Hybrid Opto‐Thermocycler for RT‐qPCR Detects SARS‐CoV‐2

Although real‐time quantitative reverse transcription polymerase chain reaction (RT‐qPCR) is the gold standard for detecting the virus severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) and other pathogens, the coronavirus disease 2019 (COVID‐19) pandemic has highlighted the scarcity of instruments, devices, and reagents for polymerase chain reaction (PCR) testing in constrained settings. At least for under‐resourced countries, it has become critical to deploy instruments that can be rapidly constructed and satisfy this demand. Instead of separating the optical system from the thermal module (typical of qPCR thermocyclers), we report a portable Hybrid Opto‐Thermocycler—dubbed HybOT Cycler—that takes advantage of the high‐temperature tolerances (>100 °C) of electronic and optical components to combine thermal control, illumination, and fluorescence detection into a highly integrated hybrid module. This simple configuration allowed us to reduce the overall number of components, thus simplifying its assembly and reducing the instrument size. The HybOT Cycler is wirelessly controlled from an application installed in a tablet. PCR assays are carried out in a bubble‐free microfluidic device that can be easily replicated from an acrylic mold. Using the HybOT Cycler, down to 100 copies/µL of genetic material of the virus SARS‐CoV‐2 with 95% sensitivity and 100% specificity is detected. The HybOT Cycler can assist in diagnosing SARS‐CoV‐2 and other pathogens in resource‐poor settings. [ FROM AUTHOR] Copyright of Advanced Materials Technologies is the property of John Wiley & Sons, Inc. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Simple hemogram to support the decision-making of COVID-19 diagnosis using clusters analysis with self-organizing maps neural network.

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is related to new coronavirus disease (COVID-19) has mobilized several scientifics to explore clinical data using soft-computing approaches. In the context of machine learning, previous studies have explored supervised algorithms to predict and support diagnosis based on several clinical parameters from patients diagnosed with and without COVID-19. However, in most of them the decision is based on a "black-box" method, making it impossible to discover the variable relevance in decision making. Hence, in this study, we introduce a non-supervised clustering analysis with neural network self-organizing maps (SOM) as a strategy of decision-making. We propose to identify potential variables in routine blood tests that can support clinician decision-making during COVID-19 diagnosis at hospital admission, facilitating rapid medical intervention. Based on SOM features (visual relationships between clusters and identification of patterns and behaviors), and using linear discriminant analysis , it was possible to detect a group of units of the map with a discrimination power around 83% to SARS-CoV-2-positive patients. In addition, we identified some variables in admission blood tests (Leukocytes, Basophils, Eosinophils, and Red cell Distribution Width) that, in combination had strong influence in the clustering performance, which could assist a possible clinical decision. Thus, although with limitations, we believe that SOM can be used as a soft-computing approach to support clinician decision-making in the context of COVID-19.

Hybrid Opto‐Thermocycler for RT‐qPCR Detects SARS‐CoV‐2

Although real‐time quantitative reverse transcription polymerase chain reaction (RT‐qPCR) is the gold standard for detecting the virus severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) and other pathogens, the coronavirus disease 2019 (COVID‐19) pandemic has highlighted the scarcity of instruments, devices, and reagents for polymerase chain reaction (PCR) testing in constrained settings. At least for under‐resourced countries, it has become critical to deploy instruments that can be rapidly constructed and satisfy this demand. Instead of separating the optical system from the thermal module (typical of qPCR thermocyclers), we report a portable Hybrid Opto‐Thermocycler—dubbed HybOT Cycler—that takes advantage of the high‐temperature tolerances (>100 °C) of electronic and optical components to combine thermal control, illumination, and fluorescence detection into a highly integrated hybrid module. This simple configuration allowed us to reduce the overall number of components, thus simplifying its assembly and reducing the instrument size. The HybOT Cycler is wirelessly controlled from an application installed in a tablet. PCR assays are carried out in a bubble‐free microfluidic device that can be easily replicated from an acrylic mold. Using the HybOT Cycler, down to 100 copies/µL of genetic material of the virus SARS‐CoV‐2 with 95% sensitivity and 100% specificity is detected. The HybOT Cycler can assist in diagnosing SARS‐CoV‐2 and other pathogens in resource‐poor settings. [ FROM AUTHOR]

