Use of Next Generation Sequencing in a State-Wide Strategy of HIV-1 Surveillance: Impact of the SARS-CoV-2 Pandemic on HIV-1 Diagnosis and Transmission.

BACKGROUND: The ongoing SARS-CoV-2 pandemic posed an unpreceded threat to the management of other pandemics such as HIV-1 in the United States. The full impact of the SARS-CoV-2 pandemic on the HIV-1 pandemic needs to be evaluated. METHODS: All individuals with newly reported HIV-1 diagnoses from NC State Laboratory of Public Health were enrolled in this prospective observational study from 2018 to 2021. We used a sequencing-based recency assay to identify recent HIV-1 infections and to determine the days post infection (DPI) for each person at the time of diagnosis. RESULTS: Sequencing was done using diagnostic serum samples from 814 individuals with new HIV-1 diagnoses spanning this 4 year period. Characteristics of individuals diagnosed in 2020 differed from those from other years. DPI analysis showed that people of color diagnosed in 2021 were on average 6 months delayed in their diagnosis compared to those diagnosed in 2020. There was a trend that genetic networks were more known for individuals diagnosed in 2021. We observed no major integrase resistance mutations over the course of the study. CONCLUSIONS: SARS-CoV-2 pandemic may contribute to the spread of HIV-1. Public health resources need to focus on restoring HIV-1 testing and interrupting active, ongoing, transmission.

Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses.

Next generation sequencing (NGS)/deep sequencing has become an important tool in the study of viruses. The use of unique molecular identifiers (UMI) can overcome the limitations of PCR errors and PCR-mediated recombination and reveal the true sampling depth of a viral population being sequenced in an NGS experiment. This approach of enhanced sequence data represents an ideal tool to study both high and low abundance drug resistance mutations and more generally to explore the genetic structure of viral populations. Central to the use of the UMI/Primer ID approach is the creation of a template consensus sequence (TCS) for each genome sequenced. Here we describe a series of experiments to validate several aspects of the Multiplexed Primer ID (MPID) sequencing approach using the MiSeq platform. We have evaluated how multiplexing of cDNA synthesis and amplicons affects the sampling depth of the viral population for each individual cDNA and amplicon to understand the relationship between broader genome coverage versus maximal sequencing depth. We have validated reproducibility of the MPID assay in the detection of minority mutations in viral genomes. We have also examined the determinants that allow sequencing reads of PCR recombinants to contaminate the final TCS data set and show how such contamination can be limited. Finally, we provide several examples where we have applied MPID to analyze features of minority variants and describe limits on their detection in viral populations of HIV-1 and SARS-CoV-2 to demonstrate the generalizable utility of this approach with any RNA virus.

A systematic review of whether COVID-19 randomized controlled trials reported on demographic and clinical characteristics.

PURPOSE: We aim to assess the reporting of key patient-level demographic and clinical characteristics among COVID-19 related randomized controlled trials (RCTs). METHODS: We queried English-language articles from PubMed, Web of Science, clinicaltrials.gov, and the CDC library of gray literature databases using keywords of "coronavirus," "covid," "clinical trial" and "randomized controlled trial" from January 2020 to June 2021. From the search, we conducted an initial review to rule-out duplicate entries, identify those that met inclusion criteria (i.e., had results), and exclude those that did not meet the definition of an RCT. Lastly, we abstracted the demographic and clinical characteristics reported on within each RCT. RESULTS: From the initial 43 627 manuscripts, our final eligible manuscripts consisted of 149 RCTs described in 137 articles. Most of the RCTs (113/149) studied potential treatments, while fewer studied vaccines (29), prophylaxis strategies (5), and interventions to prevent transmission among those infected (2). Study populations ranged from 10 to 38 206 participants (median = 100, IQR: 60-300). All 149 RCTs reported on age, 147 on sex, 50 on race, and 110 on the prevalence of at least one comorbidity. No RCTs reported on income, urban versus rural residence, or other indicators of socioeconomic status (SES). CONCLUSIONS: Limited reporting on race and other markers of SES make it difficult to draw conclusions about specific external target populations without making strong assumptions that treatment effects are homogenous. These findings highlight the need for more robust reporting on the clinical and demographic profiles of patients enrolled in COVID-19 related RCTs.

