Variation In Viral Load Research Articles

SARS-CoV-2 Viral Load in the Nasopharynx at Time of First Infection Among Unvaccinated Individuals

SARS-CoV-2 viral load (VL) in the nasopharynx is difficult to quantify and standardize across settings, but it may inform transmission potential and disease severity. To characterize VL at COVID-19 diagnosis among previously uninfected and unvaccinated individuals by evaluating the association of demographic and clinical characteristics, viral variant, and trial with VL, as well as the ability of VL to predict severe disease. This secondary cross-protocol analysis used individual-level data from placebo recipients from 4 harmonized, phase 3 COVID-19 vaccine efficacy trials sponsored by Moderna, AstraZeneca, Janssen, and Novavax. Participants were SARS-CoV-2 negative at baseline and acquired COVID-19 during the blinded phase of the trials. The setting included the US, Brazil, South Africa, Colombia, Argentina, Peru, Chile, and Mexico; start dates were July 27, 2020, to December 27, 2020; data cutoff dates were March 26, 2021, to July 30, 2021. Statistical analysis was performed from November 2022 to June 2023. Linear regression was used to assess the association of demographic and clinical characteristics, viral variant, and trial with polymerase chain reaction-measured log10 VL in nasal and/or nasopharyngeal swabs taken at the time of COVID-19 diagnosis. Among 1667 participants studied (886 [53.1%] male; 995 [59.7%] enrolled in the US; mean [SD] age, 46.7 [14.7] years; 204 [12.2%] aged 65 years or older; 196 [11.8%] American Indian or Alaska Native, 150 [9%] Black or African American, 1112 [66.7%] White; 762 [45.7%] Hispanic or Latino), median (IQR) log10 VL at diagnosis was 6.18 (4.66-7.12) log10 copies/mL. Participant characteristics and viral variant explained only 5.9% of the variability in VL. The independent factor with the highest observed differences was trial: Janssen participants had 0.54 log10 copies/mL lower mean VL vs Moderna participants (95% CI, 0.20 to 0.87 log10 copies/mL lower). In the Janssen study, which captured the largest number of COVID-19 events and variants and used the most intensive post-COVID surveillance, neither VL at diagnosis nor averaged over days 1 to 28 post diagnosis was associated with COVID-19 severity. In this study of placebo recipients from 4 randomized phase 3 trials, high variability was observed in SARS-CoV-2 VL at the time of COVID-19 diagnosis, and only a fraction was explained by individual participant characteristics or viral variant. These results suggest challenges for future studies of interventions seeking to influence VL and elevates the importance of standardized methods for specimen collection and viral load quantitation.

A quanta-independent approach for the assessment of strategies to reduce the risk of airborne infection

The Wells-Riley model is extensively used for retrospective and prospective modelling of the risk of airborne transmission of infection in indoor spaces. It is also used when examining the efficacy of various removal and deactivation methods for airborne infectious aerosols in the indoor environment, which is crucial when selecting the most effective infection control technologies. The problem is that the large variation in viral load between individuals makes the Wells-Riley model output very sensitive to the input parameters and may yield a flawed prediction of risk. The absolute infection risk estimated with this model can range from nearly 0 % to 100 % depending on the viral load, even when all other factors, such as removal mechanisms and room geometry, remain unchanged. We therefore propose a novel method that removes this sensitivity to viral load. We define a quanta-independent maximum absolute before-after difference in infection risk that is independent of quanta factors like viral load, physical activity, or the dose-response relationships. The input data needed for a non-steady-state calculation are just the removal rates, room volume, and occupancy duration. Under steady-state conditions the approach provides an elegant solution that is only dependent on removal mechanisms before and after applying infection control measures. We applied this method to compare the impact of relative humidity, ventilation rate and its effectiveness, filtering efficiency, and the use of ultraviolet germicidal irradiation on the infection risk. The results demonstrate that the method provides a comprehensive understanding of the impact of infection control strategies on the risk of airborne infection, enabling rational decisions to be made regarding the most effective strategies in a specific context. The proposed method thus provides a practical tool for mitigation of airborne infection risk.

Interaction of toll-like receptors and ACE-2 with different variants of SARS-CoV-2: A computational analysis.

