| 1. |
- Albinsson, Bo, et al.
(författare)
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Seroprevalence of tick-borne encephalitis virus and vaccination coverage of tick-borne encephalitis, Sweden, 2018 to 2019
- 2024
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Ingår i: Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin. - : European Centre for Disease Control and Prevention (ECDC). - 1560-7917 .- 1025-496X. ; 29:2
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIn Sweden, information on seroprevalence of tick-borne encephalitis virus (TBEV) in the population, including vaccination coverage and infection, is scattered. This is largely due to the absence of a national tick-borne encephalitis (TBE) vaccination registry, scarcity of previous serological studies and use of serological methods not distinguishing between antibodies induced by vaccination and infection. Furthermore, the number of notified TBE cases in Sweden has continued to increase in recent years despite increased vaccination.AimThe aim was to estimate the TBEV seroprevalence in Sweden.MethodsIn 2018 and 2019, 2,700 serum samples from blood donors in nine Swedish regions were analysed using a serological method that can distinguish antibodies induced by vaccination from antibodies elicited by infection. The regions were chosen to reflect differences in notified TBE incidence.ResultsThe overall seroprevalence varied from 9.7% (95% confidence interval (CI): 6.6-13.6%) to 64.0% (95% CI: 58.3-69.4%) between regions. The proportion of vaccinated individuals ranged from 8.7% (95% CI: 5.8-12.6) to 57.0% (95% CI: 51.2-62.6) and of infected from 1.0% (95% CI: 0.2-3.0) to 7.0% (95% CI: 4.5-10.7). Thus, more than 160,000 and 1,600,000 individuals could have been infected by TBEV and vaccinated against TBE, respectively. The mean manifestation index was 3.1%.ConclusionA difference was observed between low- and high-incidence TBE regions, on the overall TBEV seroprevalence and when separated into vaccinated and infected individuals. The estimated incidence and manifestation index argue that a large proportion of TBEV infections are not diagnosed.
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| 2. |
- Haars, Jonathan, et al.
(författare)
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Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023
- 2023
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Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 11:10
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Tidskriftsartikel (refereegranskat)abstract
- Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.
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| 3. |
- Naguib, Mahmoud, et al.
(författare)
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A Comparison of Host Responses to Infection with Wild-Type Avian Influenza Viruses in Chickens and Tufted Ducks
- 2023
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Ingår i: Microbiology Spectrum. - : American Society for Microbiology. - 2165-0497. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Cross-species transmission of influenza A virus (IAV) from wild waterfowl to poultry is the first step in a chain of events that can ultimately lead to exposure and infection of humans. Herein, we study the outcome of infection with eight different mallard-origin IAV subtypes in two different avian hosts: tufted ducks and chickens. We found that infection and shedding patterns as well as innate immune responses were highly dependent on viral subtypes, host species, and inoculation routes. For example, intraoesophageal inoculation, commonly used in mallard infection experiments, resulted in no infections in contrast to oculonasal inoculation, suggesting a difference in transmission routes. Despite H9N2 being endemic in chickens, inoculation of mallard-origin H9N2 failed to cause viable infection beyond 1 day postinfection in our study design. The innate immune responses were markedly different in chickens and tufted ducks, and despite the presence of retinoic acid-inducible gene-I (RIG-I) in tufted duck transcriptomes, it was neither up nor downregulated in response to infection. Overall, we have revealed the heterogeneity of infection patterns and responses in two markedly different avian hosts following a challenge with mallard-origin IAV. These virus-host interactions provide new insights into important aspects of interspecies transmission of IAV.IMPORTANCE Our current findings highlight important aspects of IAV infection in birds that have implications for our understanding of its zoonotic ecology. In contrast to mallards where the intestinal tract is the main site of IAV replication, chickens and tufted ducks show limited or no signs of intestinal infection suggesting that the fecal-oral transmission route might not apply to all bird IAV host species. Our results indicate that mallard-origin IAVs undergo genetic changes upon introduction into new hosts, suggesting rapid adaptation to a new environment. However, similar to the mallard, chickens and tufted ducks show a limited immune response to infection with low pathogenic avian influenza viruses. These findings and future studies in different IAV hosts are important for our understanding of barriers to IAV transmission between species and ultimately from the wild reservoir to humans. Our current findings highlight important aspects of IAV infection in birds that have implications for our understanding of its zoonotic ecology. In contrast to mallards where the intestinal tract is the main site of IAV replication, chickens and tufted ducks show limited or no signs of intestinal infection suggesting that the fecal-oral transmission route might not apply to all bird IAV host species.
