Background Hepatitis B virus (HBV) genomes integrated into human DNA significantly contribute to surface antigen (HBsAg) production and may drive hepatocellular carcinoma (HCC). Long-read sequencing methods like Nanopore offer advantages over short-read next-generation sequencing (NGS) by providing continuous reads of whole transcripts, but their application to HBV integration analysis remains limited.Objective To develop and apply a method combining semi-nested PCR with Nanopore sequencing to analyse HBV transcripts, including canonical RNA, HBV-human fusion transcripts, and spliced forms in patients with HBV- or hepatitis D virus (HDV)-induced liver disease.Methods Nine liver-transplanted patients with HBV- or HDV-related cirrhosis or HCC were studied. Semi-nested PCR was used to amplify all HBV transcripts, followed by Nanopore sequencing. The approach allowed differentiation between canonical (cccDNA-derived) and fusion transcripts. Reads containing the 3 ' redundancy beyond nucleotide 1826, exclusive to cccDNA-derived RNA, were quantified to determine the source of HBV RNA.Results Unique and total HBV-human fusion RNA reads correlated with serum levels of HBV DNA and HBsAg. Integration-derived RNA accounted for a median of 97% (range: 16%-100%) of HBV RNA. PreS1 RNA levels were much lower than preS2 but sufficient for HDV particle production in an HDV patient without cccDNA-derived transcripts.Conclusion This method enables a simplified and comprehensive analysis of HBV transcripts. The results highlight the predominance of integration-derived RNA and support the presence of cccDNA-independent hepatitis D virus production. Nanopore sequencing offers valuable insights into HBV and HDV biology, supporting its role in understanding viral pathogenesis and therapeutic targeting.

Abstract Cervical cancer from persistent HPV infection is the leading cause of cancer death among Sub-Saharan African women. We here addressed the existing knowledge gap concerning the prevalence of HPV infection and cervical lesions in asymptomatic women living with HIV (WLWH) in Addis Ababa, Ethiopia. Adult WLWH ( N = 334) were recruited at the HIV clinic of the Tikur Anbessa Specialized Hospital, Addis Ababa. Real-time PCR targeting 12 high-risk (HR) and 2 low-risk HPV types on cervical samples and Pap smear testing were performed. Logistic regression was used in IBM SPSS Statistics to identify factors associated with HPV infection and abnormal cytology. HR-HPV infections occurred in 20.6% of participants and the most prevalent HR-HPV genotypes were HPV35 (16.8%) and HPV16 (14.7%). Abnormal cytology was more common among HR-HPV–positive women than HR-HPV–negative women (36.1% vs. 12.6%, p < 0.0001). LSIL and HSIL were detected in 9.9% and 6.6% of HR-HPV–positive women, respectively. Condom use was associated with reduced odds of HPV infection and abnormal cytology. HR-HPV infections dominated by non-HPV16/18 types and abnormal cytology were common among asymptomatic WLWH in Ethiopia underscoring the need for strengthened cervical cancer screening, HPV vaccinations and safe-sex education for this high-risk population.

Deep sequencing of the whole hepatitis B virus genome increases the analytical resolution and has the potential to improve molecular epidemiology investigations. The aim of this study was to develop and evaluate the performance of such deep sequencing using the Nanopore technology. The method includes an initial PCR step to generate two overlapping amplicons that cover the whole relaxed circular HBV genome found in circulating viral particles and covalently closed circular DNA in infected hepatocytes, followed by sequencing using the Nanopore rapid barcoding kit that allows parallel analysis of several samples in one reaction. The libraries can be sequenced with the standard Nanopore flow cell on MiniIon or GridIon devices, as well as the Flongle. The performance of the method was evaluated by comparing Nanopore and Sanger sequences or qPCR results from 64 clinical samples. The Nanopore-derived consensus sequences were, on average, 99.9% similar to those from Sanger sequencing, and the full HBV genome was determined in samples with HBV DNA levels of approximately 3 log10 IU/mL with MagNA pure 96 extraction and < 2 log10 IU/mL using a high-volume manual extraction protocol on a subset of samples from patients with very low viral load (1.62-3.74 IU/mL). A perfect agreement with Sanger/qPCR-derived genotype was seen. The cost of sequencing per genome using the Nanopore method is low, ranging from 6 to 37 euros. We conclude that whole genome sequencing of HBV with Nanopore is well suited for genomic characterization, antiviral resistance mutation analysis, and genotyping of HBV in a routine laboratory setting.

