Low Levels Of Virus Research Articles

Intranasal parainfluenza virus-vectored vaccine expressing SARS-CoV-2 spike protein of Delta or Omicron B.1.1.529 induces mucosal and systemic immunity and protects hamsters against homologous and heterologous challenge.

The continuous emergence of new SARS-CoV-2 variants requires that COVID vaccines be updated to match circulating strains. We generated B/HPIV3-vectored vaccines expressing 6P-stabilized S protein of the ancestral, B.1.617.2/Delta, or B.1.1.529/Omicron variants as pediatric vaccines for intranasal immunization against HPIV3 and SARS-CoV-2 and characterized these in hamsters. Following intranasal immunization, these B/HPIV3 vectors replicated in the upper and lower respiratory tract and induced mucosal and serum anti-S IgA and IgG. B/HPIV3 expressing ancestral or B.1.617.2/Delta-derived S-6P induced serum antibodies that effectively neutralized SARS-CoV-2 of the ancestral and B.1.617.2/Delta lineages, while the cross-neutralizing potency of B.1.1.529/Omicron S-induced antibodies was lower. Despite the lower cross-neutralizing titers induced by B/HPIV3 expressing S-6P from B.1.1.529/Omicron, a single intranasal dose of all three versions of B/HPIV3 vectors was protective against matched or heterologous WA1/2020, B.1.617.2/Delta or BA.1 (B.1.1.529.1)/Omicron challenge; hamsters were protected from challenge virus replication in the lungs, while low levels of challenge virus were detectable in the upper respiratory tract of a small number of animals. Immunization also protected against lung inflammatory response after challenge, with mild inflammatory cytokine induction associated with the slightly lower level of cross-protection of WA1/2020 and B.1.617.2/Delta variants against the BA.1/Omicron variant. Serum antibodies elicited by all vaccine candidates were broadly reactive against 20 antigenic variants, but the antigenic breadth of antibodies elicited by B/HPIV3-expressed S-6P from the ancestral or B.1.617.2/Delta variant exceeded that of the S-6P B.1.1.529/Omicron expressing vector. These results will guide development of intranasal B/HPIV3 vectors with S antigens matching circulating SARS-CoV-2 variants.

Protective evaluation of the commercialized porcine reproductive and respiratory syndrome virus vaccines in piglets challenged by NADC34-like strain.

In China, the porcine reproductive and respiratory syndrome virus (PRRSV) has undergone several variations over the decades and contributed to the diversity of the clinical epidemic PRRSV strains. This has complicated the prevention and control of PRRS. In particular, the efficacy of the currently available commercial vaccines against the highly pathogenic NADC34-like strains is unclear. Therefore, the objective of this study was to evaluate the protection efficacy of three commercial PRRS modified-live virus (MLV) vaccines derived from classical PRRS VR2332 MLV and R98 MLV against challenge with a heterologous NADC34-like PRRSV strain, JS2021NADC34, which has high pathogenicity in pigs. PRRSV- and antibody-free piglets were immunized with the PRRS VR2332 MLV vaccine or either of two R98 MLV vaccines (from different manufacturers) and were challenged with the JS2021NADC34 strain 28 days after immunization. Rectal temperature, clinical symptoms, viremia and viral shedding from the nose, gross lesions in the thymus and lungs, microscopic lesions and viral distribution in the lungs, as well as the humoral immune response and mortality rates were recorded over a 14-day post-challenge period. The results showed that PRRS VR2332 MLV had better efficacy against the JS2021NADC34 challenge than PRRS R98 MLV, with vaccinated piglets in the former group showing transient and mild symptoms, mild pathological lesions in the lungs, mild thymic atrophy, and low viral levels in sera and nasal swabs, as well as better growth performance and a 100% survival rate. In contrast, two PRRS R98 MLVs exhibited limited efficacy against the JS2021NADC34 challenge, with the piglets in two R98 groups showing obvious clinical symptoms and pathological changes in the lungs and thymus; moreover, there were two deaths caused by PRRS in two R98 groups, respectively. Despite this, the mortality rate was lower than that of the unvaccinated piglets that were challenged with JS2021NADC34. The cumulative results demonstrate that PRRS VR2332 MLV was partly effective against the highly pathogenic PRRSV NADC34-like strain based on the observations over the 14-day post-challenge period. Thus, it might be a viable option among the commercially available vaccines for control of NADC34-like virus infections in swine herds.