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| 4. |
- Skog, Erik, et al.
(författare)
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An oseltamivir-resistant avian H1N1 influenza A virus can transmit from mallards to chickens similarly to a wild-type strain : implications for the risk of resistance transmission to humans
- 2023
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Ingår i: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 104:4
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Tidskriftsartikel (refereegranskat)abstract
- The neuraminidase inhibitor (NAI) oseltamivir is stockpiled globally as part of influenza pandemic preparedness. However, oseltamivir carboxylate (OC) resistance develops in avian influenza virus (AIV) infecting mallards exposed to environmental-like OC concentrations, suggesting that environmental resistance is a real concern. Herein we used an in vivo model to investigate if avian influenza H1N1 with the OC-resistant mutation NA-H274Y (51833/H274Y) as compared to the wild-type (wt) strain (51833 /wt) could transmit from mallards, which would potentially be exposed to environmentally contaminated environments, to and between chickens, thus posing a potential zoonotic risk of antiviral-resistant AIV. Regardless of whether the virus had the OC-resistant mutation or not, chickens became infected both through experimental infection, and following exposure to infected mallards. We found similar infection patterns between 51833/wt and 51833/H274Y such that, one chicken inoculated with 51833/wt and three chickens inoculated with 51833/H274Y were AIV positive in oropharyngeal samples more than 2 days consecutively, indicating true infection, and one contact chicken exposed to infected mallards was AIV positive in faecal samples for 3 consecutive days (51833/wt) and another contact chicken for 4 consecutive days (51833/H274Y). Importantly, all positive samples from chickens infected with 51833/H274Y retained the NA-H274Y mutation. However, none of the virus strains established sustained transmission in chickens, likely due to insufficient adaptation to the chicken host. Our results demonstrate that an OC-resistant avian influenza virus can transmit from mallards and replicate in chickens. NA-H274Y does not constitute a barrier to interspecies transmission per se, as the resistant virus did not show reduced replicative capacity compared to the wild-type counterpart. Thus, responsible use of oseltamivir and surveillance for resistance development is warranted to limit the risk of an OC-resistant pandemic strain.
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| 5. |
- Valeckova, Eliska, et al.
(författare)
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Intestinal colonization with Campylobacter jejuni affects broiler gut microbiota composition but is not inhibited by daily intake of Lactiplantibacillus plantarum
- 2023
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Lactobacilli may prevent broilers from colonization with Campylobacter spp. and other gram-negative zoonotic bacteria through lactic acid production and modulation of the intestinal microbiota. This study evaluated the effects of daily intake of Lactiplantibacillus plantarum 256 (LP256) on Campylobacter jejuni (C. jejuni) loads in ceca and feces of C. jejuni challenged broilers, together with the changes in the gut microbiota.Methods: Two experiments were conducted using the broilers Ross 308 (R-308; Experiment 1) for 42 days and Rowan Ranger broilers (RR; Experiment 2) for 63 days. The LP256 strain was administered either via silage inoculated with LP256 or direct supplementation in the drinking water. Concurrently, haylage as a forage similar to silage but without any inoculum was tested. C. jejuni loads in fecal matter and cecal content were determined by plate counts and qPCR, respectively. The cecal microbiota, in response to treatments and the challenge, were assessed by 16S rRNA sequencing.Results and Discussion: Culturing results displayed a significant reduction in C. jejuni colonization (2.01 log) in the silage treatment in comparison to the control at 1 dpi (day post-infection) in Experiment 1. However, no treatment effect on C. jejuni was observed at the end of the experiment. In Experiment 2, no treatment effects on C. jejuni colonization were found to be statistically significant. Colonization load comparison at the peak of infection (3 dpi) to that at the end of the trial (32 dpi) revealed a significant reduction in C. jejuni in all groups, regardless of treatment. Colonization dynamics of C. jejuni in the cecal samples analyzed by qPCR showed no difference between any of the treatments in Experiment 1 or 2. In both experiments, no treatment effects on the cecal microbiota were observed. However, proportional changes in the bacterial composition were observed after the C. jejuni challenge, suggesting that colonization affected the gut microbiota. Overall, the daily intake of LP256 was not effective in reducing C. jejuni colonization in either broiler type at the end of the rearing period and did not cause any significant changes in the birds' cecal microbiota composition.
