Average Viral Load Research Articles

Effect of rock bream iridovirus (RBIV) contained tissue intake on rock bream (Oplegnathus fasciatus) mortality and blood cell distribution

Rock bream (Oplegnathus fasciatus) is one of the highly priced cultured marine fish in Korea. Rock bream iridovirus (RBIV) outbreaks in aquaculture farms may involve environmental factors, co-infection with other pathogenic microorganisms and grounded (raw) fish feed. This study evaluated the effects of RBIV-containing tissue intake on mortality and oral transmission in rock bream. Virus-containing tissues administered to rock bream [50 mg (1.53 × 108/major capsid protein, MCP gene copies) to 2400 mg (7.34 × 109)] held at 23 °C lead to 100 % mortality by 27 days post administration. Interestingly, the mortality rates were not viral dose- or concentration dependent. Further, high MCP gene copy numbers were observed in the gill, liver, intestine, stomach, spleen, heart, kidney, brain and muscle tissues (viral load range of 3.03 × 106 to 4.01 × 107/mg, average viral load 1.70 × 107/mg) of dead rock bream. Moreover, a high viral load was detected in the intestine and stomach, where the virus was directly administered. This indicated that the intake of RBIV-containing tissue feed weakens the intestinal mucosal immunity and increases viral load in the intestine. Moreover, the levels of complete blood cell count (CBC) indicators, such as red blood cell (RBC), hemoglobin (HGB) and hematocrit (HCT) significantly decreased from 15 dpi with red blood cell distribution width (RDW), and white blood cells (lymphocyte, monocyte and granulocyte) significantly increased from the initial to later stage of infection. These results highlight the significance of blood-mediated indicators against RBIV infection in rock bream. We demonstrate the existence of an oral transmission route for RBIV in rock bream. Our findings indicate that pathogen-containing feed is an important risk factor for disease outbreaks in rock bream.

Human leukocyte antigen HLA-B*57:01 status in HIV-1 patients developing hypersensitivity reactions in Benin: a pilot study

BackgroundAntiretroviral drugs in people living with HIV-1 (PLHIV-1) often trigger side effects which may lead to discontinuation or failure of treatment. Human Leukocyte Antigen B*57:01 (HLA-B*57:01) allele is known to predict hypersensitivity reactions to Abacavir. Very few data are available on the prevalence of HLA-B*57:01 allele in PLHIV-1 in African countries. This study aimed to screen for HLA-B*57:01 allele in PLHIV-1 in Benin.MethodsThis pilot study was carried out on one hundred ten PLHIV-1 enrolled in two health facilities in Benin. Socio-demographic and clinical data were collected. Biological data were determined and HLA-B*57:01 allele was genotyped, using Single Specific Primer-Polymerase Chain Reaction in blood samples.Results70% of participants were female. PLHIV-1 were under TDF + 3TC + DTG (47.2%) or TDF + 3TC + EFV (57.3%). Their median age was 41 [36-48.75] years and the average CD4 + T cell count was 249 [130-381.25] cells/µl. The average viral load in treatment failure PLHIV-1 was 4.7 [3.9–5.2] Log10. At the inclusion date, twenty-nine (26.4%) PLHIV-1 under TDF + 3TC + EFV have developed hypersensitivity reactions. None of 110 patients had shown HLA-B*5701 allele.ConclusionOur study revealed that HLA-B*57:01 allele was very rare in PLHIV-1 in Benin, suggesting that its screening before starting the Abacavir regimen did not seem necessary.

Long-term wastewater monitoring of SARS-CoV-2 viral loads and variants at the major international passenger hub Amsterdam Schiphol Airport: A valuable addition to COVID-19 surveillance

