gag/pro and pro/pol frameshifts are indicated. Download Figure S5, TIF file, 2.9 MB.

A more detailed version of the ME tree of 128 selected avian ERV Pol sequences shown manually simplified in Fig. 1. Provirus colors: yellow, chicken; blue, turkey; red, zebra finch. Each of the 128 avian ERV branches is labeled with the chromosome number, the host (t, zebra finch; g, chicken; m, turkey), chromosomal position, ReTe-suggested genus,...

Motif usage in the 10 avian ERV clades. For each conserved retroviral motif group, ReTe has a library which covers most or all of the seven retroviral genera. The best-fitting motif is chosen during the analysis of a putative proviral chain. The average number of motifs per genus is a rough indicator of which genus the chain (provirus) belongs to....

A 900- to 1,000-bp pro/pol partial nucleotide sequence from the avian ERV consensuses and their best representatives (magenta) were aligned by MUSCLE with 136 pro/pol sequences from three publications of the Tristem group (R. Gifford et al., J. Virol. 79:6478–6486, 2005; E. Herniou et al., J. Virol. 72:5955–5966, 1998; J. Martin et al., J. Virol. 7...

Characteristics of avian retroviral clades. These clades were derived from the tree in Fig. S1. This classification is different from the initial ReTe-based classification in Table 1. Membership was determined after BLASTing the entire 1,863-provirus set with consensus sequences as described in Materials and Methods. Most of the avibeta2 and some o...

Characteristics of minor avian retroviral clades previously described by others. These proviruses were identified in the larger set of 1,863 proviruses. Clades ChirRV1 and FET1 bordered and partially overlapped avigamma1. The other clades did not overlap the clades identified in Table S1. The relationships between these clades and other avian and n...

Endogenous retroviruses (ERVs) were identified and characterized in three avian genomes to gain insight into early retroviral evolution. Using the computer program RetroTector to detect relatively intact ERVs, we identified 500 ERVs in the chicken genome, 150 in the turkey genome, and 1,200 in the zebra finch genome. Previous studies suggested that...

In contrast to ordinary PCRs, which have a limited multiplex capacity and often return false-negative results due to target variation or inhibition, our new detection strategy, VOCMA (variation-tolerant capture multiplex assay), allows variation-tolerant, target-specific capture and detection of many nucleic acids in one test. Here we demonstrate t...

Many syndromes have a large number of differential diagnoses, a situation which calls for multiplex diagnostic systems. Myalgic encephalomyelitis (ME), also named chronic fatigue syndrome (CFS), is a common disease of unknown etiology. A mouse retrovirus, xenotropic murine leukemia-related virus (XMRV), was found in ME/CFS patients and blood donors...

Feline infectious peritonitis is one of the most severe devastating diseases of the Felidae. Upon the appearance of clinical signs, a cure for the infected animal is impossible. Therefore rapid and proper diagnosis for both the presence of the causative agent, feline coronavirus (FCoV) and the manifestation of feline infectious peritonitis is of pa...

4 1 Vilniaus universiteto Medicinos fakulteto Infekcinių, krūtinės ligų, dermatovenerologijos ir alergologijos klinika 2 Upsalos universiteto Medicinos mokslų departamento Infekcinių ligų klinika, Švedija 3 Vilniaus universiteto Medicinos fakulteto Akušerijos ir ginekologijos klinika 4 Upsalos universiteto Medicinos mokslų departamento Klinikinės v...

614 Eglė Aukštuolienė VU MF Infekcinių ir krūtinės ligų, dermatovenerologijos ir alergologijos klinika Kairiūkščio g. 2, Vilnius 4 1 Vilniaus universiteto Medicinos fakulteto Infekcinių, krūtinės ligų, dermatovenerologijos ir alergologijos klinika 2 Upsalos universiteto Medicinos mokslų departamento Infekcinių ligų klinika, Švedija 3 Vilniaus unive...

Parallel Session 6: Xenozoonoses

Detailed list of the members of the G1–G3 groups. (PDF)

Xenotropic cell culture contaminating retroviruses and the uniqueness of 22RV1/XMRV. (DOC)

Phylogenetic trees supporting the G1–G3 groups, and the G3 subgroups (poly-, modified poly- and xenotropic), as well as ecotropic, MERVs. Relationship to other MLV-related gammaretroviruses. (PDF)

Development of the gag and env RTQPCR; Evolutionary conservation of target sequences. (PDF)

The G1–G3 groups. Properties and consensus sequences. (DOC)

The recent report of gammaretroviruses of probable murine origin in humans, called xenotropic murine retrovirus related virus (XMRV) and human murine leukemia virus related virus (HMRV), necessitated a bioinformatic search for this virus in genomes of the mouse and other vertebrates, and by PCR in humans. Three major groups of murine endogenous gam...

Gammaretrovirus-like sequences occur in most vertebrate genomes. Murine Leukemia Virus (MLV) like retroviruses (MLLVs) are a subset, which may be pathogenic and spread cross-species. Retroviruses highly similar to MLLVs (xenotropic murine retrovirus related virus (XMRV) and Human Mouse retrovirus-like RetroViruses (HMRVs)) reported from patients su...

Diagnosis of infectious diseases often requires demonstration of antibodies to the microbe (serology). A large set of antigens, covering viruses, bacteria, fungi and parasites may be needed. Recombinant proteins have a prime role in serological tests. Suspension arrays offer high throughput for simultaneous measurement of many different antibodies....

The following series of concise summaries addresses the evolution of infectious agents in relation to sex in animals and humans from the perspective of three specific questions: (1) what have we learned about the likely origin and phylogeny, up to the establishment of the infectious agent in the genital econiche, including the relative frequency of...

Estimation of CfERV-containing gaps distribution per chromosome in the dog genome. Chromosomal size and number of reported annotations is displayed alongside the estimation of fragment gaps which possibly contain a total or partial CfERV as well as the variation of Ns annotated in the agp file between the different categories. (DOC)