Chronic infection by human papillomavirus (HPV) is necessary for the development of almost all cervical cancers. The study assessed the prevalence of vaginal and cervical HPV infections in women living with HIV (WLWH) in Rwanda and assessed the performance of vaginal HPV screening to detect cervical HPV infections. HIV-positive women (N = 413) attending the HIV clinic at the University Teaching Hospital of Kigali, Kigali, Rwanda, were interviewed and vaginal and cervical swab samples for HPV testing and a pap smear sample were taken. RT-PCR was performed to detect twelve high-risk (HR)-HPVs (HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59 and two low-risk (LR)-HPVs (HPV6 and 11) and conventional cytology was performed. Vaginal HR-HPV/LR-HPV infections occurred in 39.2

ABSTRACT Current guidelines to prevent hepatocellular carcinoma (HCC) by chronic hepatitis B virus (HBV) infection are based on risk assessments that include age, sex, and virological and biochemical parameters. The study aim was to investigate the impact of predictive markers on long‐term outcomes. The clinical outcomes of 100 patients with chronic hepatitis B were investigated 30 years after a baseline assessment that included liver biopsy. A favourable outcome—HBsAg loss or HBeAg‐negative infection (ENI; previously termed ‘inactive carrier’)—was observed in 74% of all patients, whereas 7% developed HCC. HBsAg loss was observed in 75% of patients with genotype A, compared with 42%, 33% and 0% with genotypes D, B and C, respectively ( p < 0.0001). HCC developed in 3 patients (33%) with genotype C as compared with 3 (17%), 1 (2%) and 0 patients with genotypes B, D and A, respectively ( p < 0.0001). In multiple logistic regression analysis, both HBsAg loss and HCC were associated with HBV genotype and baseline HBV DNA level, and HCC also with histological score. The results suggest that genotyping and histological assessment may improve outcome prediction and help decisions about HCC screening, particularly in populations with HBV‐infected individuals of mixed geographic origin.

Background:Real-time polymerase chain reaction (PCR), the gold standard for viral diagnostics in children, is a sensitive but resource-intensive method. Viral antigen tests are cheaper and more rapid but have lower sensitivity. The clinical relevance of PCR positivity has been questioned because of its high sensitivity and detection in asymptomatic individuals. Thus, we hypothesized that antigen test positivity might be more indicative of active infection than PCR positivity. The aim of this study was to evaluate the antigen test mariPOC Respi test for the detection of 10 respiratory viruses versus PCR in relation to viral load, days of illness, and immunological viral response. Methods:Children 1-59 months old with lower respiratory infections were prospectively enrolled at the emergency department, Sachs' Children and Youth Hospital, Stockholm, Sweden, between 2017 and 2019. Nasopharyngeal samples were collected from all cases (n = 314). The sensitivity and specificity of the mariPOC Respi test were assessed in children with and without an immunological viral response (defined as a blood myxovirus resistance Protein A level > 430 μg/L), using PCR as the reference standard. Results:The highest sensitivity for mariPOC Respi test was attained for respiratory syncytial virus (68%; 95% confidence interval: 63-73). Restricting the analysis to cases with a viral immunological response did not alter the results considerably. Conclusion:These findings do not support the idea that mariPOC Respi test positivity to a higher degree than PCR correlates with clinical relevance, as indicated by an immunological viral response. The role of antigen tests in current clinical practice requires further discussion, particularly in the post-pandemic era. Trial Registration:ClinicalTrials.gov identifier: NCT03233516.

IntroductionPneumococcal conjugate vaccines have reduced severe disease attributed to vaccine-type pneumococci in children. However, the effect is dependent on serotype distribution in the population and disease development may be influenced by co-occurrence of viral and bacterial pathogens in the nasopharynx.MethodsFollowing introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Tanzania we performed repeated cross-sectional surveys, including 775 children below 2 years of age attending primary healthcare centers. All children were sampled from nasopharynx and pneumococci were detected by single-target PCR. Pneumococcal serotypes/groups and presence of viruses and other bacteria were determined by two multiplex PCR assays.ResultsThe prevalence of PCV13 vaccine-type pneumococci decreased by 50%, but residual vaccine-types were still detected in 21% of the children 2 years after PCV13 introduction. An increase in the non-vaccine-type 15 BC was observed. Pneumococci were often co-occurring with Haemophilus influenzae, and detection of rhino/enterovirus was associated with higher pneumococcal load.DiscussionWe conclude that presence of residual vaccine-type and emerging non-vaccine-type pneumococci in Tanzanian children demand continued pneumococcal surveillance. High co-occurrence of viral and bacterial pathogens may contribute to the disease burden and indicate the need of multiple public health interventions to improve child health in Tanzania.

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.

The causes of diarrhea after 10 years of rotavirus vaccination in Rwanda were investigated with real-time polymerase chain reaction in 496 children with diarrhea and 298 without. Rotavirus was detected in 11% of children with diarrhea (odds ratio, 2.48; P = .002). Comparison of population attributable fractions (PAFs) shows that Shigella (PAF, 11%) and enterotoxigenic Escherichia coli producing labile toxin (PAF, 12%) have replaced rotavirus as the main causative agents. The PAF for rotavirus had declined from 41% prevaccination to 6.5% postvaccination, indicating that rotavirus has become one among several similarly important causes of childhood diarrhea in Rwanda. A rotavirus genotype shift to G3P[8] points at the importance of continued genotype surveillance.

