| 1. |
- Myhrman, Sofia, et al.
(författare)
-
Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of SARS-CoV-2
- 2022
-
Ingår i: Infection Control and Hospital Epidemiology. - : Cambridge University Press (CUP). - 0899-823X .- 1559-6834. ; 43:10, s. 1403-1407
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: Effective infection prevention and control (IPC) measures are key for protecting patients from nosocomial infections and require knowledge of transmission mechanisms in different settings. We performed a detailed outbreak analysis of the transmission and outcome of coronavirus disease 2019 (COVID-19) in a geriatric ward by combining whole-genome sequencing (WGS) with epidemiological data. Design: Retrospective cohort study. Setting: Tertiary care hospital. Participants: Patients and healthcare workers (HCWs) from the ward with a nasopharyngeal sample (NPS) positive for SARS-CoV-2 RNA during the outbreak period. Methods: Patient data regarding clinical characteristics, exposure and outcome were collected retrospectively from medical records. Stored NPS from 32 patients and 15 HCWs were selected for WGS and phylogenetic analysis. Results: Median patient age was 84 years and 17/32 (53%) were male. Fourteen patients (44%) died within 30 days after sampling. Viral load was significantly higher among the deceased. WGS was successful in 28/32 (88%) patient samples and 14/15 (93%) HCW samples. Three separate viral clades were identified, whereof one clade and two subclades among both patient and HCW samples. Integrated epidemiological and genetic analysis revealed six probable transmission events between patients and supported hospital-acquired COVID-19 in 25/32 patients. Conclusion: WGS provided a deep insight into the outbreak dynamics and true extent of nosocomial COVID-19. The extensive transmission between patients and HCWs indicated that current IPC measures were insufficient. We suggest increased use of WGS in outbreak investigations for identification of otherwise unknown transmission links and evaluation of IPC measures.
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Törnell, Andreas, 1994, et al.
(författare)
-
Presence of MDSC associates with impaired antigen-specific T cell reactivity following COVID-19 vaccination in cirrhotic patients
- 2023
-
Ingår i: Frontiers in Immunology. - 1664-3224. ; 14
-
Tidskriftsartikel (refereegranskat)abstract
- Background and aims: Cirrhosis entails high risk of serious infections and abated efficiency of vaccination, but the underlying mechanisms are only partially understood. This study aimed at characterizing innate and adaptive immune functions, including antigen-specific T cell responses to COVID-19 vaccination, in patients with compensated and decompensated cirrhosis. Methods: Immune phenotype and function in peripheral blood from 42 cirrhotic patients and 44 age-matched healthy controls were analysed after two doses of the mRNA-based COVID-19 vaccines [BNT162b2 (Pfizer BioNTech) or mRNA-1273 (Moderna)]. Results: Cirrhotic patients showed significantly reduced blood counts of antigen-presenting dendritic cells (DC) and high counts of monocytic myeloid-derived suppressor cells (M-MDSC) as compared to healthy controls. In addition, monocytic cells recovered from cirrhotic patients showed impaired expression of the antigen-presenting molecule HLA-DR and the co-stimulatory molecule CD86 upon Toll-like receptor (TLR) stimulation. These features were more prominent in patients with decompensated cirrhosis (Child-Pugh classes B & C). Interestingly, while patients with compensated cirrhosis (Child-Pugh class A) showed an inflammatory profile with myeloid cells producing the proinflammatory cytokines IL-6 and TNF, decompensated patients produced reduced levels of these cytokines. Cirrhotic patients, in particular those with more advanced end-stage liver disease, mounted reduced antigen-specific T cell reactivity to COVID-19 vaccination. Vaccine efficiency inversely correlated with levels of M-MDSC. Conclusion: These results implicate MDSC as mediators of immunosuppression, with ensuing deficiency of vaccine-specific T cell responses, in cirrhosis.
|
|
| 5. |
- Al-Dury, S., et al.
