| 1. |
- Hober, Sophia, Professor, 1965-, et al.
(författare)
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Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay
- 2021
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Ingår i: Clinical & Translational Immunology. - : Wiley. - 2050-0068. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Objective. The COVID-19 pandemic poses an immense need for accurate, sensitive and high-throughput clinical tests, and serological assays are needed for both overarching epidemiological studies and evaluating vaccines. Here, we present the development and validation of a high-throughput multiplex bead-based serological assay. Methods. More than 100 representations of SARS-CoV-2 proteins were included for initial evaluation, including antigens produced in bacterial and mammalian hosts as well as synthetic peptides. The five best-performing antigens, three representing the spike glycoprotein and two representing the nucleocapsid protein, were further evaluated for detection of IgG antibodies in samples from 331 COVID-19 patients and convalescents, and in 2090 negative controls sampled before 2020. Results. Three antigens were finally selected, represented by a soluble trimeric form and the S1-domain of the spike glycoprotein as well as by the C-terminal domain of the nucleocapsid. The sensitivity for these three antigens individually was found to be 99.7%, 99.1% and 99.7%, and the specificity was found to be 98.1%, 98.7% and 95.7%. The best assay performance was although achieved when utilising two antigens in combination, enabling a sensitivity of up to 99.7% combined with a specificity of 100%. Requiring any two of the three antigens resulted in a sensitivity of 99.7% and a specificity of 99.4%. Conclusion. These observations demonstrate that a serological test based on a combination of several SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay.
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| 2. |
- Arroyo Mühr, Laila Sara, et al.
(författare)
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Does human papillomavirus-negative condylomata exist?
- 2015
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Ingår i: Virology. - : Elsevier BV. - 1096-0341 .- 0042-6822. ; 485, s. 283-288
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Tidskriftsartikel (refereegranskat)abstract
- Condylomata acuminata is caused by human papillomavirus (HPV). PCR with consensus primers will typically detect HPV in >96% of condylomata. Metagenomic sequencing has found that some "HPV-negative" condylomata do indeed contain HPV. We wished to perform a renewed evaluation of the "HPV-negative" condylomata using deeper metagenomics sequencing. Sequencing of whole genome amplified DNA from 40 apparently "HPV-negative" condylomata detected HPV in 37/40 specimens. We found 75 different HPV types, out of which 43 represented novel putative HPV types. Three types were cloned and established as HPV types 200, 201 and 202. Molluscum contagiosum virus was detected in 24 of the 40 samples. In summary, deep sequencing enables detection of HPV in almost all condylomata. "HPV-negative" condylomata might largely be explained by clinical misdiagnosis or the presence of viral variants, distantly related HPV types and/or low viral loads.
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| 3. |
- Arroyo Mühr, Laila Sara, et al.
(författare)
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Improving human papillomavirus (HPV) testing in the cervical cancer elimination era : The 2021 HPV LabNet international proficiency study
- 2022
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Ingår i: Journal of Clinical Virology. - : Elsevier BV. - 1386-6532. ; 154, s. 105237-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Proficient Human Papillomavirus (HPV) genotyping services are essential to support HPV and cervical cancer elimination strategies, in particular to support HPV vaccine research. Objectives: To perform a global HPV genotyping proficiency study, with evaluation in relation to previous proficiency studies. Study design: The proficiency panel contained 44 coded samples (40 samples containing one or more purified HPV types (HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/68a/68b) in human DNA, 1 human DNA control and 3 DNA extraction controls). Proficiency required detection of both single and multiple infections of 50 International Units of HPV 16/18, of 500 genome equivalents for other HPV types and no false positivity. Results: One hundred and thirty-two laboratories submitted 211 datasets. Most assays used (182/211 datasets) were commercially available. An all-time high of 75% of the datasets were 100% proficient. One or more false positives were found in 17.5% of datasets. Among laboratories who participated in the 2019 proficiency study, full proficiency increased from 25% in 2019 to 60% in 2021. The high overall proficiency was mostly attributable to a large number of new laboratories, which used similar assays. Conclusions: The worldwide deterioration in comparability and reliability of HPV testing found in 2019 is now reversed and an overall increase in proficiency is found.