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| 6. |
- Wasberg, Anishia, et al.
(författare)
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Assessing compatibility and viral fitness between poultry-adapted H9N2 and wild bird-derived neuraminidases
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Exchange of viral segments between one or more influenza virus subtypes can contribute to a shift in virulence and adaptation to new hosts. Among several influenza subtypes, H9N2 is widely circulating in poultry populations worldwide and has the ability to infect humans. Here, we studied the reassortant compatibility between chicken H9N2 with N1-N9 gene segments of wild bird origin, either with an intact or truncated stalk. Naturally occurring amino acid deletions in the NA stalk of the influenza virus can lead to increased virulence in both mallard ducks and chickens. Our findings show extended genetic compatibility between chicken H9Nx gene segments and the wild-bird NA with and without 20 amino acid stalk deletion. Replication kinetics in avian, mammalian and human cell lines revealed that parental chH9N2 and rH9N6 viruses with intact NA-stalk replicated significantly better in avian DF1 cells compared to human A549 cells. After introducing a stalk deletion, an enhanced preference for replication in mammalian and human cell lines could be observed for rH9N2(Delta)(H6), rH9N6(Delta) and rH9N9(Delta) compared to the parental chH9N2 virus. This highlights the potential emergence of novel viruses with variable phenotypic traits, warranting the continuous monitoring of H9N2 and co-circulating subtypes in avian hosts.
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| 7. |
- Adel, Amany, et al.
(författare)
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Genetic Variations among Different Variants of G1-like Avian Influenza H9N2 Viruses and Their Pathogenicity in Chickens
- 2022
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Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.
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| 8. |
- Mannsverk, Steinar, et al.
(författare)
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SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing
- 2022
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Ingår i: Virology Journal. - : Springer Nature. - 1743-422X. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures.Methods: We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021.Results: The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes.Conclusion: Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences.
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| 9. |
- Martinell, Mats, 1971-, et al.
(författare)
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In-Flight Transmission of a SARS-CoV-2 Lineage B.1.617.2 Harbouring the Rare S:E484Q Immune Escape Mutation
- 2022
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Ingår i: Viruses. - : MDPI. - 1999-4915. ; 14:3
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Tidskriftsartikel (refereegranskat)abstract
- We describe a flight-associated infection scenario of seven individuals with a B.1.617.2 (Delta) lineage, harbouring an S:E484Q point mutation. In Sweden, at least 10% of all positive SARS-CoV-2 samples were sequenced in each county; the B.1.717.2 + S:E484Q combination was not detected in Sweden before and was imported within the scenario described in this report. The high transmission rate of the delta lineage combined with the S:E484Q mutation, associated with immune escape in other lineages, makes this specific genetic combination a possible threat to the global fight against the COVID-19 pandemic. Even within the Omicron wave, the B.1.617.2 + S:E484Q variant appeared in community samples in Sweden, as it seems that this combination has an evolutionary gain compared to other B.1.617.2 lineages. The here described genomic combination was not detectable with the common fasta file-based Pango-lineage analysis, hence increasing the probability of the true global prevalence to be higher.