(författare)
-
Catch-up antibody responses and hybrid immunity in mRNA vaccinated patients at risk of severe COVID-19
- 2023
-
Ingår i: Infectious Diseases. - 2374-4235. ; 55:10, s. 744-750
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundThe immunogenicity of repeated vaccination and hybrid immunity in vulnerable patients remains unclear.MethodsWe studied the impact of iterative Covid-19 mRNA vaccination and hybrid immunity on antibody levels in immunosuppressed subjects. Patients with liver cirrhosis (n = 38), survivors of allogeneic haematopoietic stem cell transplantation (allo-HSCT) (n = 36) and patients with autoimmune liver disease (n = 14) along with healthy controls (n = 20) were monitored for SARS-CoV-2-S1 IgG after their 1st-3rd vaccine doses, 31 of whom became infected with the Omicron variant after the 2nd dose. Ten uninfected allo-HSCT recipients received an additional 4th vaccine dose.ResultsUnexpectedly, immunosuppressed patients achieved antibody levels in parity with controls after the 3rd vaccine dose. In all study cohorts, hybrid immunity (effect of vaccination and natural infection) resulted in approximately 10-fold higher antibody levels than vaccine-induced immunity alone.ConclusionsThree doses of the Covid-19 mRNA vaccine entailed high antibody concentrations even in immunocompromised individuals, and hybrid-immunity resulted further augmented levels than vaccination alone.
|
|
| 6. |
- Al-Dury, Samer, et al.
(författare)
-
Impaired SARS-CoV-2-specific T-cell reactivity in patients with cirrhosis following mRNA COVID-19 vaccination
- 2022
-
Ingår i: JHEP Reports. - : Elsevier BV. - 2589-5559. ; 4:7
-
Tidskriftsartikel (refereegranskat)abstract
- Background & Aims: Cirrhosis entails elevated risk of COVID-19-associated mortality. This study determined T cell-mediated and antibody reactivity against the spike 1 (S1) protein of SARS-CoV-2 among 48 patients with cirrhosis and 39 healthy controls after mRNA COVID-19 vaccination. Methods: SARS-CoV-2-specific T-cell reactivity was measured by induced level of T cell-derived interferon-gamma (IFN-gamma) in blood cells stimulated ex vivo with multimeric peptides spanning the N-terminal portion of S1. S1-induced IFN-gamma was quantified before and after the 1st and 2nd vaccination (BNT162b2, Pfizer-BioNTech or mRNA-1273, Moderna) alongside serum IgG against the receptor-binding domain (RBD) within S1 (anti-RBD-S1 IgG). Results: T-cell reactivity against S1 was reduced in patients with cirrhosis after the 1st (p < 0.001 vs. controls) and 2nd (p < 0.001) vaccination. Sixty-eight percent of patients lacked detectable S1-specific T-cell reactivity after the 1st vaccination vs. 19% in controls (odds ratio 0.11, 95% CI 0.03-0.48, p = 0.003) and 36% remained devoid of reactivity after the 2nd vaccination vs. 6% in controls (odds ratio 0.12, 95% CI 0.03-0.59, p = 0.009). T-cell reactivity in cirrhosis remained significantly impaired after correction for potential confounders in multivariable analysis. Advanced cirrhosis (Child-Pugh class B) was associated with absent or lower T-cell responses (p < 0.05 vs. Child-Pugh class A). The deficiency of T-cell reactivity was paralleled by lower levels of anti-RBD-S1 IgG after the 1st (p < 0.001 vs. controls) and 2nd (p < 0.05) vaccination. Conclusions: Patients with cirrhosis show deficient T-cell reactivity against SARS-CoV-2 antigens along with diminished levels of anti-RBD-S1 IgG after dual COVID-19 vaccination, highlighting the need for vigilance and additional preventative measures. Clinical trial registration: EudraCT 2021-000349-42 Lay summary: T cells are a pivotal component in the defence against viruses. We show that patients with cirrhosis have impaired SARS-CoV-2-specific T-cell responses and lower antibody levels after mRNA vaccination against COVID-19 compared with healthy controls. Patients with more advanced liver disease exhibited particularly inferior vaccine responses. These results call for additional preventative measures in these patients. (C) 2022 The Author(s). Published by Elsevier B.V. on behalf of European Association for the Study of the Liver (EASL).
|
|
| 7. |
- Eilard, Anders, et al.