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| 4. |
- Arroyo Mühr, Laila Sara
(författare)
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Infections in skin cancer
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The increasing prevalence of skin cancer results in that it will soon equal that of all other cancers combined. Sun exposure is a well-known risk factor for its development, but despite the growing public awareness of the harmful consequences of ultraviolet radiation, the cancer incidence continues to increase, implying that other factors might also have a role in promoting this disease. Data from immunosuppressed patients reveals a 100-fold increased incidence of nonmelanoma skin carcinoma (NMSC), but an infectious etiology has not been established. However, certain human papillomaviruses (HPVs) have previously been detected in this type of cancer. We applied high throughput sequencing to different skin lesions in order to assess which organisms were present. Most viral reads (>95%) belonged to human papillomavirus. Traditionally, viral detection was performed using PCR methods. We used degenerate “general” HPV primers and multiplexed novel “specific” HPV primers in order to amplify a broad number of HPVs by PCR. This method showed a very high sensitivity, but the HPV types with low similarity to the primer sequences might have escaped amplification. Therefore, we performed an unbiased approach based on non-PCR whole genome amplification, independent of sequence information, in order to detect those “escaping” HPV types, as well as to determine if other viruses were present in the samples. Overall, we identified almost 100 putative novel HPV types in total, and characterized 4 novel HPV types (HPV 197, 200, 201 and 202). Most of the HPV types were detected in very few patients each, and at a very low viral load (below 0.5 copies/cell), except for HPV 197, which was the most commonly found virus in skin tumors (37.4% of skin lesions). Despite the higher sensitivity of PCR methods, the unbiased approach detected HPV in 37/40 condyloma acuminata that had been reported as “HPV-negative” with specific PCR techniques. Certain HPV types, including HPV 197, were not detected by PCR and only by non-PCR based methods. Therefore, more unbiased PCR-independent methods are needed to describe which organisms are most commonly present in skin lesions. The work in this thesis has expanded our knowledge of the wide genomic diversity of HPV on the skin, and finds that PCR-independent methods are needed to describe which organisms are most commonly present in skin lesions. Further studies are needed to assess any possible role of viral infections in skin cancer, elucidation of mechanistic effects and determine the direction of causality of any associations.
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| 5. |
- Bzhalava, Davit, et al.
(författare)
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Deep sequencing extends the diversity of human papillomaviruses in human skin.
- 2014
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4:Jul 24
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Tidskriftsartikel (refereegranskat)abstract
- Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.
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| 6. |
- Bzhalava, Davit, et al.
(författare)
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Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study.
- 2016
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 138:9, s. 2212-2220
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Tidskriftsartikel (refereegranskat)abstract
- A possible role for infections of the pregnant mother in the development of childhood acute leukemias and lymphomas has been suggested. However, no specific infectious agent has been identified. Offspring of 74,000 mothers who had serum samples taken during pregnancy and stored in a large-scale biobank were followed up to the age of 15 years (750,000 person years) through over-generation linkages between the biobank files, the Swedish national population and cancer registers to identify incident leukemia/lymphoma cases in the offspring. First-trimester sera from mothers of 47 cases and 47 matched controls were retrieved and analyzed using next generation sequencing. Anelloviruses were the most common viruses detected, found in 37/47 cases and in 40/47 controls, respectively (OR: 0.6, 95% CI: 0.2-1.9). None of the detected viruses was associated with leukemia/lymphoma in the offspring. Viremia during pregnancy was common, but no association with leukemia/lymphoma risk in the offspring was found.
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| 7. |
- Eklund, Carina, et al.
(författare)
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The 2019 HPV Labnet international proficiency study : Need of global Human Papillomavirus Proficiency Testing
- 2021
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Ingår i: Journal of Clinical Virology. - : Elsevier BV. - 1386-6532. ; 141, s. 104902-
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Tidskriftsartikel (refereegranskat)abstract
- Background:: Accurate and internationally comparable human papillomavirus (HPV) testing services are essential for cervical cancer elimination programs. The WHO HPV Laboratory Network started issuing international HPV testing proficiency panels in 2008. Objectives:: We report the results of the 2019 global proficiency study and evaluate the proficiency over time. Study design:: The proficiency panel contained 40 coded samples containing mixes of purified HPV types (HPV6/11/16/18/31/33/35/39/45/51/52/56/58/59/68a/68b) and 4 controls. Proficiency required detection of both single and multiple infections of 50 International Units of HPV 16/18, of 500 genome equivalents (10x higher concentration) for other HPV types, and no false positives (stricter requirement compared to previous panels). Results:: Seventy-eight laboratories submitted 110 datasets with 38 different assays. Most samples (38/44) were reported with 100% proficiency in most datasets. Mostly commercial assays were used (88/110 datasets). Overall, 47.3% of the datasets were 100% proficient. False positivity was detected in at least one sample in 30.1% of datasets. When analysing all datasets ever since 2008 using exactly the same proficiency criteria, there was a steady improvement up to 2017 (the proportion of datasets being completely proficient increased from 25% to 73%). However, in the 2019 proficiency testing the proportion of fully proficient datasets dropped to 50%. Conclusions:: Although we initially documented a worldwide improvement in comparability and reliability of HPV testing services, the trend now appears to be reversed. In response, the International HPV Reference Center will provide support for improved quality of laboratory services, including issuing of global proficiency panels every year.