Hubungan Rendahnya Pengetahuan Tentang Imunisasi Kanker Serviks Pada Wanita Usia Subur (WUS) Di RT 05 RW 02 Kelurahan Telaga Asih Bekasi Tahun 2023

Globocan data for 2020 recorded that the total cancer cases in Indonesia in 2020 reached 396,914 cases and the total deaths were 234,511 cases. Cervical cancer (cervix) ranks second with 36,633 cases or 9.2% of total cancer cases. One of the factors that contributes to the high incidence of cervical cancer in Indonesia is the lack of awareness and access to routine examinations and vaccinations. Cervical cancer is one of the cancers that can be prevented, namely by immunization with the HPV vaccine and early detection of cervical cancer with a Pap smear or IVA examination (visual inspection using acetic acid). The aim of this research is to analyze factors related to WUS knowledge about the low level of Human Papilloma Virus (HPV) immunization in RT 05 RW 02, Telaga Asih Bekasi Village in 2023. The research method used is a cross sectional survey method. The population in this study was 50 female respondents of childbearing age in RT 05 RW 02. The sample was taken using a total sampling technique of 50 female respondents of childbearing age in RT 05 RW 02. Univariate analysis used frequency distribution and for bivariate tests used the Chi Square test. This research uses primary data from filling out questionnaires by respondents. Based on the results of the analysis of the 50 respondents, 31 people (62.0%) had the most good knowledge, 41 people aged 20-35 years (82.0%). There were 29 women whose parity was not at risk (58%), 29 people had at least high school education (58%), and 34 people got information sources electronically (68%). Variables related to knowledge are education and sources of information with a value of 0.000 < 0.05. Meanwhile, variables that are not related are age and parity. It is hoped that this research will become a reference for increasing knowledge and an intensive approach to WUS. The results of this research can also be used as an opener to wider insight into midwifery and especially in the field of reproductive health.

Computation and analysis of optimal disturbances of stationary solutions of the hepatitis B dynamics model

Abstract Optimal disturbances of a number of typical stationary solutions of the hepatitis B virus infection dynamics model have been found. Specifically optimal disturbances have been found for stationary solutions corresponding to various forms of the chronic course of the disease, including those corresponding to the regime of low-level virus persistence. The influence of small optimal disturbances of individual groups of variables on the stationary solution is studied. The possibility of transition from stable stationary solutions corresponding to chronic forms of hepatitis B to stable stationary solutions corresponding to the state of functional recovery or a healthy organism using optimal disturbances is studied. Optimal disturbances in this study were constructed on the basis of generalized therapeutic drugs characterized by one-compartment and two-compartment pharmacokinetics.

Quantification of low-level human cytomegalovirus and Epstein-Barr virus DNAemia by digital PCR

BackgroundDigital PCR (dPCR) can quantify cell-free viral DNA (DNAemia), a biomarker of active viral infection. To accelerate epidemiologic investigation into low-level viral reactivation in chronic disease, we have evaluated the performance of dPCR to detect cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNAemia across platforms and blood matrices. MethodsThe droplet-based (BioRad) dPCR platform performance was compared to chip-based (BioMark), and assay validation followed dMIQE guidelines. CMV and EBV DNA reference materials were spiked into known negative plasma and serum samples. In addition, two independent cohorts of ovarian cancer patients were evaluated for viral DNAemia (n = 65 serum and 79 plasma samples). ResultsThe limit of quantification (LOQ) was at or slightly above 100 copies/mL for both instruments: 105–135 copies/mL for droplet-based detection and 100 copies/mL for chip-based detection. DNAemia in serum had a slightly lower LOQ (105–110 copies/mL) compared to plasma (LOQ; 115–135 copies/mL). The variation (CV) coefficients for each assay and machine were less than 5 %. In patient samples, CVs ranged from 4.5 – 7.4 % and were similar for cell-free DNA derived from serum or plasma. There was good correlation between DNAemia measurements in patient samples across dPCR platforms (r > 0.90 for each assay and matrix). ConclusiondPCR can quantify low-level herpes virus DNAemia with CVs below 8 %. Our results indicate that using serum-derived cell-free DNA and droplet-based dPCR is optimal for quantitating low-level viral DNAemia; however, plasma and chip-based approaches are acceptable alternatives and suitable for epidemiologic investigation.