(författare)
-
Vertically acquired occult hepatitis B virus infection may become overt after several years
- 2019
-
Ingår i: Journal of Infection. - : Elsevier BV. - 0163-4453 .- 1532-2742. ; 78:3, s. 226-231
-
Tidskriftsartikel (refereegranskat)abstract
- © 2019 Elsevier Ltd Objectives: To study the frequency of vertically acquired occult hepatitis B virus (HBV) infection (OBI). Methods: We investigated 44 children born to hepatitis B surface antigen (HBsAg) positive mothers. They received HBV vaccine directly after birth and at 2, 6 and 52 weeks of age; eight with HBeAg-positive mothers also received hepatitis B immunoglobulin (HBIG). HBV DNA was analyzed in blood collected at 6 weeks and 12 months of age, and HBV antibodies at 12 and 18 months of age. Results: HBV DNA, but not HBsAg or anti-HBc, was detected at 12 months of age in three children. The viral sequences were almost identical with HBV DNA from their mothers who all were HBeAg-positive and had received tenofovir during pregnancy. Follow-up at 5–7 years age showed that one of the three children had become seropositive for HBsAg and anti-HBc. This child and one of the other two had detectable HBV DNA at the follow-up, with whole genome sequences identical to those in HBV from their mothers. Conclusions: Mothers-to-child transmission of HBV can, despite adequate prophylaxis, lead to OBI which may later develop into overt HBV infection. Whether such infections are of clinical importance needs to be further investigated.
|
|
| 8. |
- Einarsdottir, Sigrun, et al.
(författare)
-
Deficiency of SARS-CoV-2 T-cell responses after vaccination in long-term allo-HSCT survivors translates into abated humoral immunity.
- 2022
-
Ingår i: Blood advances. - : American Society of Hematology. - 2473-9537 .- 2473-9529. ; 6:9, s. 2723-2730
-
Tidskriftsartikel (refereegranskat)abstract
- Recipients of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for hematological diseases are at risk of severe disease and death from COVID-19. To determine the safety and immunogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines, samples from 50 infection-naive allo-HSCT recipients (median, 92 months from transplantation, range, 7-340 months) and 39 healthy controls were analyzed for serum immunoglobulin G (IgG) against the receptor binding domain (RBD) within spike 1 (S1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; anti-RBD-S1 IgG) and for SARS-CoV-2-specific T-cell immunity, reflected by induction of T-cell-derived interferon-γ in whole blood stimulated ex vivo with 15-mer SI-spanning peptides with 11 amino acid overlapS1-spanning peptides. The rate of seroconversion was not significantly lower in allo-transplanted patients than in controls with 24% (12/50) and 6% (3/50) of patients remaining seronegative after the first and second vaccination, respectively. However, 58% of transplanted patients lacked T-cell responses against S1 peptides after 1 vaccination compared with 19% of controls (odds ratio [OR] 0.17; P = .009, Fisher's exact test) with a similar trend after the second vaccination where 28% of patients were devoid of detectable specific T-cell immunity, compared with 6% of controls (OR 0.18; P = .02, Fisher's exact test). Importantly, lack of T-cell reactivity to S1 peptides after vaccination heralded substandard levels (<100 BAU/mL) of anti-RBD-S1 IgG 5 to 6 months after the second vaccine dose (OR 8.2; P = .007, Fisher's exact test). We conclude that although allo-HSCT recipients achieve serum anti-RBD-S1 IgG against SARS-CoV-2 after 2 vaccinations, a deficiency of SARS-CoV-2-specific T-cell immunity may subsequently translate into insufficient humoral responses.
|
|
| 9. |
|
|
| 10. |
|
|
| 11. |
- Lan, Pham Thi, et al.