Computational studies were performed to investigate the unknown status of endosomal and cell surface receptors in SARS-CoV-2 infection. The interactions between Toll-like receptors (TLRs)- 4/7/8/9 or ACE2 receptor and different SARS-CoV-2 variants were investigated. The RNA motifs for TLR7, TLR8 and a CpG motif for TLR9 were analyzed in different variants. Molecular docking and molecular dynamics (MD) simulations were performed to investigate receptor-ligand interactions. The number of motifs recognized by TLR7/8/9 in the Alpha, Delta and Iranian variants was lower than in the wild type (WT). Docking analysis revealed that the Alpha, Delta and some Iranian spike variants had a higher affinity for ACE2 and TLR4 than the WT, which may account for their higher transmission rate. The MD simulation also showed differences in stability and structure size between the variants and the WT, indicating potential variations in viral load. It appears that Alpha and some Iranian isolates are the variants of concern due to their higher transmissibility and rapid spread. The Delta mutant is also a variant of concern, not only because of its closer interaction with ACE2, but also with TLR4. Our results emphasize the importance of ACE2 and TLR4, rather than endosomal TLRs, in mediating the effects of different viral mutations and suggest their potential therapeutic applications.

Honey bee stocks exhibit high levels of intra-colony variation in viral loads

Colonies of the western honey bee, Apis mellifera L., are comprised of tens of thousands of genetically related individuals that can easily share and spread pathogens. Honey bee colonies exhibit variations in disease susceptibility that can translate into highly variable pathogen replication among individuals within a colony, between colonies, and between stocks. Here, we investigate the degree of variation in viral titers of common honey bee viruses (DWV-A, DWV-B, IAPV, LSV2, BQCV) within colonies and between colonies of five honey bee stocks in the United States. Our results showed high intra-colony variation in DWV-A, DWV-B, IAPV, and LSV2, but not in BQCV titers. However, the level of variation was not consistent across stocks. Here, we empirically demonstrate that there is significant intra-colony variation in viral titers and that some stocks are more prone to this variability. Our results highlight the need for further studies comparing virus susceptibility among stocks.

Large spontaneous HBV DNA fluctuations and potential usefulness of a single-point measurement of combined HBV DNA and quantitative HBsAg for the exclusion of HBeAg-negative chronic hepatitis B: A prospective Tunisian cohort study

Background and study aimDuring the natural course of HBeAg-negative chronic hepatitis B (CHB), fluctuations in hepatitis B virus (HBV) DNA and alanine aminotransferase (ALT) levels are often observed, making the classification of patients difficult. We aimed to describe spontaneous short-term HBV DNA level fluctuations and to assess the usefulness of qHBsAg in Tunisian patients with HBeAg-negative chronic HBV infection. Patients and methodsWe included 174 treatment-naive Tunisian patients with HBeAg-negative chronic HBeAg-negative HBV infection. A prospective 1-year follow-up was conducted with serial determinations of HBV DNA, ALT levels, and qHBsAg. The patients were classified into three groups: inactive carriers (G1), patients with negative HBeAg CHB (G2), and patients with an “indeterminate state” (G3). For the latter group, a liver biopsy was indicated. ResultsOnly genotype D was detected. During follow-up, 21.6% and 19.5% of patients with a low initial (<2,000 IU/ml) and intermediate viral load (2,000–20,000 IU/ml) experienced a subsequent increase in their HBV DNA levels above 2,000 and 20,000 IU/ml, respectively. Significant variations in viral load were observed in 61.1% of patients at 6-month intervals. Among the 174 patients, 89 (51.1%) belonged to G1, 33 (19%) to G2, and 52 (29.9%) to G3. Fourteen patients have undergone a liver biopsy, of whom seven showed moderate to severe liver disease. Combination of HBV DNA < 2,000 IU/ml and qHBsAg < 832 IU/ml excluded CHB in 98.4% of cases. A cutoff point for qHBsAg < 100 IU/ml associated with an annual decline of > 0.5 log 10 IU/ml is a good predictor marker of functional cure for hepatitis B. ConclusionsThis study highlights the large short-term fluctuations in HBV DNA in patients with HBeAg-negative chronic HBeAg-negative HBV infection with genotype D. Thus, using the cutoff value of 832 for qHBsAg combined with that of 2,000 for HBV DNA makes it possible to exclude CHB for most patients.