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 ≈75% of the virus particles, whereas the remaining 25% contain both RNA and DNA of lengths that reflect variable progress of the polymerase.

How common it is with the presence of human papillomavirus (HPV) in the healthy and diseased oral cavity is largely unknown for Africans. In this cross-sectional study we assessed the prevalence of oral HPV and the risk factors associated with HPV contraction including sexual practice in the urban and rural Zambian population. Urban (N = 188) and rural (N = 211) Zambian adults aged 21 years and older living in Ndola and Mansa, respectively, were interviewed about demographical data, oral and coital sexual history and tobacco and alcohol use. Participants were orally examined and underwent a buccal swab test for 12 high-risk HPVs (HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59) and two low-risk HPVs (HPV6 and 11) with real-time PCR. Alcohol consumption was higher in urban participants than rural participants, i.e., 34.1

Mother-to-child transmission (MTCT) has been the main cause of chronic hepatitis B virus (HBV) infection, particularly in East Asia. Hepatitis B immunoglobulin (HBIG) and vaccination given directly after birth effectively prevents hepatitis B surface antigen (HBsAg)-positive (overt) HBV infection, but occult hepatitis B infection (OBI) may develop despite adequate prophylaxis. The aim of this study was to investigate the long-term outcome in children born to mothers with very high HBV DNA levels with special focus on children discovered in early childhood with OBI. One-year and long-term outcome regarding overt and occult HBV infection were analysed in 66 children born to hepatitis B e antigen (HBeAg)-positive mothers, and were compared with one-year outcome in 69 children born to HBeAg-negative mothers. The children were born between 1998 and 2018. Six children born to HBeAg-positive mothers developed overt chronic HBV infection, in two cases after normal pregnancies and despite HBIG and vaccination, but never when nucleotide analogue treatment was given during pregnancy. OBI with HBV DNA detected in serum in the absence of surface antigen (HBsAg) was observed in four children at the age of 1 year. One of them was transiently HBsAg-positive at the age of 7 years. At long-term follow-up, six children had overt chronic infection, one had OBI and six had previous OBI or positive anti-HBc suggesting resolved unidentified infections. The results indicate that children born to mothers with high HBV DNA levels have approximately 10

Background: The prevalence of human papillomavirus (HPV) infections in other anatomical sites besides the uterine cervix is unknown in East Africa. Here, we assessed the prevalence and concordance of HPVs in different anatomical sites in HIV concordant couples in Rwanda. Methods: Fifty HIV-positive concordant male-female couples at the HIV clinic at the University Teaching Hospital of Kigali in Rwanda were interviewed, swabbed from the oral cavity (OC), oropharynx (OP), anal canal (AC), vagina (V), uterine cervix (UC) and penis. A pap smear test and a self-collected vaginal swab (Vself) were taken. Twelve high-risk (HR)-HPVs were analyzed. Results: HR-HPVs occurred in 10%/12% in OC, 10%/0% in OP and 2%/24% in AC (p = 0.002) in men and women, respectively. HR-HPVs occurred in 24% of UC, 32% of Vself, 30% of V and 24% of P samples. Only 22.2% of all HR-HPV infections were shared by both partners (κ −0.34 ± 0.11; p = 0.004). The type-specific HR-HPV concordance was significant between male to female OC-OC (κ 0.56 ± 0.17), V-VSelf (κ 0.70 ± 0.10), UC-V (κ 0.54 ± 0.13), UC-Vself (κ 0.51 ± 0.13) and UC-female AC (κ 0.42 ± 0.15). Conclusions: HPV infections are prevalent in HIV-positive couples in Rwanda but concordance within couples is low. Vaginal self-sampling for HPV is representative of cervical HPV status.

People who inject drugs (PWID) are exposed to serious health risks such as lethal overdoses, addiction and infections. The patterns of drug use and the prevalence of hepatitis C virus (HCV) infection vary greatly between and even within countries. Data on drugs used for injection are important to inform PWID of risks and adapt healthcare. This study aimed to determine which substances are injected in Gothenburg, Sweden, and estimate the risk of HCV transmission. A total of 150 syringes handed in at the needle and syringe exchange program (NEP) in Gothenburg over a week in November 2021 were analysed for drug content using liquid chromatography coupled with high-resolution mass spectrometry. Using a dose-adjusted comparison, the main drug(s) injected was distinguished from the impurities in the syringes containing several drugs. HCV RNA was quantified by real-time PCR in an additional set of 150 syringes. Drugs were detected in >99% of analysed syringes, and the most common drugs were amphetamine (81%), followed by buprenorphine (8.0%), heroin (6.7%) and alprazolam (4.6%). Less common findings were testosterone (2.7%), methylphenidate (2.0%), MDMA (0.7%), trenbolone (0.7%) and zopiclone (0.7%). Eleven syringes (7.3%) contained more than one drug. HCV RNA was detected in 13% of the syringes, and one in 10 contained enough to potentially transmit an infection. This study underlines the importance of access to NEPs for PWID to reduce the risks associated with drug injection.

