John H.-O Pettersson

John H.-O Pettersson
Uppsala University | UU · Department of Medical Biochemistry and Microbiology

PhD

About

75
Publications
10,830
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1,268
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Introduction
John H.-O Pettersson currently works at the Dept. of Medical Biochemistry and Microbiology, Uppsala University, Sweden; Sydney Institute for Infectious Diseases, the University of Sydney, Australia, and the Public Health Agency of Sweden. John does research in virus evolution and epidemiology, virome and pathogen discovery to which he applies NGS and bioinformatic related techniques.

Publications

Publications (75)
Article
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The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapp...
Article
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Male sex and advanced age are associated with severe symptoms of COVID-19. Sex and age also exhibit substantial associations with genome-wide DNA methylation (DNAm) differences in humans. Using a random sample of Illumina EPIC-based genome-wide methylomes from peripheral whole blood of 1,976 parents, participating in The Norwegian Mother, Father an...
Article
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The unprecedented pandemic COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with bats as original reservoirs, has once again highlighted the importance of exploring the interface of wildlife diseases and human health. In this study, we identified a novel Betacoronavirus from bank voles (Myodes glareolus) in Grimsö,...
Article
Intraspecies (homologous) phylogenetic incongruence, or ‘tree conflict’ between different loci within the same genome of mosquito-borne flaviviruses (MBFV), was first identified in dengue virus (DENV) and subsequently in Japanese encephalitis virus (JEV), St Louis encephalitis virus (SLEV), and Zika virus (ZIKV). Recently, the first evidence of phy...
Preprint
We identified a novel Betacoronavirus from bank voles (Myodes glareolus) in Grimso, Sweden. Repeated detection over three years and an overall prevalence of 3.4% suggests the virus commonly occurs in bank voles. Furthermore, phylogenetic analyses indicate the virus belongs to a highly divergent Embecovirus lineage predominantly associated with bank...
Article
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We explored how the duration, size and number of virus transmission clusters, defined as country-specific monophyletic groups in a SARS-CoV-2 phylogenetic tree, differed between the Nordic countries of Norway, Sweden, Denmark, Finland and Iceland. Our results suggest that although geographical connectivity, population density and openness influence...
Article
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The four mosquito-borne dengue virus serotypes (DENV1–DENV4) cause a high burden of disease throughout the tropical and sub-tropical regions of the world. Nevertheless, their precise epidemiological history in Africa, including when and where they originated and were distributed during the 20th century, remains unclear stressing the need for One He...
Article
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Sandfly-borne phleboviruses are distributed widely throughout the Mediterranean Basin, presenting a threat to public health in areas where they circulate. However, the true diversity and distribution of pathogenic and apathogenic sandfly-borne phleboviruses remains a key issue to be studied. In the Balkans, most published data rely on serology-base...
Article
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Background Many countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus. Aim We aimed to assess the du...
Preprint
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The Nordic countries, defined here as Norway, Sweden, Denmark, Finland and Iceland, are known for their comparable demographics and political systems. Since these countries implemented different COVID-19 intervention strategies, they provide a natural laboratory for examining how COVID-19 policies and mitigation strategies affected the propagation,...
Article
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Pathogens associated with haemorrhagic fever commonly have zoonotic origins. The first documented imported case of likely viral severe haemorrhagic fever in Sweden occurred in 1990. Despite extensive study, no aetiological agent was identified. Following retrospective investigation with total RNA-sequencing of samples collected between 7 and 36 day...
Chapter
This book is a collection of 77 expert opinions arranged in three sections. Section 1 on "Climate" sets the scene, including predictions of future climate change, how climate change affects ecosystems, and how to model projections of the spatial distribution of ticks and tick-borne infections under different climate change scenarios. Section 2 on "...
Preprint
Full-text available
Background Many countries have attempted to mitigate and control COVID-19 through the implementation of non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus. Aim To...
Article
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Background Whether type-specific human papillomavirus (HPV) infection influences the risk of acquiring infections with other HPV types is unclear. We studied concurrent HPV infections in 17-year-old girls from two birth cohorts; the first vaccine-eligible cohort in Norway and a pre-vaccination cohort. Methods Urine samples were collected and teste...