Virological Follow-up of Adults Living with HIV on Dolutegravir in an Approved Treatment Center in Douala (Cameroon)

Background: Human immunodeficiency virus infection constitutes one of the greatest contemporary human pandemics, lethal in the absence of treatment. WHO 2018 recommendations have placed Dolutegravir-based treatment as first-line treatment, particularly in resource-limited countries. The aim of this work was to study the evolution of virological parameters in people undergoing treatment with this molecule.&#x0D; Methodology: This was an analytical cross-sectional study of people aged 25 and over, received since January 2015 at the Approved Treatment center of Laquintinie Hospital in Douala (Cameroon). After plasma collection and centrifugation, viral load was determined on the Abbott m2000TM platform, targeting the Pol gene. The detection threshold was greater than or equal to 40 copies/mL. Data analysis was performed using Excel and SPSS version 20 softwares.&#x0D; Results: A total of 504 people were selected, with an average age of 48±11 years and a predominance of women (70.8%). Antiretroviral treatment had been initiated at clinical stage 1 in over 80% of participants. The TDF/3TC/EFV regimen prior to initiation of Dolutegravir was used in 93.5% of cases. Mean weight after initiation of treatment was 75.9 kg. People with a viral load &lt;40 copies/ml before starting Dolutegravir therapy accounted for 332 (65.9%) of cases, compared with 91.1% six months after starting treatment. Weight (&gt;75kg) (95% CI, OR=1.112-2.381, p=0.012) and non-adherence (95% CI, OR=2.790-25.613, p=0.001) were considered factors associated with viral load variation.&#x0D; Conclusion: The ARV protocol comprising two nucleoside reverse transcriptase inhibitors and Dolutegravir improves virological response in people living with HIV at all clinical stages.

Effectiveness of a community-based intervention (Konga model) to address factors contributing to low viral load suppression among children living with HIV in Tanzania: a preliminary, cluster, randomized clinical trial report

BackgroundDespite effective antiretroviral therapy (ART) coverage in other groups living with human immunodeficiency virus (HIV) in Tanzania, virologic suppression among HIV-positive children receiving ART remains unacceptably low. This study evaluated the effectiveness of a community-based intervention (Konga model) in addressing the factor contributing to low viral load suppression among children living with HIV in the Simiyu region, Tanzania.MethodsThis study used a parallel cluster randomized trial. The cluster was only eligible if the health facility provided HIV care and treatment. All eligible resident children aged 2‒14 years who attended the cluster with a viral load > 1,000 cells/mm were enrolled. The intervention included three distinct activities: adherence counseling, psychosocial support, and co-morbidity screening such as tuberculosis. The evaluation was based on patient-centered viral load outcomes measured at baseline and 6 months later. Using a pre- and post-test design, we compared the means of participants in the intervention and control groups. We performed an analysis of covariance. The effect of a Konga was calculated using omega-squared. We used F-tests, with their corresponding p-values, as measures of improvement.ResultsWe randomly assigned 45 clusters to the treatment (15) and control (30) groups. We enrolled 82 children with amedian age of 8.8 years(interquartile range(IQR);5.5–11.2), and a baseline median viral load of 13,150 cells/mm (interquartile range (IQR);3600–59,200). After the study, both children in each group had good adherence, with children in the treatment group scoring slightly higher than those in the control group, 40 (97.56%) versus 31(75%61), respectively. At the end of the study, the difference in viral load suppression between the two groups was significant. The median viral load suppression at the end of the study was 50 cells/mm [IQR, (20–125)]. After adjusting for the viral load before the intervention, the effect size of the Konga intervention explained 4% (95% confidence interval [0%, 14.1%]) of the viral load variation at the end of the intervention.ConclusionThe Konga model demonstrated significant positive effects that improved viral load suppression. We recommend implementing the Konga model trial in other regions to improve the consistency of results.