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| 10. |
- Mourkas, Evangelos, et al.
(författare)
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Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter
- 2022
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd.. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus Campylobacter, there are species with divergent ecologies, from rarely isolated single-host specialists to multihost generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterizing these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analyzing recipient and donor population ancestry among genomes from 30 Campylobacter species, we show that cohabitation in the same host can lead to a six-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT.
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| 11. |
- Persson, Sofia, 1988-
(författare)
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Improved methodologies for molecular detection and quantification of viruses in food
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Foodborne viruses such as norovirus, hepatitis A virus and hepatitis E virus cause a high burden of disease worldwide. Reverse transcription (RT) quantitative real-time PCR (qPCR) is the current standard method for monitoring viral contamination in the food chain. However, quantitative detection of viruses in food is challenging and RT-qPCR has several limitations, for example in terms of biased quantification and high variability of results. Therefore, there is a high need for further developments to provide reliable data for official controls, risk assessments and surveillance studies.The aim of this thesis was to develop, improve and validate methods for molecular detection and quantification of viruses in food. Particular emphasis was placed on evaluating the usefulness of a new technique, RT droplet digital PCR (ddPCR), for food virological applications. In addition, many foodborne viruses have high sequence variability, which makes assay development for PCR-based methods time-consuming and error-prone. Another important focus was therefore to simplify and improve the design process for such assays.Five articles form the basis for this work. In Paper I, we validate and evaluate RT-ddPCR for quantitative detection of noroviruses in oysters. In Paper II we show that (RT)-ddPCR can provide less biased quantification of viruses with high sequence variability compared to (RT)-qPCR. In Paper III we develop and validate a new improved assay for hepatitis A virus in food. In Paper IV we present a new tool for the design of (RT)-PCR assays for viruses with high sequence variability. In the last study, Paper V, we optimise and validate a method for quantitative detection of hepatitis E virus in pork sausages.In addition, through a combined analysis of the validation data from Papers I, III and V, we show that RT-qPCR performs somewhat better in qualitative detection, but that RT-ddPCR is superior to RT-qPCR in quantitative detection. Furthermore, we demonstrate through comparisons with data from Poisson distributions that we achieve almost ideal precision in quantification with RT-ddPCR. In summary, this work presents methodological improvements for quantitative detection of the three most important foodborne viruses in high-risk foods. I hope that such methods will help us to better understand the transmission routes and epidemiology of foodborne viruses and reduce the burden of foodborne diseases.
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| 12. |
- Persson, Sofia, et al.
(författare)
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rprimer : an R/bioconductor package for design of degenerate oligos for sequence variable viruses
- 2022
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Ingår i: BMC Bioinformatics. - : BioMed Central (BMC). - 1471-2105. ; 23:1
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Tidskriftsartikel (refereegranskat)abstract
- Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT-PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development.
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| 13. |
- Hansson, Ingrid, et al.
(författare)
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Differences in Genotype and Antimicrobial Resistance between Campylobacter spp. Isolated from Organic and Conventionally Produced Chickens in Sweden
- 2021
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Ingår i: Pathogens. - : MDPI. - 2076-0817. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Antibiotic resistance is a major challenge worldwide and increased resistance to quinolones in Campylobacter is being reported. Analysis of antibiotic resistance was performed on 157 Campylobacter strains (123 C. jejuni and 34 C. coli) from conventional and organic chickens produced in Sweden. Susceptibility for tetracycline, ciprofloxacin, erythromycin, nalidixic acid, streptomycin, and gentamycin was determined by microdilution. All 77 isolates from organic chickens were sensitive to all antibiotics, except two C. jejuni that were resistant to tetracycline. Of the 80 isolates from conventional chickens, 22.5% of C. jejuni and 11.1% of C. coli were resistant to quinolones and 5.6% of C. jejuni were resistant to tetracycline. Whole-genome sequencing resulted in 50 different sequence types of C. jejuni and six of C. coli. Nine sequence types were found in both organic and conventional chickens. Two of these (ST-19 and ST-257) included isolates from conventional broilers with different resistance phenotypes to the remaining isolates from conventional and organic broilers. There are management differences between the production systems, such as feed, breed, use of coccidiostats, and access to outdoor area. It is unlikely that quinolone resistance has arisen due to use of antimicrobials, since fluoroquinolones are not permitted in Swedish broiler production.