Article
Tick-borne encephalitis virus (TBEV) is a medically important arbovirus, widespread in Europe and Asia. The virus is primarily transmitted to humans and animals by bites from ticks and, in rare cases, by consumption of unpasteurized dairy products. The aim of this study was to sequence and characterize two TBEV strains with amplicon sequencing by d...
Preprint
Full-text available
The first imported case of severe haemorrhagic fever in Sweden was reported in 1990. Despite extensive diagnostic study, no aetiological agent was identified. Following retrospective investigation with total RNA-sequencing of plasma and urine samples collected during between 7 to 36 days from onset of symptoms, we identified dengue virus 3 (DENV-3)...
Article
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Background: Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful meth...
Article
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The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera - Hepacivirus, Pegivirus, Pestivirus and Flavivirus – each with a diverse host range. Members of the genus Hepacivirus are a...
Article
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Ticks (order: Ixodida) are a highly diverse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick (Ixodes uriae), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circump...
Article
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During an ongoing virome metagenomics project we identified hepatitis C virus (HCV) in a pool of recently blood-fed common bed bug (Cimex lectularius) nymphs sampled from domestic residences in Europe. Additional PCR and genomic analysis revealed that the virus was a member of HCV genotype 3A, one of the most prevalent genotypes in Europe. Although...
Preprint
Full-text available
The RNA virus family Flaviviridae harbours several important pathogens of humans and other animals, including Zika virus, dengue virus and hepatitis C virus. The Flaviviridae are currently divided into four genera, Hepacivirus, Pegivirus, Pestivirus and Flavivirus, each of which have a diverse host range. Members of the genus Hepacivirus are associ...
Preprint
Full-text available
Ticks (order: Ixodida) are a highly diverse and ecologically important group of ectoparasitic blood-feeding organisms. One such species, the seabird tick ( Ixodes uriae ), is widely distributed around the circumpolar regions of the northern and southern hemispheres. It has been suggested that Ix. uriae spread from the southern to the northern circu...
Article
Full-text available
Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spatial diffusion of H9N2 virus to, within, and from E...
Article
The tick‐borne encephalitis virus (TBEV), a zoonotic flaviviral infection, is endemic in large parts of Norway and Eurasia. Humans are mainly infected with TBEV via bites from infected ticks. In Norway, the main geographical distribution of ticks is along the Norwegian coastline from southeast (~59°N) and up to the southern parts of Nordland County...
Article
Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV...
Article
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Mosquitoes harbor an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes, little is known about the diversity and evolutionary history of RNA viruses sampled from mosquitoes in northerly regions. He...
Article
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Background Genomic GC content varies both within and, substantially, between microbial genomes. While some of this variation can be explained by evolutionary divergence and environmental factors, a notable portion is not understood. To investigate further, we explore a non-linear mathematical model (gcMOD) of single-nucleotide polymorphism (SNP) GC...
Preprint
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There is mounting evidence that mosquitoes harbour an extensive diversity of ‘insect-specific’ RNA viruses in addition to those important to human and animal health. However, because most studies of the mosquito virome have been conducted at lower latitudes there is a major knowledge gap on the genetic diversity, evolutionary history, and spread of...
Article
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Determining the etiological basis of central nervous system (CNS) infections is inherently challenging, primarily due to the multi-etiological nature. Using RNA sequencing, we aimed to identify microbes present in cerebrospinal fluid (CSF) of two patients suffering CNS infection, previously diagnosed with Cryptococcus sp. and Streptococcus pneumoni...
Article
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Hepatitis delta virus (HDV) is the smallest known RNA virus, encoding a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has a...
Article
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Bird-hosted viruses have the potential to be transported over large areas of the world and to be transmitted in distant geographical regions. Sindbis virus (SINV) is a mosquito-borne alphavirus that is locally amplified in a bird-mosquito enzootic cycle and distributed all over the Old World and Australia/Oceania. Sindbis virus genotype I (SINV-I)...