Pre-exposure Prophylaxis Discontinuation During the COVID-19 Pandemic Among Men Who Have Sex With Men in a Multisite Clinical Cohort in the United States.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic continues to put strain on health systems in the United States, leading to significant shifts in the delivery of routine clinical services, including those offering HIV pre-exposure prophylaxis (PrEP). We aimed to assess whether individuals discontinued PrEP use at higher rates during the COVID-19 pandemic and the extent to which disruptions to usual clinical care were mitigated through telehealth. METHODS: Using data from an ongoing prospective cohort of men who have sex with men (MSM) newly initiating PrEP in 3 mid-sized cities (n = 195), we calculated the rate of first-time discontinuation of PrEP use in the period before the COVID-19 pandemic and during the COVID-19 pandemic and compared these rates using incidence rate ratios (IRRs). Furthermore, we compared the characteristics of patients who discontinued PrEP use during these periods with those who continued to use PrEP during both periods. RESULTS: Rates of PrEP discontinuation before the COVID pandemic and during the COVID-19 pandemic were comparable [4.29 vs. 5.20 discontinuations per 100 person-months; IRR: 1.95; 95% confidence interval (CI): 0.83 to 1.77]. Although no significant differences in the PrEP discontinuation rate were observed in the overall population, the rate of PrEP discontinuation increased by almost 3-fold among participants aged 18-24 year old (IRR: 2.78; 95% CI: 1.48 to 5.23) and by 29% among participants covered by public insurance plans at enrollment (IRR: 1.29; 95% CI: 1.03 to 5.09). Those who continued to use PrEP were more likely to have had a follow-up clinical visit by telehealth in the early months of the pandemic (45% vs. 17%). CONCLUSIONS: In this study, rates of PrEP discontinuation were largely unchanged with the onset of the COVID-19 pandemic. The use of telehealth likely helped retain patients in PrEP care and should continue to be offered in the future.

Perspectives of people living with HIV-1 on implementation of long-acting cabotegravir plus rilpivirine in US healthcare settings: results from the CUSTOMIZE hybrid III implementation-effectiveness study.

INTRODUCTION: The CUSTOMIZE hybrid III implementation-effectiveness study evaluated implementation of once-monthly long-acting (LA) cabotegravir + rilpivirine in diverse US healthcare settings. Here, we report patient participant perspectives after 12 months in CUSTOMIZE. METHODS: CUSTOMIZE was a phase IIIb, 12-month study conducted from July 2019 to October 2020 at eight diverse US HIV clinics that enrolled virologically suppressed people living with HIV-1 (PLHIV) on a stable oral regimen to receive monthly cabotegravir + rilpivirine LA injections after a 1-month oral lead-in. Participants were administered quantitative surveys before injections at months 1 (baseline), 4 and 12. A randomly selected subset of participants was interviewed at baseline and month 12. Data collection at month 12 was completed by October 2020 (during the COVID-19 pandemic). RESULTS: At baseline, 109 and 34 participants completed surveys and interviews, respectively; 87% were male; 35% were Black or African American. All participants who remained in the study at month 12 (n = 102) maintained HIV-1 RNA <50 copies/ml; two participants withdrew due to injection-related reasons. Mean total scores measuring acceptability and appropriateness of cabotegravir + rilpivirine LA were high at baseline (4.5-4.6 out of 5) and month 12 (4.7-4.9). At month 12, 74% of participants reported nothing interfered with receiving LA injections; injection pain or soreness was the most common concern (15%). Time spent in the clinic and coming to the clinic for monthly injections was very or extremely acceptable after 12 months for most participants (93% and 87%, respectively), with 64% reporting having spent ≤30 minutes in the clinic for injection visits. At month 12, 92% of participants preferred LA injections to daily oral tablets (3%); 97% plan to continue LA treatment going forward. In month 12 interviews, 24 (77%) of 31 participants reported the COVID-19 pandemic did not impact their ability to receive treatment. CONCLUSIONS: Once-monthly cabotegravir + rilpivirine LA was highly acceptable among PLHIV who were virologically suppressed on a stable antiretroviral regimen and interested in trying LA therapy, with few participants reporting challenges receiving LA injections. Implementation data from CUSTOMIZE suggest that monthly LA injections provide a convenient and appealing treatment option for PLHIV.