Rotavirus vaccination has reduced mortality and hospital admissions due to rotavirus diarrhoea, but its effect on rotavirus infections and the impact of rotavirus genotypes are still unclear. Real-time PCR was used to detect rotavirus and other pathogens in faeces samples from children below five years of age with acute diarrhoea, collected before (n = 827) and after (n = 807, 92% vaccinated) the introduction of vaccination in Rwanda in 2012. Rotavirus was genotyped by targeting VP7 to identify G1, G2, G3, G4, G9 and G12 and VP4 to identify P[4], P[6] and P[8]. In vaccinated children, rotavirus infections were rarer (34% vs. 47%) below 12 months of age, severe dehydration was less frequent, and rotavirus was more often found as a co-infecting agent. (79% vs 67%, p = 0.004). Norovirus genogroup II, astrovirus, and sapovirus were significantly more often detected in vaccinated children. The predominant rotavirus genotypes were G2P[4] and G12P[6] in 2009–2010 (50% and 12%), G9P[8] and G1P[8] in 2011–2012 (51% and 22%), and G12P[8] in 2014–2015 (63%). Rotavirus vaccination in Rwanda has reduced the severity of rotavirus gastroenteritis and rotavirus infection frequency during the first year of life. Rotavirus infections were frequent in vaccinated children with diarrhoea, often as co-pathogen. Rotavirus genotype changes might be unrelated to vaccination because shifts were observed also before its introduction.

ABSTRACT Detailed knowledge regarding norovirus transmission within hospitals is limited. We investigated a norovirus hospital outbreak affecting 65 patients at five different wards. PCR showed that 61 (94%) of the patients were infected with genotype II.4 strains. Successful Ion Torrent deep sequencing of GII.4 positive samples from 59 patients followed by phylogenetic analysis revealed that all sequences but two clustered into four distinct clades. Two of the clades belonged to GII.4 Sydney 2012, while the other two belonged to GII.4 New Orleans 2009. One of the clades was predominant at two wards, while two clades were predominant at one ward each. The fourth clade was found in sporadic cases at several wards. Thus, at four out of five wards, variants from one clade were predominant. At one ward, a single clade accounted for all cases, while at three wards the predominant clade accounted for 60%–71% of cases. Analysis of quasispecies variation identified positions that could further discriminate between variants from separate wards. The results illustrate a complex transmission of healthcare-associated norovirus infections and show that sequencing can be used to discriminate between related and unrelated cases.

Abstract Hepatitis B virus (HBV) DNA and RNA were quantified by digital PCR assays in 20–30 tissue pieces from each of 4 liver explants with cirrhosis caused by HBV. The within-patient variability of HBV RNA levels between pieces was up to a 1000-fold. Core RNA and S RNA levels were similar and correlated strongly when replication was high, supporting that transcription was from covalently closed circular DNA (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.

BACKGROUND:The knowledge on the concentration of viral particles in exhaled breath is limited. The aim of this study was to explore if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be detected in aerosol from subjects with the coronavirus disease 2019 (COVID-19) during various types of breathing and coughing and how infection with SARS-CoV-2 may influence the number and size of exhaled aerosol particles. METHODS:We counted and collected endogenous particles in exhaled breath in subjects with COVID-19 disease by two different impaction-based methods, during 20 normal breaths, 10 airway opening breaths, and three coughs, respectively. Breath samples were analyzed with reverse transcription real-time polymerase chain reaction (RT-PCR). RESULTS:Detection of RNA in aerosol was possible in 10 out of 25 subjects. Presence of virus RNA in aerosol was mainly found in cough samples (n = 8), but also in airway opening breaths (n = 3) and in normal breaths (n = 4), with no overlap between the methods. No association between viral load in aerosol and number exhaled particles <5 μm was found. Subjects with COVID-19 exhaled less particles than healthy controls during normal breathing and airway opening breaths (all P < 0.05), but not during cough. CONCLUSION:SARS-CoV-2 RNA can be detected in exhaled aerosol, sampled during a limited number of breathing and coughing procedures. Detection in aerosol seemed independent of viral load in the upper airway swab as well as of the exhaled number of particles. The infectious potential of the amount of virus detected in aerosol needs to be further explored.