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| 14. |
- Mueller, Ralf C., et al.
(författare)
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A high-quality genome and comparison of short-versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)
- 2021
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome.Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families.Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long -read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.
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| 15. |
- Persson, Sofia, et al.
(författare)
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A new assay for quantitative detection of hepatitis A virus
- 2021
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Ingår i: Journal of Virological Methods. - : Elsevier BV. - 0166-0934 .- 1879-0984. ; 288
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Tidskriftsartikel (refereegranskat)abstract
- Hepatitis A virus (HAV) is mainly transmitted via contaminated food or water or through person-to-person contact. Here, we describe development and evaluation of a reverse transcription droplet digital PCR (RTddPCR) and reverse transcription real-time PCR (RT-qPCR) assay for detection of HAV in food and clinical specimens. The assay was evaluated by assessing limit of detection, precision, matrix effects, sensitivity and quantitative agreement. The 95 % limit of detection (LOD95 %) was 10 % higher for RT-ddPCR than for RTqPCR. A Bayesian model was used to estimate precision on different target concentrations. From this, we found that RT-ddPCR had somewhat greater precision than RT-qPCR within runs and markedly greater precision between runs. By analysing serum from naturally infected persons and a naturally contaminated food sample, we found that the two methods agreed well in quantification and had comparable sensitivities. Tests with artificially contaminated food samples revealed that neither RT-ddPCR nor RT-qPCR was severely inhibited by presence of oysters, raspberries, blueberries or leafy-green vegetables. For this assay, we conclude that RT-qPCR should be considered if rapid, qualitative detection is the main interest and that RT-ddPCR should be considered if precise quantification is the main interest. The high precision of RT-ddPCR allows for detection of small changes in viral concentration over time, which has direct implications for both food control and clinical studies.
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| 16. |
- Verhagen, Josanne H., et al.
(författare)
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Host Range of Influenza A Virus H1 to H16 in Eurasian Ducks Based on Tissue and Receptor Binding Studies
- 2021
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Ingår i: Journal of Virology. - : American Society of Microbiology. - 0022-538X .- 1098-5514. ; 95:6, s. 1-19
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Tidskriftsartikel (refereegranskat)abstract
- Dabbling and diving ducks partly occupy shared habitats but have been reported to play different roles in wildlife infectious disease dynamics. Influenza A virus (IAV) epidemiology in wild birds has been based primarily on surveillance programs focused on dabbling duck species, particularly mallard (Anas platyrhynchos). Surveillance in Eurasia has shown that in mallards, some subtypes are commonly (H1 to H7 and H10), intermediately (H8, H9, H11, and H12), or rarely (H13 to H16) detected, contributing to discussions on virus host range and reservoir competence. An alternative to surveillance in determining IAV host range is to study virus attachment as a determinant for infection. Here, we investigated the attachment patterns of all avian IAV subtypes (H1 to H16) to the respiratory and intestinal tracts of four dabbling duck species (Mareca and Anas spp.), two diving duck species (Aythya spp.), and chicken, as well as to a panel of 65 synthetic glycan structures. We found that IAV subtypes generally showed abundant attachment to colon of the Anas duck species, mallard, and Eurasian teal (Anas crecca), supporting the fecal-oral transmission route in these species. The reported glycan attachment profile did not explain the virus attachment patterns to tissues but showed significant attachment of duck-originated viruses to fucosylated glycan structures and H7 virus tropism for Neu5Gc-LN. Our results suggest that Anas ducks play an important role in the ecology and epidemiology of IAV. Further knowledge on virus tissue attachment, receptor distribution, and receptor binding specificity is necessary to understand the mechanisms underlying host range and epidemiology of IAV. IMPORTANCE Influenza A viruses (IAVs) circulate in wild birds worldwide. From wild birds, the viruses can cause outbreaks in poultry and sporadically and indirectly infect humans. A high IAV diversity has been found in mallards (Anas platyrhynchos), which are most often sampled as part of surveillance programs; meanwhile, little is known about the role of other duck species in IAV ecology and epidemiology. In this study, we investigated the attachment of all avian IAV hemagglutinin (HA) subtypes (H1 to H16) to tissues of six different duck species and chicken as an indicator of virus host range. We demonstrated that the observed virus attachment patterns partially explained reported field prevalence. This study demonstrates that dabbling ducks of the Anas genus are potential hosts for most IAV subtypes, including those infecting poultry. This knowledge is useful to target the sampling of wild birds in nature and to further study the interaction between IAVs and birds.