Dynamics of GFLV, GFkV, GLRaV-1, and GLRaV -3 grapevine viruses transport toward developing tissues

AbstractViral diseases in grapevine cause large economic losses due to decreased irregular yield and unbalanced ripening, and can even lead to plant mortality. There is a large number of grapevine viral agents, and a few of them have a prominent impact due to their worldwide distribution, virulence, and incidence. Although previous research has evaluated variations in viral load between organs and time since infection, there is still a lack of knowledge on how the viruses are transported toward developing tissues. In this work, we present the results of two experiments that contribute to understanding the spread dynamics of four major grapevine viruses (GFLV, GFkV, GLRaV-1, and GLRaV -3). Bud and leaf tissues were sampled from shoots obtained from cv. ‘Garnacha’ cuttings known to be infected with one of these viruses. Bud samples taken at early development stages were used to understand short-distance transport, while leaves taken from young shoots represented long-distance transport, driven mainly through the phloem. Our results show that all viruses were able to invade tissues from the beginning of development. The dissemination ability of GFLV was considerable, as the viral load detected in young organs was as high as in the dormant shoot. Furthermore, for GFLV and GFkV, it was shown that the viral load in young shoots does not follow the general assumption of older tissues accumulating a higher viral load but, conversely, a higher viral load closer to the shoot tip might be driven by the sink strength.

Effect of tecovirimat on healing time and viral clearance by emulation of a target trial in patients hospitalized for mpox.

Tecovirimat is a treatment option for severe mpox, although randomized clinical trials are ongoing. The aim of the study is to assess the effect of tecovirimat on healing time and the extent of viral clearance by target trial emulation using observational data. Clinical and virological data of patients hospitalized for mpox were collected. Samples from the upper respiratory tract (URT) were grouped in two time points: T1 (median 6 days from symptoms onset) and T2 (median 5 days from T1). Patients were followed-up until recovery. Average treatment effect (ATE) in patients untreated versus treated with tecovirimat was estimated on time to healing and variation in viral load in URT, using a weighted and cloning analysis. Among the 41 patients included, 19 completed a course of tecovirimat. The median time from symptoms onset to hospitalization and to drug-starting was 4 days and 10 days, respectively. No improvement in healing time in treated versus untreated was observed. No difference by treatment group in time to viral clearance was detected by ATE fitted in a subset of 13 patients after controlling for confounders. We found no evidence for a large effect of tecovirimat in shortening healing time and viral clearance. While awaiting the results of randomized studies, the use of tecovirimat should be restricted to the clinical trial setting.

Transposable elements are associated with the variable response to influenza infection

Influenza A virus (IAV) infections are frequent every year and result in a range of disease severity. Here, we wanted to explore the potential contribution of transposable elements (TEs) to the variable human immune response. Transcriptome profiling in monocyte-derived macrophages from 39 individuals following IAV infection revealed significant inter-individual variation in viral load post-infection. Using transposase-accessible chromatin using sequencing (ATAC-seq), we identified a set of TE families with either enhanced or reduced accessibility upon infection. Of the enhanced families, 15 showed high variability between individuals and had distinct epigenetic profiles. Motif analysis showed an association with known immune regulators (e.g., BATFs, FOSs/JUNs, IRFs, STATs, NFkBs, NFYs, and RELs) in stably enriched families and with other factorsin variable families, including KRAB-ZNFs. We showed that TEs and host factors regulating TEs were predictive of viral load post-infection. Our findings shed light on the role TEs and KRAB-ZNFs may play in inter-individual variation in immunity.

Associations of functional human leucocyte antigen class I groups with HIV viral load in a heterogeneous cohort.

Human leucocyte antigen (HLA) class I alleles are the main host genetic factors involved in controlling HIV-1 viral load (VL). Nevertheless, HLA diversity has proven a significant challenge in association studies. We assessed how accounting for binding affinities of HLA class I alleles to HIV-1 peptides facilitate association testing of HLA with HIV-1 VL in a heterogeneous cohort. Cohort from the Strategic Timing of AntiRetroviral Treatment (START) study. We imputed HLA class I alleles from host genetic data (2546 HIV+ participants) and sampled immunopeptidomes from 2079 host-paired viral genomes (targeted amplicon sequencing). We predicted HLA class I binding affinities to HIV-1 and unspecific peptides, grouping alleles into functional clusters through consensus clustering. These functional HLA class I clusters were used to test associations with HIV VL. We identified four clades totaling 30 HLA alleles accounting for 11.4% variability in VL. We highlight HLA-B∗57:01 and B∗57:03 as functionally similar but yet overrepresented in distinct ethnic groups, showing when combined a protective association with HIV+ VL (log, β -0.25; adj. P-value < 0.05). We further demonstrate only a slight power reduction when using unspecific immunopeptidomes, facilitating the use of the inferred functional HLA groups in other studies. The outlined computational approach provides a robust and efficient way to incorporate HLA function and peptide diversity, aiding clinical association studies in heterogeneous cohorts. To facilitate access to the proposed methods and results we provide an interactive application for exploring data.