(författare)
-
Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16
- 2020
-
Ingår i: Journal of Antimicrobial Chemotherapy. - : Oxford University Press. - 0305-7453 .- 1460-2091. ; 75:6, s. 1432-1438
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae, compromising gonorrhoea treatment, is a threat to reproductive health globally. South-East and East Asia have been major sources of emergence and subsequent international spread of AMR gonococcal strains during recent decades. We investigated gonococcal isolates from 2011 and 2015-16 in Vietnam using AMR testing, WGS and detection of AMR determinants.METHODS: Two hundred and twenty-nine gonococcal isolates cultured in 2015-16 (n = 121) and 2011 (n = 108) in Vietnam were examined. AMR testing was performed using Etest and WGS with Illumina MiSeq.RESULTS: Resistance among the 2015-16 isolates was as follows: ciprofloxacin, 100%; tetracycline, 79%; benzylpenicillin, 50%; cefixime, 15%; ceftriaxone, 1%; spectinomycin, 0%; and 5% were non-WT to azithromycin. Eighteen (15%) isolates were MDR. The MIC range for gentamicin was 2-8 mg/L. Among the 2015-16 isolates, 27% (n = 33) contained a mosaic penA allele, while no isolates had a mosaic penA allele in 2011. Phylogenomic analysis revealed introduction after 2011 of two mosaic penA-containing clones (penA-10.001 and penA-34.001), which were related to cefixime-resistant strains spreading in Japan and Europe, and a minor clade (eight isolates) relatively similar to the XDR strain WHO Q.CONCLUSIONS: From 2011 to 2015-16, resistance in gonococci from Vietnam increased to all currently and previously used antimicrobials except ceftriaxone, spectinomycin and tetracycline. Two mosaic penA-containing clones were introduced after 2011, explaining the increased cefixime resistance. Significantly increased AMR surveillance, antimicrobial stewardship and use of WGS for molecular epidemiology and AMR prediction for gonococcal isolates in Vietnam and other Asian countries are crucial.
|
|
| 12. |
- Lan, P. T., et al.
(författare)
-
Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16
- 2020
-
Ingår i: The Journal of antimicrobial chemotherapy. - 1460-2091. ; 75:6, s. 1432-1438
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae, compromising gonorrhoea treatment, is a threat to reproductive health globally. South-East and East Asia have been major sources of emergence and subsequent international spread of AMR gonococcal strains during recent decades. We investigated gonococcal isolates from 2011 and 2015-16 in Vietnam using AMR testing, WGS and detection of AMR determinants. METHODS: Two hundred and twenty-nine gonococcal isolates cultured in 2015-16 (n=121) and 2011 (n=108) in Vietnam were examined. AMR testing was performed using Etest and WGS with Illumina MiSeq. RESULTS: Resistance among the 2015-16 isolates was as follows: ciprofloxacin, 100%; tetracycline, 79%; benzylpenicillin, 50%; cefixime, 15%; ceftriaxone, 1%; spectinomycin, 0%; and 5% were non-WT to azithromycin. Eighteen (15%) isolates were MDR. The MIC range for gentamicin was 2-8mg/L. Among the 2015-16 isolates, 27% (n=33) contained a mosaic penA allele, while no isolates had a mosaic penA allele in 2011. Phylogenomic analysis revealed introduction after 2011 of two mosaic penA-containing clones (penA-10.001 and penA-34.001), which were related to cefixime-resistant strains spreading in Japan and Europe, and a minor clade (eight isolates) relatively similar to the XDR strain WHO Q. CONCLUSIONS: From 2011 to 2015-16, resistance in gonococci from Vietnam increased to all currently and previously used antimicrobials except ceftriaxone, spectinomycin and tetracycline. Two mosaic penA-containing clones were introduced after 2011, explaining the increased cefixime resistance. Significantly increased AMR surveillance, antimicrobial stewardship and use of WGS for molecular epidemiology and AMR prediction for gonococcal isolates in Vietnam and other Asian countries are crucial. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.
|
|
| 13. |
- Larsson, Simon B., et al.