Article
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Background Hepatitis B virus (HBV) infection remains a serious global health challenge. The widespread distribution of HBV is highlighted by multiple HBV genotypes associated with different geographical origin and transmission patterns, as well as, clinical outcomes. Investigating population HBV genotype composition and origin is therefore highly w...
Article
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Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the differen...
Preprint
Full-text available
Hepatitis delta virus (HDV) is the smallest known RNA virus and encodes a single protein. Until recently, HDV had only been identified in humans, where it is strongly associated with co-infection with hepatitis B virus (HBV). However, the recent discovery of HDV-like viruses in metagenomic samples from birds and snakes suggests that this virus has...
Article
Full-text available
On the basis of population genomic and phylogeographic analyses of 1669 Mycobacterium tuberculosis lineage 4 (L4) genomes, we find that dispersal of L4 has been completely dominated by historical migrations out of Europe. We demonstrate an intimate temporal relationship between European colonial expansion into Africa and the Americas and the spread...
Article
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Background: Tick-borne encephalitis (TBE) is one tick-transmitted disease where the human incidence has increased in some European regions during the last two decades. We aim to find the most important factors causing the increasing incidence of human TBE in Sweden. Based on a review of published data we presume that certain temperature-related va...
Article
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Background: The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species' core genome GC content...
Article
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Based on serological evidence and viral isolation, Zika virus (ZIKV) has circulated for many years relatively benignly in a sylvatic cycle in Africa and an urban cycle in South East Asia (SEA). With the recent availability of limited but novel Indian ZIKV sequences to add to the plethora of SEA sequences, we traced the phylogenetic history and spat...
Article
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RNA viruses are abundant infectious agents and present in all domains of life. Arthropods, including ticks, are well known as vectors of many viruses of concern for human and animal health. Despite their obvious importance, the extent and structure of viral diversity in ticks is still poorly understood, particularly in Europe. Using a bulk RNA-sequ...
Article
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The recent global (re)emergence of arthropod-borne viruses (arboviruses), such as chikungunya and Zika virus, was widely reported in the media as though it was a new phenomenon. This is not the case. Arboviruses and other human microbial pathogens have been (re)emerging for centuries. The major difference today is that arbovirus emergence and dispe...
Article
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Background The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding...
Article
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Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10,000 to 15,000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV pers...
Article
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The "Beijing" Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is spreading globally and has been associated with accelerated disease progression and increased antibiotic resistance. Here we performed a phylodynamic reconstruction of one of the L2 sublineages, the central Asian clade (CAC), which has recently spread to western Europe. We find that r...
Article
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The unexpected emergence of Zika virus (ZIKV) in the Pacific Islands and Latin America and its association with congenital Zika virus syndrome (CZVS) (which includes microcephaly) and Guillain-Barré syndrome (GBS) have stimulated wide-ranging research. High densities of susceptible Aedes spp., immunologically naive human populations, global populat...
Article
Background and aims: On-going risk behaviour can lead to hepatitis C virus (HCV) reinfection following successful treatment. We aimed to assess the incidence of persistent HCV reinfection in a population of people who inject drugs (PWID) who had achieved sustained virological response (SVR) seven years earlier. Methods: In 2004-2006 we conducted...
Article
Tick-borne encephalitis (TBE) is the most important viral tick-borne disease in Europe and can cause severe disease in humans. In Norway, human cases have been reported only from the southern coast. The aim of this study was to investigate the prevalence of tick-borne encephalitis virus (TBEV) in questing Ixodes ricinus ticks from the north-western...
Article
The genus Flavivirus includes some of the most important human viral pathogens and its members are found in all parts of the populated world. The temporal origin of diversification of the genus has for long been debated due to the inherent problems with dating deep RNA virus evolution. A generally accepted hypothesis suggests that Flavivirus emerge...