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxford Nanopore Technologies (ONT) long-reads to measure differential host gene expression, transcript polyadenylation and isoform usage within various epithelial cell lines permissive and non-permissive for SARS-CoV-2 infection. SARS-CoV-2-infected and mock-infected Vero (African green monkey kidney epithelial cells), Calu-3 (human lung adenocarcinoma epithelial cells), Caco-2 (human colorectal adenocarcinoma epithelial cells) and A549 (human lung carcinoma epithelial cells) were analyzed over time (0, 2, 24, 48 hours). Differential polyadenylation was found to occur in both infected Calu-3 and Vero cells during a late time point (48 hpi), with Gene Ontology (GO) terms such as viral transcription and translation shown to be significantly enriched in Calu-3 data. Poly(A) tails showed increased lengths in the majority of the differentially polyadenylated transcripts in Calu-3 and Vero cell lines (up to ~101 nt in mean poly(A) length, padj = 0.029). Of these genes, ribosomal protein genes such as RPS4X and RPS6 also showed downregulation in expression levels, suggesting the importance of ribosomal protein genes during infection. Furthermore, differential transcript usage was identified in Caco-2, Calu-3 and Vero cells, including transcripts of genes such as GSDMB and KPNA2, which have previously been implicated in SARS-CoV-2 infections. Overall, these results highlight the potential role of differential polyadenylation and transcript usage in host immune response or viral manipulation of host mechanisms during infection, and therefore, showcase the value of long-read sequencing in identifying less-explored host responses to disease.

B-cell cytopenia and time to last B-cell-depleting therapy predict response to SARS-COV-2 vaccines in patients with lymphoproliferative disorders.

Patients with B-non-Hodgkin lymphoma (NHL) are at increased risk of morbidity and mortality from SARS-CoV-2. We investigated the relationship between B cell cytopenia and the SARS-CoV-2 vaccine response in B-NHL patients. We measured anti-RBD antibodies and the lymphocyte immunophenotype in 19 controls, 22 lymphoma patients on observation (cohort 1) and 55 lymphoma patients receiving their vaccines post B-cell depleting therapy (cohort 2). Half of the lymphoma patients in both cohorts achieved seropositivity compared to 100% of controls. In cohort 2, only 5% achieved an antibody response in the first year post B-cell depleting treatment, vs 88% treated >2 years prior. Also, 28% of patients with <50 B cells/µl achieved a serologic response vs 86% of patients with B-cell >50 B cells/µl. B-cell cytopenia is profound within the first year of exposure to B-cell depleting treatment, therefore an additional dose of vaccine within that timeframe is unlikely to raise antibody levels.

Reflections from the COVID-19 pandemic on inequalities and patient and public involvement and engagement (PPIE) in social care, health and public health research.

Patient and public involvement and engagement (PPIE) has evolved to become widely established practice in social care, health and public health research in the UK. The COVID-19 pandemic has caused rapid change in practice in PPIE, notably in moving from face-to-face meetings to virtual ones. This has opened a space for reflecting on established PPIE practice, but there is a risk this is conducted too narrowly, such as only weighing our preferences and the relative pros and cons with regard to in-person versus virtual meetings. The pandemic has also demonstrated the wide inequalities in society, and hence, we argue that an inequalities lens ought to guide a deeper and wider reflection on PPIE practice. We do not seek to criticize practice pre- or during the pandemic, but to encourage using the inequalities lens as a means of encouraging debate and focusing energy on a more rigorous review of PPIE practice to widen involvement in social care, health and public health research.

Increasing efficiency in vaccine Production: A primer for change.

The COVID-19 pandemic has highlighted the importance of vaccines as public health and pandemic preparedness tools and amplified the importance of issues ranging from equitable distribution to reliable supply of quality, affordable vaccines. These issues however are not new. Delays in time from the first dose in a high-income country to introduction at scale in a low-income country can take years. These delays are driven by several challenges, some of which are unique to the vaccine development ecosystem. The patenting and overall intellectual property (IP) protection are complex, regulatory oversight is rigorous, manufacturing processes require technical support or know-how transfer from the innovator, and market dynamics create obstacles to delivering at scale. However, there are opportunities to accelerate the introduction of vaccines at scale in low and middle-income countries. To identify those opportunities, this paper provides an overview of the vaccine research and development process and where reform of the current system could increase access.