(författare)
-
Epidemiology and clinical manifestations of different enterovirus and rhinovirus types show that EV-D68 may still have an impact on severity of respiratory infections
- 2022
-
Ingår i: Journal of Medical Virology. - : Wiley. - 0146-6615 .- 1096-9071. ; 94:8, s. 3829-3839
-
Tidskriftsartikel (refereegranskat)abstract
- Respiratory infections are often caused by enteroviruses (EVs). The aim of this study was to identify whether certain types of EV were more likely to cause severe illness in 2016, when an increasing spread of upper respiratory infections was observed in Gothenburg, Sweden. The EV strain in 137 of 1341 nasopharyngeal samples reactive for EV by polymerase chain reaction could be typed by sequencing the viral 5 '-untranslated region and VP1 regions. Phylogenetic trees were constructed. Patient records were reviewed. Hospital care was needed for 46 of 74 patients with available medical records. The majority of the patients (83) were infected with the rhinovirus (RV). The remaining 54 were infected with EV A, B, C, and D strains of 13 different types, with EV-D68 and CV-A10 being the most common (17 vs. 14). Significantly more patients with EV-D68 presented with dyspnea, both when compared with other EV types (p = 0.003) and compared to all other EV and RV infections (p = 0.04). Phylogenetic analysis of the sequences revealed the spread of both Asian and European CV-A10 strains and 12 different RV C types. This study showed an abundance of different EV types spreading during a year with increased upper respiratory increased infections. EV-D68 infections were associated with more severe disease manifestation. Other EV and RV types were more evenly distributed between hospitalized and nonhospitalized patients. The EV type CV-A10 was also found in infected patients, which warrants further studies and surveillance, as this pathogen could cause more severe disease and outbreaks of hand, foot, and mouth disease.
|
|
| 14. |
|
|
| 15. |
- Prakash, Kasthuri, et al.
(författare)
-
Hepatitis B Virus RNA Profiles in Liver Biopsies by Digital Polymerase Chain Reaction
- 2020
-
Ingår i: Hepatology Communications. - : Ovid Technologies (Wolters Kluwer Health). - 2471-254X. ; 4:7, s. 973-982
-
Tidskriftsartikel (refereegranskat)abstract
- Replication of hepatitis B virus (HBV) originates from covalently closed circular DNA (cccDNA) and involves reverse transcription of pregenomic RNA (pgRNA), which is also called core RNA and encodes the capsid protein. The RNA coding for hepatitis B surface antigen (HBsAg) in the envelope of viral or subviral particles is produced from cccDNA or from HBV DNA integrated into the host genome. Because only cccDNA can generate the core and the 3 ' redundancy regions of HBV RNA, we aimed to clarify to what extent such HBV integrations are expressed by quantifying the different HBV RNA species in liver tissue. Digital droplet polymerase chain reaction (ddPCR) was employed to quantify six HBV RNA targets in 76 liver biopsies from patients with chronic infection, comprising 14 who were hepatitis B e antigen (HBeAg) positive and 62 who were HBeAg negative. In patients who were HBeAg negative, HBV RNA from the S RNA region was >1.6 log(10) units higher than in the core and 3 ' redundancy regions (P < 0.0001), indicating that >90% of S RNA was integration derived. HBeAg-negative samples showed 10 times lower levels of pgRNA (5 ' core) compared with core RNA (3 ' part of core; P < 0.0001), suggesting that a large proportion of core RNA might have a downstream shift of the transcription starting point. In multiple regression analysis, HBV DNA levels in serum were most strongly dependent on pgRNA. Conclusion: In patients who were HBeAg negative, integration-derived S RNA seemed to predominate and a large proportion of the core RNA lacked the 5 ' part. Because this part comprises the down-regulator of transcription 1 sequences, which are necessary for virus production (plus strand translocation), the finding might help to explain the low level of HBV DNA in serum that frequently is observed in patients with chronic HBV infection who are HBeAg negative.
|
|
| 16. |
- Ringlander, Johan, et al.