Wastewater-based epidemiological surveillance at municipal wastewater treatment plants has proven to play an important role in COVID-19 surveillance. Considering international passenger hubs contribute extensively to global transmission of viruses, wastewater surveillance at this type of location may be of added value as well. The aim of this study is to explore the potential of long-term wastewater surveillance at a large passenger hub as an additional tool for public health surveillance during different stages of a pandemic. Here, we present an analysis of SARS-CoV-2 viral loads in airport wastewater by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) from the beginning of the COVID-19 pandemic in Feb 2020, and an analysis of SARS-CoV-2 variants by whole-genome next-generation sequencing from Sep 2020, both until Sep 2022, in the Netherlands. Results are contextualized using (inter)national measures and data sources such as passenger numbers, clinical surveillance data and national wastewater surveillance data. Our findings show that wastewater surveillance was possible throughout the study period, irrespective of measures, as viral loads were detected and quantified in 98.6 % (273/277) of samples. Emergence of SARS-CoV-2 variants, identified in 91.0 % (161/177) of sequenced samples, coincided with increases in viral loads. Furthermore, trends in viral load and variant detection in airport wastewater closely followed, and in some cases preceded, trends in national daily average viral load in wastewater and variants detected in clinical surveillance. Wastewater-based epidemiology at a large international airport is a valuable addition to classical COVID-19 surveillance and the developed expertise can be applied in pandemic preparedness plans for other (emerging) pathogens in the future.

A label-free aptasensing method for detecting SARS-CoV-2 virus antigen by using dumbbell probe-mediated circle-to-circle amplification.

Controlling the spread of pathogen requires an efficient and accurate diagnosis. Compared with nucleic acid and antibody detection, antigen assays are more convenient to meet clinical diagnostic needs. However, antigen detection is often difficult to achieve high sensitivity in a limited time. In this work, a novel aptasensing method was designed for the purpose of SARS-CoV-2 antigen detection, using a dumbbell padlock probe-mediated circle-to-circle amplification (C2CA) approach. A sandwich complex of antibody-antigen-aptamer is first formed on the magnetic beads. Afterwards, the signal is amplified by a C2CA reaction involving two tandem rolling circle amplifications. Without special instruments or nanomaterials, a detection limit of 575fg/mL for S1 protein can be achieved in less than 2h. In the case of the spike pseudovirus SARS-CoV-2 in artificial saliva, the detection limit is 272 TU/μL, which is much lower than average viral load in patients. Therefore, our method provides a timely, efficient and accurate approach for the clinical diagnosis of SARS-CoV-2. It also opens up the application of C2CA in aptamer sensing and antigen detection.

A preliminary study on plasma concentration, short-term efficacy, and safety profile of dolutegravir in Chinese people with HIV

ABSTRACT Background This study examined the plasma concentration, clinical efficacy, and safety of dolutegravir (DTG) in Chinese people with HIV (PWH). Methods In this observational study, HIV-positive individuals on DTG-based regimens for at least 6 months were included. Plasma DTG concentrations were measured 1 month after initiating treatment. Viral loads (VL) and CD4+ T cell counts were evaluated at baseline and after 1 and 6 months of therapy. High-performance liquid chromatography was used for measuring DTG concentrations, polymerase chain reaction for VL, and flow cytometry for CD4+ T cell counts. Safety assessments included monitoring liver enzymes, serum creatinine estimated glomerular filtration rate, and adverse reactions. Results Eighty-two Chinese PWH were enrolled. Average VL decreased significantly from baseline by 3.1 log at 1 month and 3.5 log at 6 months. CD4+ T cell counts increased from 273 cells/mm3 at baseline to 378 cells/mm3 and 446 cells/mm3 after 1 and 6 months, respectively. Seventy-five percent achieved undetectable VLs (<20 copies/mL) by 6 months. Cmax and Cτ were 4.63 and 1.98 μg/mL, respectively. The safety profile was favorable with only 4.88% experiencing transient dizziness. Conclusion Preliminary findings suggest higher DTG plasma concentrations in Chinese PWH compared to Western populations, with promising short-term efficacy and safety.

Epstein‐Barr virus in tonsillar tissue of Iranian children with tonsillar hypertrophy: Quantitative measurement by real‐time PCR

AbstractBackground and ObjectivesEpstein‐Barr virus (EBV) infection is ubiquitous all around the world. Tonsils seem to be candidate replication sites for EBV, and these tissues can be infected acutely or chronically. Some studies reported an association between EBV infection and tonsillar hypertrophy. In this study, we aimed to evaluate the presence and copy number of the EBV genome in tonsil tissue specimens of patients with tonsillar hypertrophy.MethodsA cross‐sectional study was performed on 50 fresh tonsil tissue samples from children, who underwent tonsillectomy because of tonsillar hypertrophy. Patients' tonsil tissues were evaluated using real‐time polymerase chain reaction for EBV genome and viral load. Finally, the results were analyzed using SPSS software.ResultsEBV genome was detected in 58% (29/50) of tonsillar tissues. The relationship between EBV genome detection rate and age groups was in the statistical significance range (P = 0.051). Among 29 positive cases, the average EBV viral load was (3.1 × 105) copy/g ± (0.5 × 105) copy/g. No significant difference was observed among different sex and age groups for EBV viral load.ConclusionHerein, EBV genome detection could support the colonization of EBV in the tonsils, which may have a direct or indirect association with the pathogenesis of tonsillar hypertrophy.

