Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation

Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies.

Prevalence of Hepatitis C Virus Infection, Genotypes and Subtypes in Migrants from Pakistan in Barcelona, Spain

Background

Hepatitis C virus (HCV) is a major cause of chronic liver infection with 71 million people infected worldwide. Pakistan has the second highest prevalence of HCV infection and more than half (52%) of Pakistani living in Spain reside in Barcelona. The aim of this study was to analyse the seroprevalence and viraemic rate and determine the genotypes and subtypes of HCV among Pakistanis living in the southern metropolitan area of Barcelona.

Methods

We included all Pakistani patients seeking primary healthcare in the southern metropolitan area of Barcelona from August 2011 to July 2014. Serum samples were screened for HCV antibodies. HCV viral load was determined by reverse transcription polymerase chain reaction and genotypes and subtypes were performed using Versant HCV Genotype and/or deep-sequencing. Screening for hepatitis B virus (HBV) was also carried out.

Results

Among 5877 Pakistani patients, 565 (9.61%) were screened for anti-HCV antibodies, with 68 (12.04%) being positive. The viral load was determined in 65, with 31 presenting active infection and the viraemic rate was 47.69% (95% confidence interval 36.02-59.62). HCV genotyping and subtyping were performed in 24 individuals. Most infections corresponded to HCV genotype 3 (91.67%), and high resolution HCV subtyping was performed in 18 samples, 16 of which presented subtype 3a. One subject presented HBV coinfection with undetectable HBV DNA. During the study period, we identified a possible case of HCV vertical transmission followed by spontaneous viraemia clearance in a chronically infected mother with a C/T IL28B genetic polymorphism.

Conclusion

These results suggest that general HCV screening protocols in patients from high prevalence countries, such as Pakistan, would be helpful to identify and treat active HCV infections. This could avoid further transmission and contribute to building targeted health policies for micro-elimination of HCV infection in specific communities.

Evaluation of Humoral and Cellular Immune Responses to the SARS-CoV-2 Vaccine in Patients With Common Variable Immunodeficiency Phenotype and Patient Receiving B-Cell Depletion Therapy

Introduction

SARS-CoV-2 vaccines' effectiveness is not yet clearly known in immunocompromised patients. This study aims to assess the humoral and cellular specific immune response to SARS-CoV-2 vaccines and the predictors of poor response in patients with common variable immunodeficiency (CVID) phenotype and in patients treated with B-cell depletion therapies (BCDT), as well as the safety of these vaccines.

Methods

From March to September 2021, we performed a prospective study of all adult patients who would receive the SARS-CoV-2 vaccination and were previously diagnosed with (i) a CVID syndrome (CVID phenotype group; n=28) or (ii) multiple sclerosis (MS) treated with B-cell depleting therapies three to six months before vaccination (BCD group; n=24). Participants with prior SARS-CoV-2 infection; or prior SARS-CoV-2 vaccine administration; or use of any immunosuppressant (except BCDT in MS group) were excluded. A group of subjects without any medical condition that confers immunosuppression and who met all study criteria was also assessed (control group; n=14). A chemiluminescence immunoassay was used to determine pre- and post-SARS-CoV-2 vaccine anti-S IgG antibodies. T-cell specific response was assessed by analysis of pre- and post-SARS-CoV-2 vaccination blood samples with an interferon-gamma release assay. The baseline blood sample also included several biochemical, haematological and immunological analyses.

Results

SARS-CoV-2 vaccines are safe in immunocompromised patients, although their effectiveness was lower than in healthy individuals. CVID phenotype patients showed impaired humoral (29%) and cellular (29%) response, while BCD patients fundamentally presented humoral failure (54%). Low IgA values, low CD19+ peripheral B cells, low switched memory B cells, and a low CD4+/CD8+ ratio were predictors of inadequate specific antibody response in CVID phenotype patients. No factor was found to predict poor cellular response in CVID phenotype patients, nor a defective humoral or cellular response in BCD patients.