Exploring Tomato Fruit Viromes through Transcriptome Data Analysis.

This study delves into the complex landscape of viral infections in tomatoes (Solanum lycopersicum) using available transcriptome data. We conducted a virome analysis, revealing 219 viral contigs linked to four distinct viruses: tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato yellow leaf curl virus (TYLCV), and cucumber mosaic virus (CMV). Among these, ToCV predominated in contig count, followed by STV, TYLCV, and CMV. A notable finding was the prevalence of coinfections, emphasizing the concurrent presence of multiple viruses in tomato plants. Despite generally low viral levels in fruit transcriptomes, STV emerged as the primary virus based on viral read count. We delved deeper into viral abundance and the contributions of RNA segments to replication. While initially focused on studying the impact of sound treatment on tomato fruit transcriptomes, the unexpected viral presence underscores the importance of considering viruses in plant research. Geographical variations in virome communities hint at potential forensic applications. Phylogenetic analysis provided insights into viral origins and genetic diversity, enhancing our understanding of the Korean tomato virome. In conclusion, this study advances our knowledge of the tomato virome, stressing the need for robust pest control in greenhouse-grown tomatoes and offering insights into virus management and crop protection.

Environmental transmission of influenza A virus in mallards.

Wild birds are the natural reservoir hosts of influenza A viruses. Highly pathogenic strains of influenza A viruses pose risks to wild birds, poultry, and human health. Thus, understanding how these viruses are transmitted between birds is critical. We conducted an experiment where we experimentally infected mallards which are ducks that are commonly exposed to influenza viruses. We exposed several contact ducks to the experimentally infected duck to estimate the probability that a contact duck would become infected from either exposure to the virus shed directly from the infected duck or shared water contaminated with the virus from the infected duck. We found that environmental transmission from contaminated water best predicted the probability of transmission to naïve contact ducks, relatively low levels of virus in the water were sufficient to cause infection, and the probability of a naïve duck becoming infected varied over time.

Plasma metabolomics by nuclear magnetic resonance reveals biomarkers and metabolic pathways associated with the control of HIV-1 infection/progression.

How the human body reacts to the exposure of HIV-1 is an important research goal. Frequently, HIV exposure leads to infection, but some individuals show natural resistance to this infection; they are known as HIV-1-exposed but seronegative (HESN). Others, although infected but without antiretroviral therapy, control HIV-1 replication and progression to AIDS; they are named controllers, maintaining low viral levels and an adequate count of CD4+ T lymphocytes. Biological mechanisms explaining these phenomena are not precise. In this context, metabolomics emerges as a method to find metabolites in response to pathophysiological stimuli, which can help to establish mechanisms of natural resistance to HIV-1 infection and its progression. We conducted a cross-sectional study including 30 HESN, 14 HIV-1 progressors, 14 controllers and 30 healthy controls. Plasma samples (directly and deproteinized) were analyzed through Nuclear Magnetic Resonance (NMR) metabolomics to find biomarkers and altered metabolic pathways. The metabolic profile analysis of progressors, controllers and HESN demonstrated significant differences with healthy controls when a discriminant analysis (PLS-DA) was applied. In the discriminant models, 13 metabolites associated with HESN, 14 with progressors and 12 with controllers were identified, which presented statistically significant mean differences with healthy controls. In progressors, the metabolites were related to high energy expenditure (creatinine), mood disorders (tyrosine) and immune activation (lipoproteins), phenomena typical of the natural course of the infection. In controllers, they were related to an inflammation-modulating profile (glutamate and pyruvate) and a better adaptive immune system response (acetate) associated with resistance to progression. In the HESN group, with anti-inflammatory (lactate and phosphocholine) and virucidal (lactate) effects which constitute a protective profile in the sexual transmission of HIV. Concerning the significant metabolites of each group, we identified 24 genes involved in HIV-1 replication or virus proteins that were all altered in progressors but only partially in controllers and HESN. In summary, our results indicate that exposure to HIV-1 in HESN, as well as infection in progressors and controllers, affects the metabolism of individuals and that this affectation can be determined using NMR metabolomics.