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| 17. |
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| 18. |
- Pettersson, John H.-O. 1981-, et al.
(författare)
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Circumpolar diversification of the Ixodes uriae tick virome
- 2020
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 16:8
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Tidskriftsartikel (refereegranskat)abstract
- 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 thatIx.uriaespread from the southern to the northern circumpolar region millions of years ago and has remained isolated in these regions ever since. Such a profound biographic subdivision provides a unique opportunity to determine whether viruses associated with ticks exhibit the same evolutionary patterns as their hosts. To test this, we collectedIx.uriaespecimens near a Gentoo penguin (Pygoscelis papua) colony at Neko harbour, Antarctica, and from migratory birds-the Razorbill (Alca torda) and the Common murre (Uria aalge)-on Bonden island, northern Sweden. Through meta-transcriptomic next-generation sequencing we identified 16 RNA viruses, seven of which were novel. Notably, we detected the same species, Ronne virus, and two closely related species, Bonden virus and Piguzov virus, in both hemispheres indicating that there have been at least two cross-circumpolar dispersal events. Similarly, we identified viruses discovered previously in other locations several decades ago, including Gadgets Gully virus, Taggert virus and Okhotskiy virus. By identifying the same or closely related viruses in geographically disjunct sampling locations we provide evidence for virus dispersal within and between the circumpolar regions. In marked contrast, our phylogenetic analysis revealed no movement of theIx.uriaetick hosts between the same locations. Combined, these data suggest that migratory birds are responsible for the movement of viruses at both local and global scales. Author summary As host populations diverge, so may those microorganisms, including viruses, that are dependent on those hosts. To examine this key issue in host-microbe evolution we compared the co-phylogenies of the seabird tick,Ixodes uriae, and their RNA viruses sampled from the far northern and southern hemispheres. Despite the huge geographic distance between them, phylogeographic analysis reveals that the same and closely related viruses were found both within and between the northern and southern circumpolar regions, most likely reflecting transfer by virus-infected migratory birds. In contrast, genomic data suggested that theIx.uriaepopulations were phylogenetically distinct between the northern and southern hemispheres. This work emphasises the importance of migratory birds and ticks as vectors and sources of virus dispersal and introduction at both the local and global scales.
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| 19. |
- Valečková, Eliška, et al.