Conclusion

The effectiveness of SARS-CoV-2 vaccines in CVID phenotype and BCD patients is lower than in healthy individuals. Knowledge of predictive factors of humoral and cellular response failure in immunocompromised patients could be very useful in clinical practice, and thus, studies in this regard are clearly needed.

Monitoring of SARS-CoV-2 seroprevalence among primary healthcare patients in the Barcelona Metropolitan Area: the SeroCAP sentinel network protocol

INTRODUCTION

SARS-CoV-2 seroprevalence studies are currently being recommended and implemented in many countries. Forming part of the COVID-19 monitoring and evaluation plan of the Catalan Government Health Department, our network aims to initiate a primary healthcare sentinel monitoring system as a surrogate of SARS-CoV-2 exposure in the Barcelona Metropolitan Area.

METHODS AND ANALYSIS

The seroCAP is a serial cross-sectional study, which will be performed in the Barcelona Metropolitan Area to estimate antibodies against SARS-CoV-2. From February 2021 to March 2022, the detection of serum IgG antibodies against SARS-CoV-2 trimeric spike protein will be performed on a monthly basis in blood samples collected for diverse clinical purposes in three reference hospitals from the three Barcelona healthcare areas (BCN areas). The samples (n=2588/month) will be from patients attended by 30 primary healthcare teams at 30 basic healthcare areas (BHA). A lab software algorithm will systematically select the samples by age and sex. Seroprevalence will be estimated and monitored by age, sex, BCN area and BHA. Descriptive and cluster analysis of the characteristics and distribution of SARS-CoV-2 infections will be performed. Sociodemographic, socioeconomic and morbidity-associated factors will be determined using logistic regression. We will explore the association between seroprevalence, SARS-CoV-2 confirmed cases and the implemented measures using interrupted time series analysis.

ETHICS AND DISSEMINATION

Ethical approval was obtained from the University Institute Foundation for Primary Health Care Research Jordi Gol i Gurina ethics committee. An informed consent is not required regarding the approval of the secondary use of biological samples within the framework of the COVID-19 pandemic. A report will be generated quarterly. The final analysis, conclusions and recommendations will be shared with the stakeholders and communicated to the general public. Manuscripts resulting from the network will be submitted for publication in peer-reviewed journals.

Building on gAMBI in ports for a challenging biological invasions scenario: Blue-gNIS as a proof of concept

The status of aquatic ecosystems has historically been monitored by the use of biotic indices. However, few biotic measures consider the presence of non-indigenous species as a sign of anthropogenic pollution and habitat disturbance even when this may seriously affect the metric scores and ecological status classifications of an environment. Today, biological invasions are currently one of the greatest threats to biodiversity and sustainable blue economies around the world. In this work, environmental assessments were conducted in the Port of Gijon, Northern Spain, using eDNA metabarcoding, and the gAMBI (genetics based AZTI Marine Biotic Index) was estimated. Results indicate a high/good ecological status within the port. However, nine non-indigenous species and five invasive species were found, and a modification of the gAMBI that includes species invasiveness was proposed: Blue-gNIS. The index was preliminary tested against existing validated indices such as gAMBI, BENTIX (based on the ecology of macroinvertebrates) and ALEX (based on the invasiveness of the species). Blue-gNIS classified the port in a good ecological status and showed its potential usefulness to achieve more complete water quality assessments of ports.

Perspectives on the marine environment and biodiversity in recreational ports: The marina of Gijon as a case study

Recreational ports are known to be sources of pollution to the coastal marine environment due to the pouring of pollutants or the transfer of invasive species to neighboring areas. Nonetheless, the responsibility of protecting the marine environment does not lie solely on the users of the ports, but also affects the rest of citizens. Thus, an effective communication is necessary between scientists and citizens to avoid the lack of knowledge and boost cooperation against these environmental problems. In this study, (focused on the marina of Gijon, Northwestern Spain) citizens set education and social media as the main sources of information, rarely considering science outreach. Also, their environmental knowledge showed to be based on a visual perception, rather than on a cognitive one, as marine litter was considered a great environmental problem, while invasive species and biofouling went unnoticed, remarking the lack of an effective communication from scientific sources.

