Efficient SARS-CoV-2 Surveillance during the Pandemic-Endemic Transition Using PCR-Based Genotyping Assays.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOC) pose an increased risk to public health due to higher transmissibility and/or immune escape. In this study, we assessed the performance of a custom TaqMan SARS-CoV-2 mutation panel consisting of 10 selected real-time PCR (RT-PCR) genotyping assays compared to whole-genome sequencing (WGS) for identification of 5 VOC circulating in The Netherlands. SARS-CoV-2 positive samples (N = 664), collected during routine PCR screening (15 ≤ ≤ 32) between May-July 2021 and December 2021-January 2022, were selected and analyzed using the RT-PCR genotyping assays.

Diagnostic accuracy of SARS-CoV-2 rapid antigen self-tests in asymptomatic individuals in the omicron period: a cross-sectional study.

Objectives: To assess the performances of three commonly used antigen rapid diagnostic tests used as self-tests in asymptomatic individuals in the Omicron period.

Methods: We performed a cross-sectional diagnostic test accuracy study in the Omicron period in three public health service COVID-19 test sites in the Netherlands, including 3600 asymptomatic individuals aged ≥ 16 years presenting for SARS-CoV-2 testing for any reason except confirmatory testing after a positive self-test. Participants were sampled for RT-PCR (reference test) and received one self-test (either Acon Flowflex [Flowflex], MP Biomedicals (MPBio), or Siemens-Healthineers CLINITEST [CLINITEST]) to perform unsupervised at home.

Diagnostic accuracy of covid-19 rapid antigen tests with unsupervised self-sampling in people with symptoms in the omicron period: cross sectional study.

Objective: To assess the performance of rapid antigen tests with unsupervised nasal and combined oropharyngeal and nasal self-sampling during the omicron period.

Design: Prospective cross sectional diagnostic test accuracy study.

Setting: Three public health service covid-19 test sites in the Netherlands, 21 December 2021 to 10 February 2022.

Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands.

In the first wave of the COVID-19 pandemic (April 2020), SARS-CoV-2 was detected in farmed minks and genomic sequencing was performed on mink farms and farm personnel. Here, we describe the outbreak and use sequence data with Bayesian phylodynamic methods to explore SARS-CoV-2 transmission in minks and humans on farms. High number of farm infections (68/126) in minks and farm workers (>50% of farms) were detected, with limited community spread.

Validation of Dried Tube Sample Format Quality Controls for the Monitoring of Viral Load and Blood Screening Assays.

HIV viral load (VL) and donor screening assays experience variation and require quaity assurance (QA). NRL sought to confirm a dried tube sample format (HIVDTS) sample type for use in quality control (QC) programs for HIV molecular testing. 50 μL of HIV supernatant at 1 × 10 copies per millilitre (copies/mL)) was dried for 48 hours at room temperature.

Usutu virus infection in Dutch blood donors.

Background: The screening of Dutch blood donations for West Nile virus (WNV) may be imminent, as WNV emerges in nearby countries and more donors travel to WNV-affected regions. Since 2016 the related, mosquito-borne Usutu virus (USUV) causes seasonal mortality in Dutch birds. To what extent will human USUV infections affect Dutch WNV donor screening?

Study Design And Methods: From April through September 2018, plasma samples from blood donations in blackbird-rich regions were stored.

Absence of zoonotic hepatitis E virus infection in Flemish dairy cows.

Recently, infectious HEV particles were discovered in milk and fecal samples of dairy cows in China. Given the recent increase of autochthonous HEV infections in Europe, we wanted to assess whether cows constitute an HEV reservoir in this region and hence may be responsible for the advance of HEV through consumption of cow produce. To verify the zoonotic risk cows potentially pose towards European consumers, we screened >10% of dairy milk farms in Flanders, Belgium for the presence of HEV.

Zika virus RNA polymerase chain reaction on the utility channel of a commercial nucleic acid testing system.

Background: Several countries have implemented safety strategies to reduce the risk of Zika virus (ZIKV) transmission through blood transfusion. These strategies have included nucleic acid amplification testing (NAT) of blood donations. In this study, a new real-time polymerase chain reaction (PCR) assay including internal control for the detection of ZIKV on the cobas omni Utility Channel (UC) on the cobas 6800 system is presented.

Acute and Chronic Hepatitis E Virus Infection in Human Immunodeficiency Virus-Infected U.S. Women.

Unlabelled: Exposure to hepatitis E virus (HEV) is common in the United States, but there are few data on prevalence of HEV/human immunodeficiency virus (HIV) coinfection in U.S.

Populations: We tested 2,919 plasma samples collected from HIV-infected (HIV(+)) women and men enrolled in U.

Validation of new real-time polymerase chain reaction assays for detection of hepatitis A virus RNA and parvovirus B19 DNA.

Background: To meet European guidelines for plasma for fractionation, plasma fractionators have implemented parvovirus B19 (B19V) and hepatitis A virus (HAV) nucleic acid test (NAT) screening on test pools. In this study we evaluate recently developed in-house NAT assays for B19V DNA and HAV RNA. The B19V NAT was designed to target two different regions of the B19V genome.

Inclusion of human immunodeficiency virus Type 2 (HIV-2) in a multiplex transcription-mediated amplification assay does not affect detection of HIV-1 and hepatitis B and C virus genotypes: a multicenter performance evaluation study.