A Retrospective Study on COVID-19 Infections Caused by Omicron Variant with Clinical, Epidemiological, and Viral Load Evaluations in Breakthrough Infections.

Purpose: To explore the clinical, epidemiological, and viral load characteristics of COVID-19 caused by the omicron variant. Methods: Based on the COVID-19 epidemic caused by SARS-CoV-2 Omicron BA.2 broke out in Shanghai, China. To analyze whether there is any association between clinical symptoms and viral load of COVID-19 with age, sex, and combined disease and whether the clinical symptoms and viral load are associated with vaccine-breakthrough infections. Results: The most common symptoms were cough, expectoration, and fatigue, which were more common in women than males (p < 0.001). The average viral clearance time in the > 75 years group was the longest (6.64 days). The viral load in the 60-75 years group was significantly higher than that in the other groups (p < 0.001). The 18-45 years old group had the most clinical symptoms at admission (45.39%). The days of nucleic acid-negative conversion, average viral load, highest viral load, and clinical symptoms in comorbid chronic disease patients are longer (p < 0.001). The average and highest viral loads in the unvaccinated group were longer than those in the vaccine breakthrough infection groups (p < 0.001). However, the clinical symptoms in the vaccine breakthrough infection group were significantly more severe than those in the unvaccinated group (p < 0.001). Conclusions: We found that female patients, the elderly, and those with underlying comorbidities had longer clinical positive symptoms and viral loads. Although vaccination may not reduce clinical symptoms, it can shorten the viral load and the time required for virus clearance.

Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay - Shenzhen City, Guangdong Province, China, 2023.

The emergence of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineage, BA.2.86, has sparked global public health concerns for its potential heightened transmissibility and immune evasion. Utilizing data from Shenzhen's city-wide wastewater surveillance system, we highlight the presence of the BA.2.86 lineage in Shenzhen. A mediator probe polymerase chain reaction (PCR) assay was developed to detect the BA.2.86 lineage in wastewater by targeting a specific mutation (Spike: A264D). Between September 19 and December 10, 2023, 781 wastewater samples from 38 wastewater treatment plants (WWTPs) and 9 pump stations in ten districts of Shenzhen were examined. Through multiple short-amplicon sequencing, three positive samples were identified. The BA.2.86 lineage was identified in the wastewater of Futian and Nanshan districts in Shenzhen on December 2, 2023. From December 2 to 10, a total of 21 BA.2.86-positive wastewater samples were found across 6 districts (Futian, Nanshan, Longhua, Baoan, Longgang, and Luohu) in Shenzhen. The weighted average viral load of the BA.2.86 lineage in Shenzhen's wastewater was 43.5 copies/L on December 2, increased to 219.8 copies/L on December 4, and then decreased to approximately 100 copies/L on December 6, 8, and 10. The mediator probe PCR assay, designed for swift detection of low viral concentrations of the BA.2.86 lineage in wastewater samples, shows promise for detecting different SARS-CoV-2 variants. Wastewater surveillance could serve as an early detection system for promptly identifying specific SARS-CoV-2 variants as they emerge.

Hepatitis C viral load and genotypes distribution among chronically infected patients in Morocco