Perspectives of healthcare providers on implementation of long-acting cabotegravir plus rilpivirine in US healthcare settings from a Hybrid III Implementation-effectiveness study (CUSTOMIZE).

INTRODUCTION: CUSTOMIZE evaluated the implementation of long-acting (LA) cabotegravir + rilpivirine, a novel healthcare provider-administered injectable antiretroviral therapy regimen, in diverse US healthcare settings. Findings from staff-study participants (SSPs) through 12 months of implementation are reported. METHODS: CUSTOMIZE was a phase IIIb, 12-month, single-arm, hybrid III implementation-effectiveness study conducted from July 2019 to October 2020 at eight US clinics of five clinic types: private practice (n = 2), federally qualified health centre (n = 2), university (n = 2), AIDS Healthcare Foundation (n = 2) and health maintenance organization (n = 1). Eligible patient participants received monthly cabotegravir + rilpivirine LA injections after a 1-month oral lead-in. At baseline, month 4 and month 12, SSPs (n = 3 each per clinic), including physicians, nurses or injectors, and administrators, completed quantitative surveys and semi-structured interviews to assess implementation outcomes (acceptability, appropriateness and feasibility of intervention measures), programme sustainability and SSP perceptions of, attitudes towards, and expectations for cabotegravir + rilpivirine LA. Month 12 data collection occurred during the COVID-19 pandemic. RESULTS: In surveys, SSPs reported high mean total scores for acceptability, appropriateness and feasibility of cabotegravir + rilpivirine LA implementation at baseline (4.43, 4.52 and 4.38 of 5, respectively) and month 12 (4.45, 4.61 and 4.46 of 5, respectively), regardless of clinic type. At month 12, SSPs were positive about the implementation sustainability (mean Program Sustainability Assessment Tool score, 5.83 out of 7). At baseline, SSPs' top concern was patients' ability to maintain monthly appointments (81%); at month 12, 39% had this concern. The proportion of SSPs reporting patient injection pain or soreness as a barrier was consistent at month 12 versus baseline (48% vs. 46%). Most (78%) SSPs reported optimal implementation of cabotegravir + rilpivirine LA in their clinics was achieved in 1-3 months. In interviews, SSP-reported strategies for successful implementation included teamwork, using a web-based treatment planner and having a designated person to track appointment scheduling. In month 12 interviews, SSP-reported structural changes needed for implementation included changing clinic hours and purchasing refrigerators. CONCLUSIONS: In CUSTOMIZE, cabotegravir + rilpivirine LA was successfully implemented across a range of US healthcare settings. Barriers were mitigated with minor process adjustments.

Projected Effects of Disruptions to Human Immunodeficiency Virus (HIV) Prevention Services During the Coronavirus Disease 2019 Pandemic Among Black/African American Men Who Have Sex With Men in an Ending the HIV Epidemic Priority Jurisdiction.

Background: Disruptions in access to in-person human immunodeficiency virus (HIV) preventive care during the coronavirus disease 2019 (COVID-19) pandemic may have a negative impact on our progress towards the Ending the HIV Epidemic goals in the United States. Methods: We used an agent-based model to simulate HIV transmission among Black/African American men who have sex with men in Mississippi over 5 years to estimate how different reductions in access affected the number of undiagnosed HIV cases, new pre-exposure prophylaxis (PrEP) starts, and HIV incidence. Results: We found that each additional 25% decrease in HIV testing and PrEP initiation was associated with decrease of 20% in the number of cases diagnosed and 23% in the number of new PrEP starts, leading to a 15% increase in HIV incidence from 2020 to 2022. Conclusions: Unmet need for HIV testing and PrEP prescriptions during the COVID-19 pandemic may temporarily increase HIV incidence in the years immediately after the disruption period.