An Advax-CpG55.2™ adjuvanted recombinant spike protein vaccine protects cynomolgus macaques from a homologous SARS-CoV-2 virus challenge

Traditional protein-based vaccine approaches to COVID-19 were overshadowed by the new mRNA and adenoviral vector vaccine approaches which were first to receive marketing authorization. The current study tested for the first time in repurposed aged (median 15.4 years) cynomolgus macaques, a novel Advax-CpG55.2™ adjuvanted recombinant extracellular domain spike protein trimer antigen for immunogenicity, protection and safety. Nine animals received two intramuscular injections 10 days apart of recombinant spike protein (25 μg) with Advax-CpG55.2™ (10 mg/200 μg) and 5 controls received saline injections. Serum antibody levels were followed for 3 months and then the animals were challenged with SARS-CoV-2 virus. Clinical signs, local reactions, body weight, food consumption and antibody levels were monitored till termination on either day 3 or 7 post-infection. Two weeks after the second dose, 8/9 immunized macaques had high serum spike and receptor binding domain binding antibodies that were able to cross-neutralize Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and, to a lesser extent, Omicron variants (B.1.1.529 ). Antibody levels decayed over the subsequent 3 months, and minimal neutralizing antibody was detectable immediately prior to the challenge which used a vaccine-homologous Wuhan-like ancestral virus. Of the nine vaccinated animals, only one 18-year-old female sacrificed at d3 had low levels of lung virus, versus 100 % of the control animals. Four of 5 (80 %) control animals had positive lung staining for SARS-CoV-2 virus versus just 1 of 9 (11 %) in the immunized group. The immunized animals exhibited better maintenance of appetite post-challenge. Neutralizing antibody levels rebounded rapidly in immunized animals, post-challenge. This data supports the benefits of Advax-CpG adjuvanted recombinant spike protein vaccine in protecting against a homologous SARS-CoV-2 infection.

Improved recovery of SARS-CoV-2 from wastewater through application of RNA and DNA stabilising agents.

Wastewater Based Epidemiology (WBE) has become an integral part of the public health effort to track the levels of SARS-CoV-2 within communities. Detection of SARS-CoV-2 in wastewater can be challenging due to relatively low levels of virus within the sample. The wastewater matrix is also comprised of commercial and domestically derived contaminants, as well as RNases, all of which can adversely affect RT-qPCR analysis. To improve SARS-CoV-2 detection within wastewater samples we investigated both the effect of template dilution (as a means to reduce RT-qPCR inhibition) and sample stabilisation via addition of DNA/RNA Shield™ and/or RNA Later™ (to prevent RNA degradation via RNases) as a means to improve viral fragment detection. Using both methodologies, a significant improvement in SARS-CoV-2 detection from wastewater samples was observed. No adverse effects of stabilising agent addition on downstream Next-Generation Sequencing workflows were detected.

Sensitivity of rapid antigen tests for Omicron subvariants of SARS-CoV-2.

Diagnosis by rapid antigen tests (RATs) is useful for early initiation of antiviral treatment. Because RATs are easy to use, they can be adapted for self-testing. Several kinds of RATs approved for such use by the Japanese regulatory authority are available from drug stores and websites. Most RATs for COVID-19 are based on antibody detection of the SARS-CoV-2 N protein. Since Omicron and its subvariants have accumulated several amino acid substitutions in the N protein, such amino acid changes might affect the sensitivity of RATs. Here, we investigated the sensitivity of seven RATs available in Japan, six of which are approved for public use and one of which is approved for clinical use, for the detection of BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1, as well as the delta variant (B.1.627.2). All tested RATs detected the delta variant with a detection level between 7500 and 75 000 pfu per test, and all tested RATs showed similar sensitivity to the Omicron variant and its subvariants (BA.5, BA.2.75, BF.7, XBB.1, and BQ.1.1). Human saliva did not reduce the sensitivity of the RATs tested. Espline SARS-CoV-2 N showed the highest sensitivity followed by Inspecter KOWA SARS-CoV-2 and V Trust SARS-CoV-2 Ag. Since the RATs failed to detect low levels of infectious virus, individuals whose specimens contained less infectious virus than the detection limit would be considered negative. Therefore, it is important to note that RATs may miss individuals shedding low levels of infectious virus.

Measuring hepatitis B pgRNA stability using an updated automated HBV pgRNA assay with increased sensitivity.