PurposeIn Morocco, the hepatitis C virus (HCV) genotypic distribution is poorly studied and not continuously updated. The aim of this study is to characterize HCV genotypes diversity and dynamics in Morocco. MethodsA retrospective study carried out between 2003 and 2020 on 2101 patients HCV-positive at the molecular biology laboratory of Pasteur Institute of Morocco (IPM), involving HCV quantification through real-time PCR (RT-PCR) and HCV genotyping through reverse hybridization. All the 2101 patients had a viral load higher than 15 IU/mL. Alanine transaminase (ALT) levels and Fibrotest were performed in 150 patients. ResultsThe 2101 analyzed patients had a mean age of 59.52 ± 12.98 years. The average viral load was 5.23 ± 0.82 log IU/mL, and females were more affected than males (sex-ratio = 0.75, p < 0.05). Genotypes 1 (54.18 %) and 2 (42.98 %) were the most prevalent, while genotypes 3, 4 and 5 were rarely found. HCV subtypes were distributed as follows: 1b (37.74 %), 2a/2c (28.18 %), 2 UC (14.80 %), 1 UC (9.47 %), 1a (5.14 %), 1a/1b (2.43 %), 4 UC (0.90 %), 3 UC (0.57 %), 3a (0.48 %), 4a (0.14 %), 5 UC (0.10 %), and 5a (0.05 %). Genotype 3 was detected for the first time in our country in 2013 and increased over time. Advanced liver fibrosis was associated with genotype 1b followed by genotype 2a/2c, with genotype 1b demonstrates a propensity for heightened virulence (p < 0.05) in the present study. ConclusionOur study reports the most recent data on HCV genotypes distribution in Morocco and the importance of analyzing HCV variability as it offers insights into the virus's dynamics in the population, enabling the monitoring of new migratory flows and their influence on the transition's rate to chronic infection.

Environmental monitoring of SARS-CoV-2 in the metropolitan area of Porto Alegre, Rio Grande do Sul (RS), Brazil

Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.

The impact of the COVID-19 pandemic on routine HIV care and cervical cancer screening in North-Central Nigeria

IntroductionCervical cancer is the fourth most diagnosed cancer among women globally, with much of the burden being carried by women in limited-resource settings often worsened by the high prevalence of HIV. Furthermore, the COVID-19 pandemic disrupted organized screening efforts and HIV management regimens worldwide, and the impact of these disruptions have not been examined in these settings. The purpose of this paper is to describe whether uptake of cervical cancer screening and HIV management changed before, during, and since the COVID-19 pandemic in North-Central Nigeria.MethodsLongitudinal healthcare administration data for women who obtained care between January 2018 and December 2021 were abstracted from the AIDS Prevention Initiative Nigeria (APIN) clinic at Jos University Teaching Hospital. Patient demographics, pap smear outcomes, and HIV management indicators such as viral load and treatment regimen were abstracted and assessed using descriptive and regression analyses. All analyses were conducted comparing two years prior to the COVID-19 pandemic, the four quarters in 2020, and the year following COVID-19 restrictions.ResultsWe included 2304 women in the study, most of whom were between 44 and 47 years of age, were married, and had completed secondary education. About 85% of women were treated with first line highly active retroviral therapy (HAART). Additionally, 84% of women screened using pap smear had normal results. The average age of women who sought care at APIN was significantly lower in Quarter 3, 2020 (p = 0.015) compared to the other periods examined in this study. Conversely, the average viral load for women who sought care during that period was significantly higher in adjusted models (p < 0.0001). Finally, we determined that the average viral load at each clinic visit was significantly associated with the period in which women sought care.ConclusionsOverall, we found that COVID-19 pandemic mitigation efforts significantly influenced women’s ability to obtain cervical cancer screening and routine HIV management at APIN clinic. This study buttresses the challenges in accessing routine and preventive care during the COVID-19 pandemic, especially in low-resource settings. Further research is needed to determine how these disruptions to care may influence long-term health in this and similar at-risk populations.

930. COVID-19 symptom and viral load rebound among individuals reporting nirmatrelvir/ritonavir use compared to propensity score matched individuals not taking COVID-19 treatment

930. COVID-19 symptom and viral load rebound among individuals reporting nirmatrelvir/ritonavir use compared to propensity score matched individuals not taking COVID-19 treatment

Pathogenicity of white spot syndrome virus (WSSV) after multiple passages in mud crab, Scylla olivacea