(författare)
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Silage and haylage as forage in slow and fast-growing broilers - effects on performance in Campylobacter jejuni infected birds
- 2020
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Ingår i: British Poultry Science. - : Informa UK Limited. - 0007-1668 .- 1466-1799. ; 61:4, s. 433-441
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Tidskriftsartikel (refereegranskat)abstract
- 1. This study investigated the effects of daily intake of silage or haylage on broiler production performance and organ development. Furthermore, effects of daily intake of Lactobacillus plantarum either via silage or by supplemented drinking water, on Campylobacter jejuni loads in faeces were studied.2. To test this, a 42-d experiment using Ross 308 and a 63-d experiment with Rowan Rangers hybrids, were performed. Silage inoculated with L. plantarum strain 256 and haylage were fed in total mixed rations with mixtures of 85% of pellets and 15% of respective forage (DM-based weight). Feed intake (FI), forage intake, body weight (BW) and feed conversion ration (FCR) were monitored weekly. Mortality was recorded daily, and organ weights were registered at slaughter. Quantification of C. jejuni was performed by colony counts from faecal samples after culture on agar plates.3. There was a negative effect of haylage on BW and FI in the fast-growing Ross 308 hybrid. Silage had a negative effect on BW only on week four and six. Water inoculated with L. plantarum 256 increased BW in the starter period. Interestingly, no significant adverse effect of forage inclusion was observed in the Rowan Ranger birds.4. Relative weight of the emptied gizzard was higher in both Ross 308 and Rowan Ranger birds fed haylage and silage than in the control group. In Ross 308 birds, both forages significantly reased the relative weight of gizzard with digestive content when compared to birds fed solely pellets.5. In both studies, higher consumption of silage than haylage was observed.6. In conclusion, daily intake of L. plantarum 256 either via silage or supplemented in drinking water, was not effective in reducing the shedding of C. jejuni in either Ross 308 or Rowan Ranger hybrids at the end of the rearing period.
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| 20. |
- Wang, Helen, et al.
(författare)
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Chlamydia psittaci in Fulmars on The Faroe Islands : A Causative Link to South American Psittacines Eight Decades After a Severe Epidemic
- 2020
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Ingår i: Microbes and infection. - : Elsevier BV. - 1286-4579 .- 1769-714X. ; 22:8, s. 356-359
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Tidskriftsartikel (refereegranskat)abstract
- A psittacosis epidemic linked to fulmar hunting occurred on the Faroe Islands in the 1930s. This study investigates a plausible explanation to the 20% human mortality in this outbreak. Phylogenetic analysis showed that C. psittaci isolated from fulmars were closely related to the highly virulent 6BC strains from psittacines and is compatible with an acquisition by fulmars of an ancestor of the 6BC clade in the 1930s. This supports the hypothesis that the outbreak on the Faroe Islands started after naïve fulmars acquired C. psittaci from infected dead parrots thrown overboard when shipped to Europe in the 1930s.
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| 21. |
- Eriksson, Per, et al.
(författare)
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Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species - Support for the Community Concept
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.
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| 22. |
- Eriksson, Per
(författare)
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Avian Influenza Virus : Deciphering receptor interactions and their role in interspecies transmission
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Influenza A virus (IAV) annually infects approximately 5–15 % of the human population, causing ~500,000 deaths globally. Novel IAVs have emerged and spread pandemically in the human population, but have over time established endemic circulation with reduced pathogenicity causing seasonal influenza. The natural reservoir of IAVs is wild waterfowl. The past pandemics have been associated with host switch and have partly or entirely originated from birds, or adapted via passage through pigs (postulated IAV mixing vessel). Understanding IAV interspecies transmission mechanisms is essential for pandemic preparedness. Enzootic circulation of avian IAV (AIV) is concentrated to a few waterfowl species, while other bird species seldom are infected. A species barrier preventing IAV interspecies transmission has been suggested. To investigate IAV host range and mixing vessels, histochemistry studies were conducted with tissues from avian species, pigs, and humans. Virus adaptation to new hosts was studied by challenging tufted ducks and chickens with mallard-derived AIVs, together with AIV receptor tropism and glycoproteomic analysis of receptor distribution. Finally, receptor and tissue tropism in ducks was studied systematically for AIV (H1–16). More abundant AIV attachment to human than pig tissues was observed, questioning the pig mixing vessel theory. Attachment patterns of AIVs to bird tissues was generally broad with abundant attachment to trachea. However, among ducks, pronounced attachment was observed to colon of Anas spp., suggesting that intestinal infection might be restricted to Anas spp., whereas other species may be susceptible to respiratory infection. Tufted ducks and chickens could not be infected by intraesophageal inoculation further supporting this hypothesis. Glycan array analysis revealed 3’SLN, 3’STF, and their fucosylated and sulfated analogues as main AIV receptors. Moreover, AIV Neu5Acα2,6 recognition was widespread. Avian respiratory and intestinal tracts glycoproteomic analysis revealed that avian and mammalian receptor structures are much more similar than earlier thought. Furthermore, observed AIV subtype titer variation in challenged tufted ducks and chickens did not correlate with virus receptor tropism. In summary, this thesis suggests that IAV receptor recognition, in particular α2,3 vs. α2,6 sialylated receptor structures, is less important for the IAV interspecies barrier than previously thought.