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| 8. |
- Elfstrom, K. Miriam, et al.
(författare)
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Differences in risk for SARS-CoV-2 infection among healthcare workers
- 2021
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Ingår i: Preventive Medicine Reports. - : Elsevier BV. - 2211-3355. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Healthcare workers (HCWs) are a risk group for SARS-CoV-2 infection, but which healthcare work that conveys risk and to what extent such risk can be prevented is not clear. Starting on April 24th, 2020, all employees at work (n = 15,300) at the Karolinska University Hospital, Stockholm, Sweden were invited and 92% consented to participate in a SARS-CoV-2 cohort study. Complete SARS-CoV-2 serology was available for n = 12,928 employees and seroprevalences were analyzed by age, sex, profession, patient contact, and hospital department. Relative risks were estimated to examine the association between type of hospital department as a proxy for different working environment exposure and risk for seropositivity, adjusting for age, sex, sampling week, and profession. Wards that were primarily responsible for COVID-19 patients were at increased risk (adjusted OR 1.95 (95% CI 1.65-2.32) with the notable exception of the infectious diseases and intensive care units (adjusted OR 0.86 (95% CI 0.66-1.13)), that were not at increased risk despite being highly exposed. Several units with similar types of work varied greatly in seroprevalences. Among the professions examined, nurse assistants had the highest risk (adjusted OR 1.62 (95% CI 1.38-1.90)). Although healthcare workers, in particular nurse assistants, who attend to COVID-19 patients are a risk group for SARS-CoV-2 infection, several units caring for COVID-19 patients had no excess risk. Large variations in seroprevalences among similar units suggest that healthcare work-related risk of SARS-CoV-2 infection may be preventable.
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| 9. |
- Garcia-Serrano, Ainhoa, et al.
(författare)
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Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing
- 2023
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Ingår i: Cancer Medicine. - 2045-7634. ; 12:18, s. 19291-19300
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Tidskriftsartikel (refereegranskat)abstract
- Background: Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non-targeted deep-sequencing strategies enable nowadays full microbiome characterization up to species level. Aim: We aimed to analyze both bacterial and viral communities in CRC using these strategies. Materials & Methods: We analyzed bacterial and viral communities using both DNA and RNA deep-sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples. Results: No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002). Discussion: Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC. Conclusion: Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.
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| 10. |
- Hultin, Emilie, et al.
(författare)
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Viremia preceding multiple sclerosis : Two nested case-control studies
- 2018
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Ingår i: Virology. - : Elsevier. - 0042-6822 .- 1096-0341. ; 520, s. 21-29
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Tidskriftsartikel (refereegranskat)abstract
- Infections have been suggested to be involved in Multiple Sclerosis (MS). We used metagenomic sequencing to detect both known and yet unknown microorganisms in 2 nested case control studies of MS. Two different cohorts were followed for MS using registry linkages. Serum samples taken before diagnosis as well as samples from matched control subjects were selected.In cohort1 with 75 cases and 75 controls, most viral reads were Anelloviridae-related and >95% detected among the cases. Among samples taken up to 2 years before MS diagnosis, Anellovirus species TTMV1, TTMV6 and TTV27 were significantly more common among cases. In cohort2, 93 cases and 93 controls were tested under the pre-specified hypothesis that the same association would be found. Although most viral reads were again related to Anelloviridae, no significant case-control differences were seen. We conclude that the Anelloviridae-MS association may be due to multiple hypothesis testing, but other explanations are possible.
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