Background: The Ultrio Elite assay (Hologic/Grifols) runs on the Panther blood screening system and is comparable to the Ultrio Plus assay apart from the addition of oligonucleotides for human immunodeficiency virus Type 2 (HIV-2) detection. In this multicenter evaluation study the analytical sensitivity and genotype detection efficiency of the two assay versions were compared.

Study Design And Methods: The analytical sensitivity and genotype detection efficiency were analyzed by replicate (18-303) testing of 27 hepatitis B virus (HBV), hepatitis C virus (HCV), HIV-1, and HIV-2 standard dilution panels calibrated in international units (IUs) and copies/mL.

Seroprevalence of hepatitis E virus (HEV) and detection of HEV RNA with a transcription-mediated amplification assay in blood donors from Catalonia (Spain).

Background: Hepatitis E virus (HEV) is an emerging threat to the safety of blood transfusion. The aim of this study was to determine HEV immunoglobulin (Ig)G and RNA prevalence in Catalan blood donors.

Study Design And Methods: Nearly 10,000 samples were collected from anonymized, unpaid donors at the Banc de Sang i Teixits (Barcelona, Spain) from June to December 2013.

Multicenter evaluation of a commercial multiplex polymerase chain reaction test for screening plasma donations for parvovirus B19 DNA and hepatitis A virus RNA.

Background: Three European laboratories evaluated the TaqScreen DPX test (DPX test), a multiplex nucleic acid test assay for the simultaneous detection and quantitation of parvovirus B19 (B19V) DNA and the detection of hepatitis A virus (HAV) RNA.

Study Design And Methods: The 95% limit of detection of the test for B19V and HAV was determined using the respective WHO International Standards. The reproducibility of the test was evaluated by testing replicate samples of B19V at log 4.

Efficacy of hepatitis B virus (HBV) DNA screening and characterization of acute and occult HBV infections among blood donors from Madrid, Spain.

Background: Screening of blood units for hepatitis B virus (HBV) DNA identifies donations collected during the window period (WP) of the acute infection and may improve viral safety of the blood supply. It also leads to the detection of occult hepatitis B infection (OBI).

Study Design And Methods: From January 2005 to December 2006, a total of 383,267 blood units were screened for hepatitis B surface antigen (HBsAg) and HBV DNA in two transfusion centers in Madrid, using either individual-donation nucleic acid testing (ID-NAT) or minipool (MP-NAT) of eight donations (MP8).

Independent evolution of overlapping polymerase and surface protein genes of hepatitis B virus.

The genome of hepatitis B virus (HBV) provides a striking example of gene overlapping. In particular, the surface protein gene S is overlapped completely by the polymerase gene P. Evolutionary constraints in overlapping genes have been demonstrated for many viruses, with one of the two overlapping genes being subjected to positive selection (adaptive evolution), while the other one is subjected to purifying selection.

Diversity and origin of hepatitis C virus infection among unpaid blood donors in the Netherlands.

Background: To improve transfusion policy and to increase understanding of the spread of hepatitis C virus (HCV) in the general population, HCV infections among voluntary Dutch blood donors were examined with molecular epidemiologic techniques.

Study Design And Methods: During 6 years, 1997 through 2002, confirmed anti-HCV-positive donors were interviewed on HCV-associated risk behavior with a standardized questionnaire. Additionally, HCV isolates were genotyped, partially sequenced, and compared to sequences obtained from Dutch injecting drug users (IDUs).

Multicenter performance evaluation of a transcription-mediated amplification assay for screening of human immunodeficiency virus-1 RNA, hepatitis C virus RNA, and hepatitis B virus DNA in blood donations.

Background: The performance of the recently launched Procleix Ultrio (Chiron/Gen-Probe) human immunodeficiency virus-1 (HIV-1), hepatitis C virus (HCV), and hepatitis B virus (HBV) blood screening assay was evaluated in a European multicenter study.

Study Design And Methods: Serial dilutions of reference materials were tested to determine the detection limits. Robustness and specificity were assessed by testing alternating high-load HCV RNA-positive and -negative samples, and 2912 test pools of eight donations.

Quantitative real-time detection of parvovirus B19 DNA in plasma.

Background: As of 2004, the European Pharmacopoeia demands that plasma pools for production of anti-D immunoglobulin should not contain more than 104 IU per mL of parvovirus B19 (B19V) DNA. Hence, before pooling, highly viremic donations have to be identified, and after pooling the level of B19V DNA must be determined. The performance of a new real-time B19V DNA PCR test (Roche, Mannheim, Germany) was studied, using a DNA extractor (NucliSens, bioMerieux, Boxtel, the Netherlands) for isolation of nucleic acid, and using a DNA quantification test (LightCycler apparatus, Roche, Mannheim, Germany) for amplification and detection.

Novel strategy for the selection of human recombinant Fab fragments to membrane proteins from a phage-display library.

Traditionally, the selection of phage-display libraries is performed on purified antigens (Ags), immobilized to a solid substrate. However, this approach may not be applicable for some Ags, such as membrane proteins, which for structural integrity strongly rely on their native environment. Here we describe an approach for the selection of phage-libraries against membrane proteins.