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of open reading frame 1ab (ORF1ab) containing nsp1 joins to ORF10, and the 3' untranslated region (UTR) upregulates at 48 h post-infection in human cell lines. We identify double-junction sgRNA containing both TRS-dependent and -independent junctions. We find multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA and that sgRNA modifications are stable across transcript clusters, host cells, and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle.

Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome.

Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses. In this report we describe a protocol using Primer ID sequencing to study the mutations induced by antivirals in a coronavirus genome from an in vitro cell culture model and an in vivo mouse model. Viral RNA or total lung tissue RNA is tagged with Primer ID-containing cDNA primers during the initial reverse transcription step, followed by two rounds of PCR to amplify viral sequences and incorporate sequencing adaptors. Purified and pooled libraries are sequenced using the MiSeq platform. Sequencing data are processed using the template consensus sequence (TCS) web-app. The Primer ID approach provides an accurate sequencing protocol to measure mutation error rates in viral RNA genomes and host mRNA. Sequencing results suggested that ß-D-N4-hydroxycytidine (NHC) greatly increased the transition substitution rate but not the transversion substitution rate in the viral RNA genomes, and cytosine (C) to uridine (U) was found as the most frequently seen mutation.

Evaluation of a primary care-based collaborative care model (PARTNERS2) for people with diagnoses of schizophrenia, bipolar, or other psychoses: study protocol for a cluster randomised controlled trial.

BACKGROUND: Current NHS policy encourages an integrated approach to provision of mental and physical care for individuals with long term mental health problems. The 'PARTNERS2' complex intervention is designed to support individuals with psychosis in a primary care setting. AIM: The trial will evaluate the clinical and cost-effectiveness of the PARTNERS2 intervention. DESIGN & SETTING: This is a cluster randomised controlled superiority trial comparing collaborative care (PARTNERS2) with usual care, with an internal pilot to assess feasibility. The setting will be primary care within four trial recruitment areas: Birmingham & Solihull, Cornwall, Plymouth, and Somerset. GP practices are randomised 1:1 to either (a) the PARTNERS2 intervention plus modified standard care ('intervention'); or (b) standard care only ('control'). METHOD: PARTNERS2 is a flexible, general practice-based, person-centred, coaching-based intervention aimed at addressing mental health, physical health, and social care needs. Two hundred eligible individuals from 39 GP practices are taking part. They were recruited through identification from secondary and primary care databases. The primary hypothesis is quality of life (QOL). Secondary outcomes include: mental wellbeing, time use, recovery, and process of physical care. A process evaluation will assess fidelity of intervention delivery, test hypothesised mechanisms of action, and look for unintended consequences. An economic evaluation will estimate its cost-effectiveness. Intervention delivery and follow-up have been modified during the COVID-19 pandemic. CONCLUSION: The overarching aim is to establish the clinical and cost-effectiveness of the model for adults with a diagnosis of schizophrenia, bipolar, or other types of psychoses.

Investigating the risks of removing wild meat from global food systems.

The COVID-19 pandemic has brought humanity's strained relationship with nature into sharp focus, with calls for cessation of wild meat trade and consumption, to protect public health and biodiversity.1,2 However, the importance of wild meat for human nutrition, and its tele-couplings to other food production systems, mean that the complete removal of wild meat from diets and markets would represent a shock to global food systems.3-6 The negative consequences of this shock deserve consideration in policy responses to COVID-19. We demonstrate that the sudden policy-induced loss of wild meat from food systems could have negative consequences for people and nature. Loss of wild meat from diets could lead to food insecurity, due to reduced protein and nutrition, and/or drive land-use change to replace lost nutrients with animal agriculture, which could increase biodiversity loss and emerging infectious disease risk. We estimate the magnitude of these consequences for 83 countries, and qualitatively explore how prohibitions might play out in 10 case study places. Results indicate that risks are greatest for food-insecure developing nations, where feasible, sustainable, and socially desirable wild meat alternatives are limited. Some developed nations would also face shocks, and while high-capacity food systems could more easily adapt, certain places and people would be disproportionately impacted. We urge decision-makers to consider potential unintended consequences of policy-induced shocks amidst COVID-19; and take holistic approach to wildlife trade interventions, which acknowledge the interconnectivity of global food systems and nature, and include safeguards for vulnerable people.