HBV pregenomic RNA (pgRNA) is a circulating biomarker for covalently closed circular DNA activity in HBV-infected individuals and has been studied for treatment efficacy, disease staging, and off-therapy outcomes; however, data on the stability are scarce. Increasing HBV pgRNA assay sensitivity may improve its predictive value and provide additional insights at low viral levels. Modifications to a fully automated first (v1) generation HBV pgRNA assay improved sensitivity up to 15-fold over the previous assay. Flexible sample input volumes yielded lower limits of quantitation of 10 and 22 copies/mL for 0.6 and 0.2mL assays, respectively. Results are standardized to secondary standards that are traceable to the WHO HBV DNA standard, and internal and external controls are included. Comparison between v1 and modified v2 assays showed increased sensitivity from 152 copies/mL with v1 to 10 (0.6mL) and 22 (0.2mL) copies/mL with v2, respectively. Quantitated v2 results were indistinguishable from v1, indicating that comparisons can be made to previous studies. Single timepoint treatment-naive blood donors or longitudinal draws from patients with chronic hepatitis B on AB-729, an investigational siRNA therapy, showed improved detection and quantifiable pgRNA with v2 compared with v1. Stability testing demonstrated excellent HBV pgRNA plasma stability after 3 freeze-thaw cycles, for at least 7 days at 25-37°C and at least 30 days at 4°C, with ≤0.25 Log U/mL decrease. HBV pgRNA v2 assays with increased sensitivity and flexible input volumes demonstrated increased detection and quantitation of low viral titer samples. Highly sensitive HBV pgRNA assays may be useful in refining predictive treatment outcomes based on this marker. HBV pgRNA was stable under multiple conditions, which increases the reliability of this marker.

Detection of Apparent Early Rabies Infection by LN34 Pan-Lyssavirus Real-Time RT-PCR Assay in Pennsylvania.

The Pennsylvania Department of Health Bureau of Laboratories (PABOL) tested 6855 animal samples for rabies using both the direct fluorescent antibody test (DFA) and LN34 pan-lyssavirus reverse transcriptase quantitative PCR (RT-qPCR) during 2017–2019. Only two samples (0.03%) were initially DFA negative but positive by LN34 RT-qPCR. Both cases were confirmed positive upon re-testing at PABOL and confirmatory testing at the Centers for Disease Control and Prevention by LN34 RT-qPCR and DFA. Rabies virus sequences from one sample were distinct from all positive samples processed at PABOL within two weeks, ruling out cross-contamination. Levels of rabies virus antigen and RNA were low in all brain structures tested, but were higher in brain stem and rostral spinal cord than in cerebellum, hippocampus or cortex. Taken together, the low level of rabies virus combined with higher abundance in more caudal brain structures suggest early infection. These cases highlight the increased sensitivity and ease of interpretation of LN34 RT-qPCR for low positive cases.

Effects of Acute Dengue Infection on Sperm and Virus Clearance in Body Fluids of Men.

We investigated the effects of dengue virus (DENV) on semen using samples collected 7, 15, 30, 60, and 90 days after symptom onset from 10 infected volunteers on Réunion Island. We assessed characteristics of semen and reproductive hormones and isolated motile spermatozoa from semen. We assayed semen for DENV using reverse transcription PCR and searched for DENV RNA by virus isolation in Vero E6 cell cultures. Four volunteers had >1 DENV RNA-positive semen samples; 2 volunteers had DENV RNA–positive semen at day 15 and 1 at day 30. No motile sperm were DENV positive. After exposure to positive semen, few Vero E6 cells stained positive for DENV antigens, indicating low levels of replicative virus. We found DENV had shorter duration in semen than in blood. These findings support the possibilities that DENV is sexually transmissible for a short period after acute dengue illness and that acute dengue induces reversible alterations in sperm.