White spot syndrome virus (WSSV) is a highly virulent shrimp pathogen with a broad host range. Among the hosts, though mud crab, Scylla olivacea is reported to be more susceptible to WSSV than S. serrata and S. paramamosain, a detailed study on the pathogenicity and genome stability of the virus after multiple passages has yet to be reported. Firstly, to test the pathogenicity of the virus, WSSV was intramuscularly injected into healthy shrimp, Penaeus vannamei. Experimentally infected P. vannamei showed the first mortality at 36 h post-injection (hpi), followed by 100 % cumulative mortality in 7 days post-injection (dpi). However, S. olivacea injected with the WSSV inoculum derived from infected shrimp showed the first mortality at 48 hpi and a cumulative mortality of 70 % at the end of the ten days experiment. Subsequently, WSSV was sequentially passaged five times in Scylla olivacea to find out any change in the virulence of the virus in each passage. S. olivacea groups injected with 1st, second, third and fourth passages derived from the crab recorded the first mortality between 48 and 56 hpi and the cumulative mortality of 60 to 70 % at the end of the ten days experiment. Injection of WSSV inoculum in P. vannamei derived from multiple passages in S. olivaceae revealed the retention of the pathogenicity of the virus. Shrimp groups injected with WSSV derived from different passages showed first mortality between 24 and 36 hpi and cumulative mortality of 100 % between 6 and 7 dpi. The average viral load in the shrimp groups injected with WSSV inoculum derived from shrimp was 3.6 × 108, whereas in shrimp injected with the inoculum derived from 1st, third and fifth passages from crab showed 4.0 × 108, 4.7 × 108 and 4.3 × 108 copies per 100 ng DNA. Histological examination of the gill and stomach tissue of shrimp injected with inoculum prepared from shrimp as well as the inoculum derived from 1st, third and fifth passages in S. olivacea revealed characteristic pathological manifestations of the WSSV infection in gill and stomach tissues such as hypertrophied nuclei, Cowdry A-type inclusions as well as massive basophilic intranuclear inclusions. Further, to study the genome stability, the primers targeting highly variable regions of the WSSV genome (ORF94, ORF125, ORF75, variable region (VR) 14/15 and VR 23/24) were used to amplify WSSV derived from different passages and the amplified PCR products were sequenced. The sequence analysis revealed the WSSV genome stability after multiple passages in mud crab, S. olivacea.

Assessing Self-Care Practises of People Living With HIV/AIDS Attending the Antiretroviral Clinic of the University of Abuja Teaching Hospital, Nigeria

In pursuance of the Global and National Goals of achieving HIV-AIDS epidemic control, it’s imperative to explore the Promotion of self-care management among people living with HIV/AIDS. Self-care management involves adhering to treatment regimens, good dietary patterns, increased physical exercise, social support, and health-seeking behaviours. The study reviewed five core pillars of self-care management: physical, psychological, emotional, spiritual, and workplace/professional. A cross-sectional descriptive, analytical study with a quantitative approach was conducted at the Antiretroviral Clinic of the University of Abuja Teaching Hospital from October to December 2020. Using random sampling, 372 people living with AIDS participated in the study. Trained research assistants collected data through a structured questionnaire administered at the antiretroviral clinic. The data was analysed using SPSS version 25.0, employing frequencies, computations, percentages, averages, means, standard deviation, and correlations, with a confidence interval of 95%. The study’s findings indicate that the weighted matrix scores (WMS) for various aspects of self-care were significantly above average, suggesting that PLHIV attending the antiretroviral clinic at the University of Abuja Teaching Hospital exhibit good self-care practices. However, psychological and workplace self-care requires some strengthening. The study revealed differences between self-reported appointment adherence and the calculated average appointment gap (3 visits). Associations were found between the average appointment gap and viral load among participants. The study did not establish any significant association between Total Matrixed self-care scores, adherence (appointment gap), or viral load suppression. The COVID epidemic and the nationwide ENDSARS protest in Nigeria during the study period were significant confounders and limitations. Keywords: Antiretroviral drugs, appointment adherence, HIV/AIDS, psychological health, self-care management.

Detection of Alpha- and Betacoronaviruses in Small Mammals in Western Yunnan Province, China.