Epidemiology of congenital Chagas disease 6 years after implementation of a public health surveillance system, Catalonia, 2010 to 2015

Background

Chagas disease is endemic in Latin America and affects 8 million people worldwide. In 2010, Catalonia introduced systematic public health surveillance to detect and treat congenital Chagas disease.

Aim

The objective was to evaluate the health outcomes of the congenital Chagas disease screening programme during the first 6 years (2010–2015) after its introduction in Catalonia.

Methods

In a surveillance system, we screened pregnant women and newborns and other children of positive mothers, and treated Chagas-positive newborns and children. Diagnosis was confirmed for pregnant women and children with two positive serological tests and for newborns with microhaematocrit and/or PCR at birth or serology at age 9 months.

Results

From 2010 to 2015, the estimated screening coverage rate increased from 68.4% to 88.6%. In this period, 33,469 pregnant women were tested for Trypanosoma cruzi and 937 positive cases were diagnosed. The overall prevalence was 2.8 cases per 100 pregnancies per year (15.8 in Bolivian women). We followed 82.8% of newborns until serological testing at age 9–12 months and 28 were diagnosed with Chagas disease (congenital transmission rate: 4.17%). Of 518 siblings, 178 (34.3%) were tested and 14 (7.8%) were positive for T. cruzi. Having other children with Chagas disease and the heart clinical form of Chagas disease were maternal risk factors associated with congenital T. cruzi infection (p < 0.05).

Conclusion

The increased screening coverage rate indicates consolidation of the programme in Catalonia. The rate of Chagas disease congenital transmission in Catalonia is in accordance with the range in non-endemic countries.

Infection by Strongyloides stercoralis in immigrants with Chagas disease: evaluation of eosinophilia as screening method in primary care

OBJECTIVES

To evaluate co-infection of Strongyloides stercoralis and Trypanosoma cruzi and to assess eosinophilia as a screening test for the detection of S. stercoralis infection in patients with Chagas disease (CD).

METHODS

A retrospective diagnostic validation study was performed on serum samples from primary care patients diagnosed with CD in the southern Barcelona metropolitan area. All samples with eosinophilia (n = 87) and a random sample of non-eosinophilic sera (n = 180) were selected. Diagnosis of CD was based on positive serology by means of two tests: ORTHO® T. cruzi ELISA test, and BIO-FLASH® Chagas or Bioelisa CHAGAS. SCIMEDX ELISA STRONGY-96 was used to diagnose strongyloidiasis.

RESULTS

Strongyloides stercoralis serology was positive in 15% of patients of whom 95% showed eosinophilia, vs. 21% of those with negative serology (P < 0.001), with differences in the mean eosinophil count (0.49 vs. 0.27 × 10⁹ /l). Only 1.1% of patients with CD but without eosinophilia presented positive serology for S. stercoralis, whereas 44% of patients with CD and eosinophilia did (P < 0.001). Sensitivity and specificity values for eosinophilia were thus 95% and 79%, respectively. PPV was 42.5% and NPV, 98.9%.

CONCLUSIONS

The prevalence of co-infection by T. cruzi and S. stercoralis is not negligible and has probably been underestimated for years in many areas, due to frequently subclinical infections. Therefore, serology seems mandatory for these patients and the use of eosinophilia as initial screening could facilitate the task, decreasing the number of analyses to be performed.