(författare)
-
Deep sequencing of hepatitis B virus using Ion Torrent fusion primer method
- 2022
-
Ingår i: Journal of Virological Methods. - : Elsevier BV. - 0166-0934. ; 299
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Hepatitis B virus (HBV) infection is worldwide a major cause of liver cirrhosis and hepatocellular carcinoma. Thousands of years ago, several HBV genotypes (A-I) evolved and have, as a result of human migration, become globally disseminated. Sequencing of HBV is used for genotyping, and investigation of out -breaks or of antiviral resistance. The present study describes a simplified deep sequencing of the whole HBV genome. Methods: Sequencing by Ion Torrent was evaluated and its performance compared with Sanger sequencing on clinical samples. Results: Amplification of overlapping segments spanning the entire HBV genome was successful at HBV DNA levels in serum as low as 100 IU/mL. The use of primers carrying adapter tags generated libraries without the need for fragmentation and ligation steps, and inclusion of barcode sequences allowed parallel analysis of multiple samples. A streamlined bioinformatic platform generated consensus sequences and superior mutation assessment as compared with Sanger sequencing, with which there was a 99.8 % average agreement. Conclusion: Deep sequencing of the whole HBV genome by using PCR primers tagged with adapters that prepare overlapping amplicons for Ion Torrent analysis was efficient and accurate.
|
|
| 17. |
- Ringlander, Johan, et al.
(författare)
-
Deep sequencing of liver explant transcriptomes reveals extensive expression from integrated hepatitis B virus DNA
- 2020
-
Ingår i: Journal of Viral Hepatitis. - : Wiley. - 1352-0504 .- 1365-2893. ; 27:11, s. 1162-1170
-
Tidskriftsartikel (refereegranskat)abstract
- Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). Integration of HBV DNA into the human genome may contribute to oncogenesis and to the production of the hepatitis B surface antigen (HBsAg). Whether integrations contribute to HBsAg levels in the blood is poorly known. Here, we characterize the HBV RNA profile of HBV integrations in liver tissue in patients with chronic HBV infection, with or without concurrent hepatitis D infection, by transcriptome deep sequencing. Transcriptomes were determined in liver tissue by deep sequencing providing 200 million reads per sample. Integration points were identified using a bioinformatic pipeline. Explanted liver tissue from five patients with end-stage liver disease caused by HBV or HBV/HDV was studied along with publicly available transcriptomes from 21 patients. Almost all HBV RNA profiles were devoid of reads in the core and the 3 ' redundancy (nt 1830-1927) regions, and contained a large number of chimeric viral/human reads. Hence, HBV transcripts from integrated HBV DNA rather than from covalently closed circular HBV DNA (cccDNA) predominated in late-stage HBV infection, in particular in cases with hepatitis D virus co-infection. The findings support the suggestion that integrated HBV DNA can be a significant source of HBsAg in humans.
|
|
| 18. |
- Ringlander, Johan, et al.
(författare)
-
Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients
- 2024
-
Ingår i: JOURNAL OF INFECTIOUS DISEASES. - 0022-1899 .- 1537-6613.
-
Tidskriftsartikel (refereegranskat)abstract
- Background. Hepatitis B virus (HBV) DNA may become integrated into the human genome of infected human hepatocytes. Expression of integrations can produce the surface antigen (HBsAg) that is required for synthesis of hepatitis D virus (HDV) particles and the abundant subviral particles in the blood of HBV- and HDV-infected subjects. Knowledge about the extent and variation of HBV integrations and impact on chronic HDV is still limited. Methods. We investigated 50 pieces of liver explant tissue from 5 patients with hepatitis D-induced cirrhosis, using a deep-sequencing strategy targeting HBV RNA. Results. We found that integrations were abundant and highly expressed, with large variation in the number of integration-derived (HBV/human chimeric) reads, both between and within patients. The median number of unique integrations for each patient correlated with serum levels of HBsAg. However, most of the HBV reads represented a few predominant integrations. Conclusions. The results suggest that HBV DNA integrates in a large proportion of hepatocytes, and that the HBsAg output from these integrations vary >100-fold depending on clone size and expression rate. A small proportion of the integrations seems to determine the serum levels of HBsAg and HDV RNA in HBV/HDV coinfected patients with liver cirrhosis.