Remdesivir Influence on SARS-CoV-2 RNA Viral Load Kinetics in Nasopharyngeal Swab Specimens of COVID-19 Hospitalized Patients: A Real-Life Experience

There are still conflicting data on the virological effects of the SARS-CoV-2 direct antivirals used in clinical practice, in spite of the documented clinical efficacy. The aim of this monocentric retrospective study was to compare virologic and laboratory data of patients admitted due to SARS-CoV-2 infection from March to December 2020 treated with either remdesivir (R), a protease inhibitor (lopinavir or darunavir/ritonavir (PI)) or no direct antiviral drugs (NT). Viral load variation was indirectly assessed through PCR cycle threshold (Ct) values on the nasopharyngeal swab, analyzing the results from swabs obtained at ward admission and 7 (±2) days later. Overall, 253 patients were included: patients in the R group were significantly older, more frequently males with a significantly higher percentage of severe COVID-19, requiring more often intensive care admission, compared to the other groups. Ct variation over time did not differ amongst the three treatment groups and did not seem to be influenced by corticosteroid use, even after normalization of the treatment groups for disease severity. Non-survivors had lower Ct on admission and showed a significantly slower viral clearance compared to survivors. CD4 T-lymphocytes absolute count assessed at ward admission correlated with a reduced Ct variation over time. In conclusion, viral clearance appears to be slower in COVID-19 non-survivors, while it seems not to be influenced by the antiviral treatment received.

Risk factors associated with response to highly active antiretroviral therapy after 24 months of administration to HIV, HIV/HBV and HCV patients in Kumba Health District, South West Region of Cameroon

Hepatitis B (HBV) and C (HCV) are two other forms of infections for which co-infection in HIV has been associated with alteration of the immune response, increased risk of progression to liver diseases, and increased risk of hepatotoxicity associated with antiretroviral therapy. This study aimed to establish the prevalence of hepatitis B surface antigen (HBsAg) and hepatitis C antibody (HCVAb) among HIV patients, evaluate response to treatment between the different categories and identify the possible risk factors associated with this burden of hepatitis B/C among HIV patients and the resulting responses to HAART in Kumba Health, in the South West Region of Cameroon. Method: We performed a systematic screening using Rapid Diagnostic Test, for HBsAg and HCVAb among 299 HIV patients enrolled at the treatment centers in Kumba Health District (District hospital Kumba, Kumba Town Sub-Divisional hospital, and the Apostolic hospital Banga Bakundu), with all positives for HBV or HCV confirmed by the ELISA and results analyzed using SPSS version 20. Out of the 299 participants, 52 HIV patients, 36 HIV/HBV, and 12 HIV/HCV patients were involved in the prospective cohort study for 24 months which permitted monitored the immune response (CD4 counts and viral load test), as well as variation of biochemical parameters (ALAT/ASAT, albumin, bilirubine, creatinine) and weights of the studied participants. Result: Out of the 100 HIV patients involved in the prospective cohort, 36 and 12 were hepatitis B and C virus-positive respectively. Following the analysis of the viral load and CD4 cell counts, there were differences in response to HAART after 24 months between the mono-infected and co-infected patients, taking into consideration the, CD4 cell counts (HIV: 930.846 cells/mm3, HIV/HBV: 595.139 cells/mm3 and HIV/HCV: 678.500cells/mm3), and viral load (HIV: 1777.85copies/ml, HIV/HBV: 2232.61copies/ml and HIV/HCV: 750.83copies/ml). There were variations in biomarkers of the liver (ALAT/ASAT, bilirubin, and albumine) and renal function (creatinine) for both patients. There were also variations of the different biomarkers linked to the infection status of the different participants. Conclusion: There were positive variations in viral load and CD4 cell counts among the studied participants, with a more rapid response to the mono-infected HIV patients compared to the co-infected patients. Similar strength was observed in the variation of the different biomarkers and such variation indicates that co-infection of HIV patients with either hepatitis B or C virus can affect rapid response to HAART and the variations in the level of Biochemical markers among the different categories are linked to the alteration of the functions of the respective organs and so this result could be used for health decisions regarding co-infections.