Projected Effects of Disruptions to HIV Prevention Services During the COVID-19 Pandemic Among Black/African American Men Who Have Sex with Men in an Ending the HIV Epidemic Priority Jurisdiction

Disruptions in access to in-person HIV preventive care during the COVID-19 pandemic may have a negative impact on our progress towards the Ending the HIV Epidemic goals in the United States. We used an agent-based model to simulate HIV transmission among Black/African American men who have sex with men (MSM) in Mississippi over five years to estimate how different reductions in access affected the number of undiagnosed HIV cases, new PrEP starts, and HIV incidence. We found that each additional 25% decrease in HIV testing and PrEP initiation was associated with decrease of 20% in the number of cases diagnosed and 23% in the number of new PrEP starts, leading to a 15% increase in HIV incidence from 2020 to 2022. Unmet need for HIV testing and PrEP prescriptions during the COVID-19 pandemic may temporarily increase HIV incidence in the years immediately following the disruption period.

Infection in asymptomatic carriers of SARS-CoV-2 can interfere with the achievement of robust immunity on a population scale

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread worldwide as a severe pandemic, and a significant portion of the infected population may remain asymptomatic. Given this, five surveys were carried out between May and September 2020 with a total of 3585 volunteers in the municipality of Foz do Igua..u, State of Paran.., a triple border region between Brazil/Argentina/Paraguay. Five months after the first infection, volunteers were re-analysed for the production of IgG anti-Spike and anti-RBD-Spike, in addition to analyses of cellular immunity. Seroconversion rates ranged from 4.4% to a peak of 37.21% followed by a reduction in seroconversion to 21.1% in September, indicating that 25% of the population lost their circulating anti-SARS-CoV-2 antibodies 3 months after infection. Analyses after 5 months of infection showed that only 17.2% of people still had anti-RBD-Spike antibodies, however, most volunteers had some degree of cellular immune response. The strategy of letting people become naturally infected with SARS-CoV-2 to achieve herd immunity is flawed, and the first contact with the virus may not generate enough immunogenic stimulus to prevent a possible second infection.

Human Immunodeficiency Virus/Sexually Transmitted Infection Testing Preferences for Young Black Men Who Have Sex With Men in the Southeastern United States: Implications for a Post-COVID-19 Era.

BACKGROUND: Little is known regarding human immunodeficiency virus (HIV)/sexually transmitted infection (STI) testing preferences for location, staffing, and hours of operation among Young Black men who have sex with men (YBMSM) in the Southeastern United States, a population at high risk for HIV/STIs. We used a discrete choice experiment to explore these preferences. METHODS: Young Black men who have sex with men ages 16 to 35 years in Birmingham, AL and Jackson, MS completed online surveys evaluating their preferences (best/worst) for HIV/STI testing locations, staffing, hours, method of results notification, and cost. They also selected preferred combinations of these variables through choice tasks. Results were analyzed using joint best/worst and discrete choice experiment models. RESULTS: Between June 2018 and December 2019, participants in Alabama (n = 54) and Mississippi (n = 159) completed online surveys. Both groups preferred stationary testing locations over mobile testing vans, with the most significant difference favoring STI testing-only clinics in Mississippi and local health departments in Alabama (P < 0.001). Technician-performed tests or self-testing were significantly less preferred compared with clinician-performed testing for both groups (P < 0.0001 and P < 0.0001, respectively). Free testing and phone results notification (versus text) were preferred by both groups. The most desirable combination among all participants was weekday clinician-performed testing at the health department for $5. CONCLUSIONS: Young Black men who have sex with men in the Southeastern United States prefer traditional testing locations staffed by experienced personnel. Combination choices are influenced by services that are low or no cost. More research is needed to inform the best way(s) to provide affordable, high-quality HIV/STI testing services for YBMSM, particularly in the post-COVID-19 era when sexual health care delivery models are evolving toward home-based and remote health-focused strategies.

Online adaptation strategies for active learning methodologies in STEM education

Due to Covid-19 pandemic, adaptations for carrying out remote work have become necessary in various sectors of society. Among these, the educational area was one of the most impacted and, with the goal of creating a "new normal", activities that used to be face-to-face are now performed online. Considering the importance of society-university integration, the university outreach programs, which form one of the pillars of the public university, also had to be adapted so the activities would continue. This paper presents the planning and execution strategies adopted by the Fast Girls outreach project team. This project is an initiative of the Faculty of Technology in partnership with other units of the University of Brasília and has the purpose of motivating girls and young women, students of basic public education from the outskirts of Brasília to pursue careers in the STEM areas (Science, Technology, Engineering and Mathematics). In this process, active teaching-learning strategies based on pedagogical workshops with hands-on activities, games, interactive lectures, women’s testimonials, and conversation rounds were used. Meanwhile the difficulties encountered, as well as the results achieved were identified and discussed, highlighting the enriching character of these procedures for the undergraduate students in terms of their ability to adapt to the execution of the teaching-learning methods in face of the new reality. In this conception, the work presents positive results, extending the benefits of the use of active learning strategies beyond basic education, reaching undergraduate students, even in times of distance education. © 2021 University of Minho. All rights reserved.