The genetic diversity of coronaviruses (CoVs) is high, and their infection in animals has not yet been fully revealed. By RT-PCR detection of the partial RNA-dependent RNA polymerase (RdRp) gene of CoVs, we screened a total of 502 small mammals in the Dali and Nujiang prefectures of Western Yunnan Province, China. The number of overall CoV positives was 20, including β-CoV (n = 13) and α-CoV (n = 7), with a 3.98% prevalence in rectal tissue samples. The identity of the partial RdRp genes obtained for 13 strains of β-CoV was 83.42-99.23% at the nucleotide level, and it is worth noting that the two strains from Kachin red-backed voles showed high identity to BOV-36/IND/2015 from Indian bovines and DcCoV-HKU23 from dromedary camels (Camelus dromedarius) in Morocco; the nucleotide identity was between 97.86 and 98.33%. Similarly, the identity of the seven strains of α-CoV among the partial RdRp sequences was 94.00-99.18% at nucleotide levels. The viral load in different tissues was measured by quantitative RT-PCR (qRT-PCR). The average CoV viral load in small mammalian rectal tissue was 1.35 × 106 copies/g; differently, the mean CoV viral load in liver, heart, lung, spleen, and kidney tissue was from 0.97 × 103 to 3.95 × 103 copies/g, which revealed that CoV has extensive tropism in rectal tissue in small mammals (p < 0.0001). These results revealed the genetic diversity, epidemiology, and infective tropism of α-CoV and β-CoV in small mammals from Dali and Nujiang, which deepens the comprehension of the retention and infection of coronavirus in natural hosts.

Identification of HPV16 positive cervical cancer subsets characterized by divergent immune and oncogenic phenotypes with potential implications for immunotherapy.

Cervical cancers (CaCx), like many other cancer types, portray high molecular heterogeneity that affects response to therapy, including immunotherapy. In India and other developing countries, CaCx mortality rates are very high because women report to the clinics with advanced cancers in absence of organized screening programs. This calls for implementation of newer therapeutic regimens for CaCx, like immunotherapy, which is again not used commonly in such countries. Therefore, we focused on dissecting tumour immune heterogeneity, if any, identify immune gene-based biomarkers of heterogeneity and subsets of such cancers with the potential for immunotherapy. We also attempted to characterize the cancer-associated phenotypes of such subsets, including viral load, to decipher the relationship of tumour immunogenicity with oncogenicity. Employing RNA-seq analysis of 44 HPV16 positive CaCx patients, immune subtypes were identified by unsupervised hierarchical clustering of global immune-gene expression profiles. Proportions of tumor infiltrating immune cells in the tumor milieu were estimated, employing Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT), using gene expression data from RNA-seq. The oncogenic phenotypes of the immune subtypes of CaCx were deciphered through differential gene expression (DEGs) and pathway enrichment analysis. Viral load was estimated through TaqMan-based qRT-PCR analysis. Analysis revealed the presence of two immune subtypes of CaCx, A (26/44; 59.09%) and B (18/44; 40.90%). Compared to Subtype-A, Subtype-B portrayed overexpression of immune genes and high infiltration of immune cells, specifically CD8+ T cells (p < 0.0001). Besides, a significant correlation between PD-1 and PD-L1 co-expression among Subtype-B, as opposed to Subtype-A, confirmed the interactive roles of these immune checkpoint molecules in Subtype B. Stepwise discriminant analysis pin-pointed ten immune-genes that could classify 100% of the patients significantly (p < 0.0001) into the two immune subtypes and serve as potential biomarkers of CaCx immunity. Differential gene expression analysis between the subtypes unveiled that Subtype-B was more biologically aggressive than Subtype-A, reflecting loss of structural integrity and promotion of cancer progression. The viral load was significantly lower in Subtype-B (average viral load = 10.74/100 ng of genomic DNA) compared to Subtype-A (average viral load = 14.29/100 ng of genomic DNA). Thus viral load and the ten-gene panel underscore their association with immunogenicity and oncogenicity. Our study provides strong evidence that only a subset, about 41% of HPV16 positive CaCx patients in India, portray immune enrichment of the tumor milieu coupled with aggressive phenotypes. Such subtypes are therefore likely to benefit through checkpoint molecule-based or tumor infiltrating lymphocyte-based immunotherapy, which could be a leap forward in tackling aggressive forms of such CaCx in India and other developing countries.