Development of a sensitive, quantitative assay with broad subtype specificity for detection of total HIV-1 nucleic acids in plasma and PBMC

An LTR-based quantitative PCR (qPCR) assay was modified and optimized for the quantification of total HIV-1 nucleic acids in plasma and PBMC. TaqMan qPCR primers and probes were designed against the NCBI/LANL HIV-1 compendium database by analyzing sequences used in assays for sensitive cross-clade detection of HIV-1 as reported in the literature and elucidating regions of improved cross-subtype specificity. Inosine and mixed nucleotide bases were included at polymorphic sites. Real-time RT-qPCR and qPCR were performed on plasma viral RNA and cellular lysates. A step-up amplification approach to allow binding of primers across polymorphic regions showed improved sensitivity compared to universal cycling. Unlike a lead competing laboratory-developed assay, all major HIV-1 subtypes, and a wide range of recombinants from a 127-member diversity panel were detected and accurately quantified in spiked plasmas. Semi-nested PCR increased detection sensitivity even further. The assay was able to detect down to 88 copies/mL of HIV-1 in plasma with 95% efficiency or the equivalent of a single infected cell. The PCR assay will be valuable in studies that monitor very low viral levels including residual or break through HIV-1 in patients receiving antiretroviral therapy, in HIV-1 cure, and in other research studies.

Alternative hepatitis B virus DNA confirmatory algorithm identified occult hepatitis B virus infection in Chinese blood donors with non-discriminatory nucleic acid testing.

Multiplex viral nucleic acid testing (NAT) and a discriminatory testing algorithm have been used to detect viral infections in blood donors. Non-discriminated reactive (NDR) results may arise from low hepatitis B virus (HBV) DNA levels and are challenging for donor management by blood services. The aim of this study was to evaluate the performance and feasibility of alternative viral particle concentration methods to confirm and to characterise HBV infection status in NDR donors from Dalian, China, in order to improve routine donor management according to the potential residual risk estimate. Individual donations were tested with ULTRIO Plus, and discriminated when reactive. Virions were concentrated from 12 and 6 mL plasma samples by ultracentrifugation (UC) and polyethylene glycol (PEG) precipitation, respectively. HBV DNA was detected with four nested polymerase chain reactions (95% limit of detection: 5-25 IU/mL). Amplified products were sequenced for definitive confirmation. Anti-HBc and anti-HBs were tested. Of 77,556 donors, 79 (0.1%) were NAT NDR. After viral particle concentration by UC and PEG precipitation, HBV DNA was detected in 46 (58.2%) and 34 (43.0%) NDR donors, respectively, including 61.7% of samples that were repeatedly non-reactive with multiple NAT testing. Anti-HBc and anti-HBs (median titre: 37 mIU/mL) were detected in 87.3% and 46.8% of NDR donors, respectively. Sequencing confirmed HBV DNA in 65.8% of NDR donors, of whom 96.2% were occult HBV carriers with rare mutations in S and core proteins. A HBV DNA confirmatory procedure with limited technical constraints was implemented successfully. The majority of NDR donors had occult HBV infections with extremely low viral DNA levels, which may constitute a potential residual threat for blood safety. Only a minority of anti-HBc+ NDR donors had anti-HBs levels high enough to consider their reinstatement as donors. The data support the permanent deferral of NDR donors to ensure maximum blood safety in areas of high HBV endemicity.

Human Monocyte-Derived Macrophages (MDM): Model 1 (GM-CSF).

Monocytes/macrophages play critical roles in HIV transmission, viral spread (early in infection), and as a reservoir of virus throughout infection. In the current research area in HIV, there has been a recent resurgence of interest in the biology of monocyte subsets and macrophages and their role in HIV pathogenesis, and as long-lived HIV reservoir. Thus, sensitive and specific techniques are needed to measure the impact of these cells in the establishment of the "hard-core" reservoir, and in their capacity to cause a low-level virus production during cART. Here, a protocol is presented for cell culture and HIV-1 infection of granulocyte-macrophage colony-stimulating factor (GM-CSF) differentiated human monocyte-derived macrophages.

Confirmed COVID-19 Cases per Economic Activity during Autumn Wave in Belgium.