|
|
| 19. |
- Ringlander, Johan
(författare)
-
Genomic and transcriptomic profiles in chronic hepatitis B infection
- 2023
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Chronic infection with hepatitis B virus (HBV) affects >250 million people globally and is the most common cause of hepatocellular carcinoma and liver cirrhosis worldwide. Approximately one million deaths each year are attributed to HBV infection. The virus is adapted to the human host and has developed mechanisms to evade immunity. For example, integration of HBV DNA into the chromosomal DNA of hepatocytes yields the formation of HBV surface antigen (HBsAg). HBsAg derived from integrated HBV DNA is not required for virus replication but may facilitate viral persistence by dampening antiviral immunity. In paper I we utilized deep sequencing to show that HBV integrations, with ensuing production of HBsAg, are much more common than previously appreciated. We also found that integrated HBV DNA may facilitate co-infection with the hepatitis delta virus (HDV), which propagates only in the presence of HBsAg. In paper II we show that samples from patients lacking HBV replication still carried HBV DNA integrations along with HDV RNA, implying that HDV replication may utilize integration-derived HBsAg. Accordingly, we observed that HBsAg levels in blood correlated with the number of HBV integrations in liver tissue samples from HDV-infected patients. By combining sequencing methods and digital PCR we provide evidence to support that the HBV particle often contains both degraded RNA as well as incomplete HBV DNA genomes (paper III). The thesis additionally includes deep sequencing-based methods for HBV whole genome sequencing, which generated highly accurate consensus sequences much faster and less costly compared to Sanger sequencing (paper IV and V). In conclusion, we show that HBV integrations are highly expressed and contribute to HBsAg levels in blood, may support HDV replication and that novel deep sequencing methods may be valuable in routine diagnostics.
|
|
| 20. |
- Ringlander, Johan, et al.
(författare)
-
Hepatitis B virus particles in serum contain minus strand DNA and degraded pregenomic RNA of variable and inverse lengths
- 2024
-
Ingår i: LIVER INTERNATIONAL. - 1478-3223 .- 1478-3231.
-
Tidskriftsartikel (refereegranskat)abstract
- This study utilized digital PCR to quantify HBV RNA and HBV DNA within three regions of the HBV genome. Analysis of 75 serum samples from patients with chronic infection showed that HBV RNA levels were higher in core than in S and X regions (median 7.20 vs. 6.80 and 6.58 log copies/mL; p < .0001), whereas HBV DNA levels showed an inverse gradient (7.71 vs. 7.73 and 7.77 log copies/mL, p < .001). On average 80% of the nucleic acid was DNA by quantification in core. The core DNA/RNA ratio was associated with viral load and genotype. In individual patients, the relations between RNA levels in core, S and X were stable over time (n = 29; p = .006). The results suggest that pregenomic RNA is completely reverse transcribed to minus DNA in approximate to 75% of the virus particles, whereas the remaining 25% contain both RNA and DNA of lengths that reflect variable progress of the polymerase.
|
|
| 21. |
- Ringlander, Johan, et al.
(författare)
-
Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2
- 2022
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 119:6
-
Tidskriftsartikel (refereegranskat)abstract
- Adenosine deaminases acting on RNA (ADAR) are RNA-editing enzymes that may restrict viral infection. We have utilized deep sequencing to determine adenosine to guanine (AfiG) mutations, signifying ADAR activity, in clinical samples retrieved from 93 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)- infected patients in the early phase of the COVID-19 pandemic. AfiG mutations were detected in 0.035% (median) of RNA residues and were predominantly nonsynonymous. These mutations were rarely detected in the major viral population but were abundant in minor viral populations in which AfiG was more prevalent than any other mutation (P < 0.001). The AfiG substitutions accumulated in the spike protein gene at positions corresponding to amino acids 505 to 510 in the receptor binding motif and at amino acids 650 to 655. The frequency of AfiG mutations in minor viral populations was significantly associated with low viral load (P < 0.001). We additionally analyzed AfiG mutations in 288,247 SARSCoV- 2 major (consensus) sequences representing the dominant viral population. The AfiG mutations observed in minor viral populations in the initial patient cohort were increasingly detected in European consensus sequences between March and June 2020 (P < 0.001) followed by a decline of these mutations in autumn and early winter (P < 0.001). We propose that ADAR-induced deamination of RNA is a significant source of mutated SARS-CoV-2 and hypothesize that the degree of RNA deamination may determine or reflect viral fitness and infectivity. © 2022 National Academy of Sciences. All rights reserved.
|
|
| 22. |
- Ringlander, Johan, et al.