Variation in within-host replication kinetics among virus genotypes provides evidence of specialist and generalist infection strategies across three salmonid host species.

Theory of the evolution of pathogen specialization suggests that a specialist pathogen gains high fitness in one host, but this comes with fitness loss in other hosts. By contrast, a generalist pathogen does not achieve high fitness in any host, but gains ecological fitness by exploiting different hosts, and has higher fitness than specialists in nonspecialized hosts. As a result, specialist pathogens are predicted to have greater variation in fitness across hosts, and generalists would have lower fitness variation across hosts. We test these hypotheses by measuring pathogen replicative fitness as within-host viral loads from the onset of infection to the beginning of virus clearance, using the rhabdovirus infectious hematopoietic necrosis virus (IHNV) in salmonid fish. Based on field prevalence and virulence studies, the IHNV subgroups UP, MD, and L are specialists, causing infection and mortality in sockeye salmon, steelhead, and Chinook salmon juveniles, respectively. The UC subgroup evolved naturally from a UP ancestor and is a generalist infecting all three host species but without causing severe disease. We show that the specialist subgroups had the highest peak and mean viral loads in the hosts in which they are specialized, and they had low viral loads in nonspecialized hosts, resulting in large variation in viral load across hosts. Viral kinetics show that the mechanisms of specialization involve the ability to both maximize early virus replication and avoid clearance at later times, with different mechanisms of specialization evident in different host-virus combinations. Additional nuances in the data included different fitness levels for nonspecialist interactions, reflecting different trade-offs for specialist viruses in other hosts. The generalist UC subgroup reached intermediate viral loads in all hosts and showed the smallest variation in fitness across hosts. The evolution of the UC generalist from an ancestral UP sockeye specialist was associated with fitness increases in steelhead and Chinook salmon, but only slight decreases in fitness in sockeye salmon, consistent with low- or no-cost generalism. Our results support major elements of the specialist-generalist theory, providing evidence of a specialist-generalist continuum in a vertebrate pathogen. These results also quantify within-host replicative fitness trade-offs resulting from the natural evolution of specialist and generalist virus lineages in multi-host ecosystems.

Subtype distribution and expression of the koala retrovirus in the Japanese zoo koala population.

We investigated the proviral copies and RNA expression in koala retrovirus (KoRV)-infected koalas. To ascertain any variation in viral load by institution, age, sex, or body condition score, we quantified KoRV proviral DNA and RNA loads in captive koalas (n = 37) reared in Japanese zoos. All koalas were positive for KoRV genes (pol, LTRs, and env of KoRV-A) in genomic DNA (gDNA), and 91.89% were positive for the pol gene in RNA. In contrast, the distribution rates of KoRV-B, KoRV-C, KoRV-D, and KoRV-F env genes in gDNA were 94.59%, 27.03%, 67.57%, and 54.05%, respectively. A wide inter-individual variation and/or a significant inter-institutional difference in proviral DNA (p < 0.0001) and RNA (p < 0.001) amounts (copies/103 koala β-actin copies) were observed in Awaji Farm England Hill Zoo koalas, which were obtained from southern koala populations, suggesting exogenous incorporation of KoRV in these koalas. Significant (p < 0.05) age differences were noted in KoRV RNA load (p < 0.05) and median total RNA load (p < 0.001), with loads higher in younger koalas (joeys and juveniles). Thus, the current study provides the distribution of KoRV subtypes in Japanese zoo koala populations and identifies several additional risk factors (sex, age, and body condition) associated with KoRV expression.

THU345 - Hepatitis B viral load variation between the first and third trimesters of pregnancy

THU345 - Hepatitis B viral load variation between the first and third trimesters of pregnancy

Viral communities in the parasite Varroa destructor and in colonies of their honey bee host (Apis mellifera) in New Zealand