Genetic differences in variants of the AMD virus at the site of a disease outbreak

Aleutian Mink Disease Virus (AMDV) results in mink breeding losses due to frequent abortion, low fecundity and high juvenile mortality. Due to the high persistence of pathogen in the environment and lack of causative treatment there is a need for research on alternative methods to eliminate the pathways of the spread of the virus and extinguish current outbreaks. The aim of the study was to investigate molecular variation of AMDV on a farm where mass deaths of mink took place.The material for the research was obtained from a mink farm located in Latvia. Mass deaths had occurred on the farm among symptoms typical of Aleutian disease. Spleen samples were collected from the dead animals during post-mortem examination. Sequencing and bioinformatic analysis made it possible to distinguish the variants occurring in the groups.The presence of the genetic material of the virus was confirmed by PCR and qPCR in each of the spleen samples. The isolates were divided into two main groups: the dominant group A, with more than 83% of all isolates, and group B. Comparison of the variants with the nonpathogenic strain AMDV-G revealed that isolates from group A were more than 95% similar to that strain, whereas the similarity of group B isolates was just over 86%. The average viral load in both groups was 108 copies; no differences in viral load were noted between groups.Testing based on serological analysis produces fairly effective screening results, but these methods do not enable complete elimination of the virus from a population. Only their use in combination with modern testing techniques as tools for identification of vectors and the directions of the spread of the AMD virus can make it possible to block the routes of its spread and to extinguish its current outbreaks.

Impact of GVHD prophylaxis on CMV reactivation and disease after HLA-matched peripheral blood stem cell transplantation.

The kinetics of early and late cytomegalovirus (CMV) reactivation after hematopoietic cell transplantation using various methods of graft-versus-host-disease (GVHD) prophylaxis are poorly defined. We retrospectively compared CMV reactivation and disease among 780 seropositive patients given HLA-matched peripheral blood stem cell (PBSC) grafts and calcineurin inhibitor plus posttransplantation cyclophosphamide (PTCy; n= 44), mycophenolate mofetil (MMF; n= 414), or methotrexate (MTX; n= 322). Transplantation occurred between 2007 and 2018; CMV monitoring/management followed uniform standard practice. Hazards of CMV reactivation at various thresholds were compared. Spline curves were fit over average daily viral load and areas under the curve (AUC) within 1 year were calculated. PTCy and MMF were associated with an increased risk of early (day ≤100) CMV reactivation ≥250 IU/mL after multivariate adjustment. The viral load AUC at 1 year was highest with MMF (mean difference= 0.125 units vs MTX group) and similar between PTCy and MTX (mean difference= 0.016 units vs MTX group). CMV disease risk was similar across groups. There was no interaction between GVHD prophylaxis and CMV reactivation on chronic GVHD risk. Despite PTCy-associated increased risk of early CMV reactivation, the CMV disease risk by 1 year was low in HLA-matched PBSC transplant recipients. In contrast, MMF was associated with higher overall CMV viral burden in the 1 year posttransplant. Although different mechanisms of immunosuppressive agents may affect CMV reactivation risk, effective prevention of GVHD may reduce corticosteroid exposure and mitigate infection risk over time.

Cost of improved test and treat strategies in Indonesia.

To estimate and compare the cost of improved test and treat strategies in Indonesia under HIV Awal (Early) Testing and Treatment Indonesia (HATI) implementation trial in community-based and hospital-based clinics. The cost and outcome [i.e. CD4 + cell count] and viral load (VL) at the beginning of interventions and their change overtime) analysis of Simplifying ART Initiation (SAI), Community-based Organization and community-based ART Service (CBO), Motivational Interviewing (MI), Oral Fluid-based Testing (OFT), and Short Message Service (SMS) reminder in community-based and hospital-based clinics in 2018-2019. We estimated the total and unit costs per patient (under HATI implementation trial interventions) per year from societal perspective in various settings, including costs from patients' perspective for SAI and MI. We also analyzed the outcome variables (i.e. CD4 + cell count and VL at the beginning of each intervention, the change in CD4 + cell count and VL over time, and adherence rate). The unit cost per patient per year of SAI and SMS were lower at the community-based clinics, and more patients visited community-based clinics. The cost per patient visit from patient perspective for SAI and MI was mostly lower than 10% of the patients' household monthly expenditure. Average CD4 + cell count was higher and average VL was lower at the start of interventions at the community-based clinics, while average CD4 + cell count and VL changes and adherence rate were similar between the two types of clinics. Community-based clinics hold the potential for scaling up the interventions as it costs less from societal perspective and showed better outcome improvement during the HATI implementation trial.

Low incidence and morbidity of Epstein-Barr virus reactivation following donor lymphocyte infusions.

Low incidence and morbidity of Epstein-Barr virus reactivation following donor lymphocyte infusions.