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| 23. |
- Naguib, Mahmoud, et al.
(författare)
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Global patterns of avian influenza A (H7) : virus evolution and zoonotic threats
- 2019
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Ingår i: FEMS Microbiology Reviews. - : Oxford University Press. - 0168-6445 .- 1574-6976. ; 43:6, s. 608-621
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Forskningsöversikt (refereegranskat)abstract
- Avian influenza viruses (AIVs) continue to impose a negative impact on animal and human health worldwide. In particular, the emergence of highly pathogenic AIV H5 and, more recently, the emergence of low pathogenic AIV H7N9 have led to enormous socioeconomical losses in the poultry industry and resulted in fatal human infections. While H5N1 remains infamous, the number of zoonotic infections with H7N9 has far surpassed those attributed to H5. Despite the clear public health concerns posed by AIV H7, it is unclear why specifically this virus subtype became endemic in poultry and emerged in humans. In this review, we bring together data on global patterns of H7 circulation, evolution and emergence in humans. Specifically, we discuss data from the wild bird reservoir, expansion and epidemiology in poultry, significant increase in their zoonotic potential since 2013 and genesis of highly pathogenic H7. In addition, we analysed available sequence data from an evolutionary perspective, demonstrating patterns of introductions into distinct geographic regions and reassortment dynamics. The integration of all aspects is crucial in the optimisation of surveillance efforts in wild birds, poultry and humans, and we emphasise the need for a One Health approach in controlling emerging viruses such as AIV H7.
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| 24. |
- Naguib, Mahmoud M., et al.
(författare)
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Avian influenza viruses at the wild–domestic bird interface in Egypt
- 2019
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Ingår i: Infection Ecology & Epidemiology. - : Taylor & Francis Group. - 2000-8686. ; 9:1, s. 1-9
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Forskningsöversikt (refereegranskat)abstract
- Wild birds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) constitute the natural reservoir for low pathogenic avian influenza (LPAI) viruses. In Egypt, highly pathogenic avian influenza (HPAI) H5N1 and LPAI H9N2 viruses are endemic in domestic poultry, forming a threat to animal and human health and raising questions about the routes of introduction and mechanisms of persistence. Recently, HPAI H5N8 virus was also introduced into Egyptian domestic birds. Here we review the literature on the role of wild birds in the introduction and endemicity of avian influenza viruses in Egypt. Dabbling ducks in Egypt harbor an extensive LPAI virus diversity and may constitute the route of introduction for HPAI H5N1 and HPAI H5N8 viruses into Egypt through migration, however their role in the endemicity of HPAI H5N1, LPAI H9N2 and potentially other avian influenza virus (AIV) strains–by means of reassortment of viral genes–is less clear. Strengthened surveillance programs, in both domestic and wild birds, that include all LPAI virus subtypes and full genome sequencing are needed to better assess the wild–domestic bird interface and form a basis for evidence-based measures to limit and prevent AIV transmission between wild and domestic birds. © 2019, © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
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| 25. |
- Persson, Sofia, et al.
(författare)
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Missing the Match Might Not Cost You the Game : Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants
- 2019
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Ingår i: Food and Environmnetal Virology. - : Springer Science and Business Media LLC. - 1867-0334 .- 1867-0342. ; 11:3, s. 297-308
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Tidskriftsartikel (refereegranskat)abstract
- Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3 '-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique.
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