Barcodes of marine invertebrates from north Iberian ports: Native diversity and resistance to biological invasions

Ports are gateways for many marine organisms transported by ships worldwide, especially non-indigenous species (NIS). In this study carried out in North Iberian ports (Cantabrian Sea, Bay of Biscay) we have observed 38% of exotic macroinvertebrates. Four species, namely the barnacle Austrominius modestus, the tubeworm Ficopomatus enigmaticus, the Pacific oyster Crassostrea gigas and the pygmy mussel Xenostrobus securis, exhibited clear signs of invasiveness. A total of 671 barcode (cytochrome oxidase subunit I or 18S rRNA) genes were obtained and confirmed the species status of some cryptic NIS. Negative and significant correlation between diversity estimators of native biota and proportion of NIS suggests biotic resistance in ports. This could be applied to management of port biota for contributing to prevent the settlement of biopollutants in these areas which are very sensitive to biological invasions.

Food control and a citizen science approach for improving teaching of Genetics in universities

A Citizen Science approach was implemented in the laboratory practices of Genetics at the University of Oviedo, related with the engaging topic of Food Control. Real samples of food products consumed by students at home (students as samplers) were employed as teaching material in three different courses of Genetics during the academic year 2014-2015: Experimental Methods in Food Production (MBTA) (Master level), and Applied Molecular Biology (BMA) and Conservation Genetics and Breeding (COMGE) (Bachelor/Degree level). Molecular genetics based on PCR amplification of DNA markers was employed for species identification of 22 seafood products in COMGE and MBTA, and for detection of genetically modified (GM) maize from nine products in BMA. In total six seafood products incorrectly labeled (27%), and two undeclared GM maize (22%) were found. A post-Laboratory survey was applied for assessing the efficacy of the approach for improving motivation in the Laboratory Practices of Genetics. Results confirmed that students that worked on their own samples from local markets were significantly more motivated and better evaluated their Genetic laboratory practices than control students (χ(2)  = 12.11 p = 0.033). Our results suggest that citizen science approaches could not be only useful for improving teaching of Genetics in universities but also to incorporate students and citizens as active agents in food control. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):450-462, 2016.

[Group B streptococcal early-onset neonatal sepsis in the area of Barcelona (2004-2010). Analysis of missed opportunities for prevention]

OBJECTIVES

To study the evolution of the incidence of early-onset neonatal sepsis (EOS) by Streptococcus agalactiae in the area of Barcelona and to analyze failure of compliance with the prevention protocol.

METHODS

A retrospective review was carried out on EOS cases in 8 Health-Care Centers in the Barcelona area between 2004 and 2010.

RESULTS

Forty-nine newborns from 48 mothers were diagnosed with EOS. The incidence was 0.29‰ living newborns (0.18-0.47‰), with no significant differences in the fluctuations along the 7 years. The mortality rate was 8.16%. In 68.5% cases the maternal colonization studies were negative, and in 21% these studies were not performed. No risk factors were detected in 58.3% of pregnant women, and 22.9% of births were premature. In 58% of cases intra-partum antibiotic prophylaxis was not administered because it was not indicated, and in 42% due to failure to follow the protocol (3 strains were resistant to erythromycin). Resistance to clindamycin was 33.3%. The Streptococcus agalactiae serotypes more frequently isolated were iii, v, and ia.

CONCLUSIONS

No significant changes were detected in the incidence of Streptococcus agalactiae EOS in the 7 years of the study. The increased sensitivity of screening methods with the use of molecular techniques, the performance of susceptibility testing of strains isolated from pregnant women, and the improvement of communication between Health-Care Centers, can contribute to a better implementation of the protocol, as well as to reduce the incidence of EOS.

Two vs. three sputum samples for microscopic detection of tuberculosis in a high HIV prevalence population

SETTING

A busy urban hospital in Cameroon.

OBJECTIVES

To compare the yield in bacteriologically proven tuberculosis (TB) cases examining two morning vs. three spot-morning-spot sputum specimens (MM vs. SMS) by direct microscopy for acid-fast bacilli (AFB).

DESIGN

Repeated temporal cross-over between MM and SMS sampling for successive TB suspects, using culture as gold standard.