Some occupational sectors, such as human health and care, food service, cultural and sport activities, have been associated with a higher risk of SARS-CoV-2 infection than other sectors. To curb the spread of SARS-CoV-2, it is preferable to apply targeted non-pharmaceutical interventions on selected economic sectors, rather than a full lockdown. However, the effect of these general and sector-specific interventions on the virus circulation has only been sparsely studied. We assess the COVID-19 incidence under different levels of non-pharmaceutical interventions per economic activity during the autumn 2020 wave in Belgium. The 14-day incidence of confirmed COVID-19 cases per the Statistical Classification of Economic Activities in the European Community (NACE–BEL) sector is modelled by a longitudinal Gaussian-Gaussian two-stage approach. This is based on exhaustive data on all employees in all sectors. In the presence of sanitary protocols and minimal non-pharmaceutical interventions, many sectors with close contact with others show considerably higher COVID-19 14-day incidences than other sectors. The effect of stricter non-pharmaceutical interventions in the general population and non-essential sectors is seen in the timing of the peak incidence and the width and height of the post-peak incidence. In most sectors incidences returned to higher levels after the peak than before and this decrease took longer for the health and care sector. Sanitary protocols for close proximity occupations may be sufficient during periods of low-level virus circulation, but progressively less with increasing circulation. Stricter general and sector-specific non-pharmaceutical interventions adequately decrease COVID-19 incidences, even in close proximity in essential sectors under solely sanitary protocols.

Development and Evaluation of a Nested PCR for Improved Diagnosis and Genetic Analysis of Peste des Petits Ruminants Virus (PPRV) for Future Use in Nascent PPR Eradication Programme.

Simple SummaryPeste des petits ruminants (PPR) is a highly contagious and economically important viral disease of small ruminants and a large number of wildlife species. The causative agent, PPR virus (PPRV) is mainly circulating across large areas in Africa, the Middle East and Asia and is, fortunately, currently subject to a global eradication program. A robust vaccination program along with a rapid and accurate laboratory diagnosis play a major role in the effective control and eradication of the disease. Furthermore, a genetic analysis of the circulating PPRV can help to identify the epidemiological linkage of the virus spread between neighboring countries. Here, we have developed an improved polymerase chain reaction (PCR) that can detect low viral loads and help in genetic identification, particularly in resource-limited settings.Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants caused by PPR virus (PPRV). PPR is endemic in Asia, the Middle East and across large areas of Africa and is currently targeted for global eradication by 2030. The virus exists as four different lineages that are usually limited to specific geographical areas. However, recent reports of spread of PPRV, in particular of lineage IV viruses to infection-free countries and previously PPR endemic areas are noteworthy. A rapid and accurate laboratory diagnosis and reports on its epidemiological linkage for virus spread play a major role in the effective control and eradication of the disease. Currently, molecular assays, including conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR (RT-qPCR) are usually used for diagnosis of PPR while the sequencing of part of the nucleocapsid gene is usually carried out for the viral lineage identification. However, it is difficult to diagnose and sequence the genetic material if the animal excreted a low level of virus at the initial stage of infection or if the PPRV is degraded during the long-distance transportation of samples to the reference laboratories. This study describes the development of a novel nested RT-PCR assay for the detection of the PPRV nucleic acid by targeting the N-protein gene, compares the performance of the assay with the existing conventional RT-PCR and also provides good-quality DNA suitable for sequencing in order to identify circulating lineages. The assay was evaluated using cell culture propagated PPRVs, field samples from clinically infected animals and samples from experimentally infected animals encompassing all four lineages (I–IV) of PPRV. This assay provides a solution with an easy, accurate, rapid and cost-effective PPR diagnostic and partial genome sequencing for use in resource-limited settings.

Clonal Expansion of Infected CD4+ T Cells in People Living with HIV.

HIV infection is not curable with current antiretroviral therapy (ART) because a small fraction of CD4+ T cells infected prior to ART initiation persists. Understanding the nature of this latent reservoir and how it is created is essential to development of potentially curative strategies. The discovery that a large fraction of the persistently infected cells in individuals on suppressive ART are members of large clones greatly changed our view of the reservoir and how it arises. Rather than being the products of infection of resting cells, as was once thought, HIV persistence is largely or entirely a consequence of infection of cells that are either expanding or are destined to expand, primarily due to antigen-driven activation. Although most of the clones carry defective proviruses, some carry intact infectious proviruses; these clones comprise the majority of the reservoir. A large majority of both the defective and the intact infectious proviruses in clones of infected cells are transcriptionally silent; however, a small fraction expresses a few copies of unspliced HIV RNA. A much smaller fraction is responsible for production of low levels of infectious virus, which can rekindle infection when ART is stopped. Further understanding of the reservoir will be needed to clarify the mechanism(s) by which provirus expression is controlled in the clones of cells that constitute the reservoir.