The parasitic mite Varroa destructor is a leading cause of mortality for Western honey bee (Apis mellifera) colonies around the globe. We sought to confirm the presence and likely introduction of only one V. destructor haplotype in New Zealand, and describe the viral community within both V. destructor mites and the bees that they parasitise. A 1232 bp fragment from mitochondrial gene regions suggests the likely introduction of only one V. destructor haplotype to New Zealand. Seventeen viruses were found in bees. The most prevalent and abundant was the Deformed wing virus A (DWV-A) strain, which explained 95.0% of the variation in the viral community of bees. Black queen cell virus, Sacbrood virus, and Varroa destructor virus 2 (VDV-2) played secondary roles. DWV-B and the Israeli acute paralysis virus appeared absent from New Zealand. Ten viruses were observed in V. destructor, with > 99.9% of viral reads from DWV-A and VDV-2. Substantially more variation in viral loads was observed in bees compared to mites. Where high levels of VDV-2 occurred in mites, reduced DWV-A occurred in both the mites and the bees co-occurring within the same hive. Where there were high loads of DWV-A in mites, there were typically high viral loads in bees.

A Comparative Analysis of Different HIV Viral Load Suppression Definitions Among Clients Receiving Care in the Miami-Dade Ryan White HIV/AIDS Program.

The study's objective was to examine variations in viral load (VL) suppression definitions among clients in the Ryan White Program (RWP). Data from clients enrolled in the RWP during 2017 were examined to calculate the proportion of virally suppressed clients using three definitions: recent viral suppression, defined as having a suppressed VL (< 200 copies/mL) in the last test in 2017; maintained viral suppression, having a suppressed VL for both the first and last tests in 2017; and sustained viral suppression, having all tests in 2017 showing suppression. Relative differences across all three definitions were computed. Recent viral suppression measures were higher than maintained and sustained viral suppression measures by 7.0% and 10.1%, respectively. Significant relative differences in definitions by demographic, socioeconomic and clinical status were observed. It may be beneficial for care planning to report not only estimates of recent viral suppression but maintained and sustained viral suppression as well.

Viruses associated with ill health in wild chimpanzees.

Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.

HIV Viral Suppression among People Living with HIV on Antiretroviral Therapy in Haut-Katanga and Kinshasa Provinces of Democratic Republic of Congo.

Human immunodeficiency virus (HIV) infections and less-than-optimal care of people living with HIV (PLHIV) continue to challenge public health and clinical care organizations in the communities that are most impacted by HIV. In the era of evidence-based public health, it is imperative to monitor viral load (VL) in PLHIV according to global and national guidelines and assess the factors associated with variation in VL levels. Purpose: This study had two objectives—(a) to describe the levels of HIV VL in persons on antiretroviral therapy (ART), and (b) to analyze the significance of variation in VL by patients’ demographic and clinical characteristics, outcomes of HIV care, and geographic characteristics of HIV care facilities. Methods: The study population for this quantitative study was 49,460 PLHIV in the Democratic Republic of Congo (DRC) receiving ART from 241 CDC-funded HIV/AIDS clinics in the Haut-Katanga and Kinshasa provinces of the DRC. Analysis of variance (ANOVA) was performed, including Tamhane’s T2 test for pairwise comparisons using de-identified data on all patients enrolled in the system by the time the data were extracted for this study by the HIV programs in May 2019. Results: The VL was undetectable (<40 copies/mL) for 56.4% of the patients and 24.7% had VL between 40 copies/mL and less than 1000 copies per mL, indicating that overall, 81% had VL < 1000 and were virologically suppressed. The remaining 19% had a VL of 1000 copies/mL or higher. The mean VL was significantly (p < 0.001) higher for males than for females (32,446 copies/mL vs. 20,786, respectively), persons <15 years of age compared to persons of ages ≥ 15 years at the time of starting ART (45,753 vs. 21,457, respectively), patients who died (125,086 vs. 22,090), those who were lost to follow-up (LTFU) (69,882 vs. 20,018), those with tuberculosis (TB) co-infection (64,383 vs. 24,090), and those who received care from urban clinics (mean VL = 25,236) compared to rural (mean VL = 3291) or semi-rural (mean VL = 26,180) clinics compared to urban. WHO clinical stages and duration on ART were not statistically significant at p ≤ 0.05 in this cohort. Conclusions: The VL was >1000 copies/mL for 19% of PLHIV receiving ART, indicating that these CDC-funded clinics and programs in the Haut-Katanga and Kinshasa provinces of DRC have more work to do. Strategically designed innovations in services are desirable, with customized approaches targeting PLHIV who are younger, male, those LTFU, with HIV/TB co-infection, and those receiving care from urban clinics.