RESULTS

A total of 799 suspects were screened using the MM strategy, identifying 223 smear-positives, and 808 suspects with the SMS strategy, yielding 236 smear-positives. Of the MM, 256 were culture-positive, of whom 195 (76%) were smear-positive. For SMS, these figures were respectively 281 and 206 (73%), a non-significant difference. The MM and SMS strategies also detected respectively 28 and 30 smear-positive cases not confirmed by culture. No cases were lost to treatment with either strategy.

CONCLUSIONS

In this population with a high prevalence of human immunodeficiency virus (HIV) with late case presentation, smear microscopy of two morning specimens detected at least as many positive cases as the classical strategy, and no cases were lost before treatment. Two specimens for initial TB suspect screening can thus be recommended, also without excessive workload. Comparative studies in populations presenting with paucibacillary sputum are needed to determine the equivalent quality and yield of an alternative strategy with two spot specimens at consultation.

[Decreasing incidence of perinatal group B streptococcal disease (Barcelona 1994-2002). Relation with hospital prevention policies]

INTRODUCTION

To analyze the incidence of perinatal sepsis due to group B streptococcus (GBS) as related to compliance with recommendations for its prevention issued by the Catalan Societies for Obstetrics, for Pediatrics, and for Infectious Diseases and Clinical Microbiology in 1997.

METHODS

The study was conducted from 1994 to 2001 in 10 Barcelona-area hospitals, where 157,848 live infants were born.

RESULTS

GBS disease was diagnosed in 129 neonates. Incidence decreased by 86.1% over the study period, from 1.92 cases per 1000 live births in 1994 to 0.26 per 1000 in 2001 (p < 0.001). Changes in the characteristics of perinatal GBS disease were observed in the 18 cases diagnosed in the last 3 years, the time when prevention policies were operative. The incidence was lower (0.28 per 1000 vs. 1.19 for the previous 5 years, p <.00006), the proportion of mothers without risk factors was greater (77.8% vs. 55.9%, p 5 0.009), and premature neonates were not affected (0% vs. 12.6%, p 5 0.003); nevertheless, mortality was similar (5.5% vs. 4.5%, p 5 0.8). Among these 18 cases of sepsis, 9 can be considered failures inherent to the prevention policy and 9 failures of compliance. Only 3 hospitals had prevention policies in 1994, whereas all 10 used intrapartum prophylaxis based on screening results in 2001.

CONCLUSIONS

A substantial decrease in the incidence of perinatal GBS disease coinciding with the application of prevention measures for this pathology has been registered in 10 participating hospitals over the 1994-2001 period.

[Neonatal infection by Streptococcus agalactiae. Multicenter study in the area of Barcelona, Spain]

BACKGROUND

Streptococcus agalactiae or streptococcus group B (SGB) is the main etiologic agent of early neonatal sepsis. A multicenter study was performed with the aim of determining the incidence and characteristics of this disease in our medium and contribute the design of an adequate prevention protocol.

METHODS

Ten hospitals and two primary health care centers were implicated in the study; 103 microbiology confirmed episodes of SGB neonatal sepsis (blood and/or LCR positive) were reported from 1994 to 1996.

RESULTS

The incidence of early SGB neonatal sepsis was 1.48/1,000 live births with a mortality of 8.7%. The cultures, for detecting the state of the SGB carrier were performed in only 26 (25%) of the patients. At least one of the factors described for risk of perinatal SGB infection was observed in 46% of the mothers, with the most frequent being prolonged amniorrhea (26%), intrapartum fever (17%), and early delivery (14%). At the time of delivery only 10.7% of the mothers received endovenous antibiotherapy.

CONCLUSIONS

From these results the following recommendations have been made: a) detection of SGB carriers by the systematic practice of blood cultures in the last weeks of gestation and b) the administration of intrapartum antibiotic prophylaxis in both early births (< 37 weeks) and in all the SGB carriers should be undertaken. With these measures we aim to decrease the neonatal infections by streptococcus group B.