(författare)
-
Recurrent and persistent infection with SARS-CoV-2-epidemiological data and case reports from Western Sweden, 2020
- 2021
-
Ingår i: Infectious Diseases. - : Informa UK Limited. - 2374-4235 .- 2374-4243. ; 53:12, s. 900-907
-
Tidskriftsartikel (refereegranskat)abstract
- Background Reinfections with SARS-CoV-2 have been reported and most cases were classified as mild. Reports of persistent infection with SARS-CoV-2 are rare. Aim To investigate the frequency of recurrent and persistent infection with SARS-CoV-2. Methods Possible cases of reinfection and persistent infection were retrospectively identified in a database of 59,998 patients. Deep sequencing of SARS-CoV-2 genomes was performed. Results We report the first case of COVID-19 reinfection in Sweden and three cases of infection with persistence over several months. The rate of sequencing-verified reinfection was 0.02% (one patient out of 6014 patients testing positive during the period). Conclusions The reinfected patient had mild symptoms during the second episode, which might reflect partial immunity. The frequency of reinfection during the first wave of the pandemic in western Sweden was very low. Our results indicate that elderly with a putative reinfection more likely have persistent COVID-19.
|
|
| 23. |
- Rydell, Gustaf E, et al.
(författare)
-
Quantification of viral RNA in multiple pieces of explant liver tissue shows distinct focal differences of hepatitis B infection.
- 2022
-
Ingår i: The Journal of infectious diseases. - : Oxford University Press (OUP). - 1537-6613 .- 0022-1899. ; 226:6, s. 1036-1040
-
Tidskriftsartikel (refereegranskat)abstract
- Hepatitis B virus (HBV) DNA and RNA were quantified by digital PCR assays in 20-30 tissue pieces from each of four liver explants with cirrhosis caused by HBV. The within-patient variability of HBV RNA levels between pieces was up to thousand-fold. Core RNA and S RNA levels were similar and correlated strongly when replication was high, supporting transcription from cccDNA. By contrast, enhanced expression of S RNA relative to cccDNA and core RNA in patients with medium-high or low replication supports that HBV surface antigen (HBsAg) can be expressed mainly from integrated HBV DNA in such patients.
|
|
| 24. |
- Sengpiel, Verena, 1977, et al.
(författare)
-
Confirmed reinfection with SARS-CoV-2 during a pregnancy: A case report.
- 2022
-
Ingår i: Clinical case reports. - : Wiley. - 2050-0904. ; 10:2
-
Tidskriftsartikel (refereegranskat)abstract
- Pregnancy might impact immunity after SARS-CoV-2 infection and/or vaccination. We describe the first case of reinfection with SARS-CoV-2 during a pregnancy. While the mother lacked detectable antibodies 2months after the first infection, both mother and baby had IgG antibodies at delivery. Infection did not cause any adverse pregnancy outcome.
|
|
| 25. |
- Törnell, Andreas, 1994, et al.
(författare)
-
Induction and subsequent decline of S1-specific T cell reactivity after COVID-19 vaccination
- 2023
-
Ingår i: Clinical Immunology. - : Elsevier BV. - 1521-6616. ; 248
-
Tidskriftsartikel (refereegranskat)abstract
- We analyzed magnitude and duration of SARS-CoV-2-specific T cell responses in healthy, infection-naive subjects receiving COVID-19 vaccines. Overlapping peptides spanning the N-terminal spike 1 (S1) domain of the spike protein triggered secretion of the T cell-derived cytokine interleukin-2 ex vivo in 94/94 whole blood samples from vaccinated subjects at levels exceeding those recorded in all 45 pre-vaccination samples. S1-specific T cell reactivity was stronger in vaccinated subjects compared with subjects recovering from natural COVID-19 and decayed with an estimated half-life of 134 days in the first six months after the 2nd vaccination. We conclude that COVID-19 vaccination induces robust T cell immunity that subsequently declines.EudraCT 2021-000349-42. https://www.clinicaltrialsregister.eu/ctr-search/search?query=2021-000349-42
|
|