Epidemiology, Clinical Features, and Outcomes of Hospitalized Adults with COVID-19: Early Experience from an Academic Medical Center in Mississippi.

OBJECTIVES: To describe the demographics, clinical characteristics, and outcomes of hospitalized adults with coronavirus disease 2019 (COVID-19) in an academic medical center in the southern United States. METHODS: Retrospective, observational cohort study of all adult patients (18 years and older) consecutively admitted with laboratory-confirmed severe acute respiratory syndrome-coronavirus-2 infection between March 13 and April 25, 2020 at the University of Mississippi Medical Center. All of the patients either survived to hospital discharge or died during hospitalization. Demographics, body mass index, comorbidities, clinical manifestations, and laboratory findings were collected. Patient outcomes (need for invasive mechanical ventilation and in-hospital death) were analyzed. RESULTS: One hundred patients were included, 53% of whom were women. Median age was 59 years (interquartile range 44-70) and 66% were younger than 65. Seventy-five percent identified themselves as Black, despite representing 58% of hospitalized patients at our institution in 2019. Common comorbid conditions included hypertension (68%), obesity (65%), and diabetes mellitus (31%). Frequent clinical manifestations included shortness of breath (76%), cough (75%), and fever (64%). Symptoms were present for a median of 7 days (interquartile range 4-7) on presentation. Twenty-four percent of patients required mechanical ventilation and, overall, 19% died (67% of those requiring mechanical ventilation). Eighty-four percent of those who died were Black. On multivariate analysis, ever smoking (odds ratio [OR] 5.9, 95% confidence interval [CI] 1.2-28.6) and history of diabetes mellitus (OR 5.9, 95% CI 1.5-24.3) were associated with mortality, and those admitted from home were less likely to die (vs outside facility, OR 0.2, 95% CI 0.0-0.7). Neither age, sex, race, body mass index, insurance status, nor rural residence was independently associated with mortality. CONCLUSIONS: Our study adds evidence that Black patients appear to be overrepresented in those hospitalized with and those who die from COVID-19, likely a manifestation of adverse social determinants of health. These findings should help guide preventive interventions targeting groups at higher risk of acquiring and developing severe COVID-19 disease.

Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets.

The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worldwide. Willing to contribute with this fight to defeat COVID-19, we performed a virtual screening study on a library containing Food and Drug Administration (FDA) approved drugs, in a search for molecules capable of hitting three main molecular targets of SARS-CoV-2 currently available in the Protein Data Bank (PDB). Our results were refined with further molecular dynamics (MD) simulations and MM-PBSA calculations and pointed to 7 multi-target hits which we propose here for experimental evaluation and repurposing as potential drugs against COVID-19. Additional rounds of docking, MD simulations and MM-PBSA calculations with remdesivir suggested that this compound can also work as a multi-target drug against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

REINVENTADO LA OPERACIÓN MINORISTA DESPUÉS DEL COVID-19

Many retailers -who were not authorized to market through the Internet-, had to lower their blinds. [...]only hypermarkets that commercialize these types of products could gain some ground. [...]Amazon is developing a brick-and-mortar network, proposing an omnichannel presence (Adhi et al., 2019 and IProfesional, 2020). Shoppers continue to buy groceries and cleaning supplies and food retailers will have a critical role to play in the near future, protecting employee health and safety, prioritizing in-store cleanliness, and dealing with demand surges and operational/supply chain shocks. * Matching the rapid demand, a challenge for retailers: Paper towels, toilet paper and cleaning products doubled in sales, and other non essentials items like cosmetics and office supplies plummeted. * Changes in consumer attitudes: they are considering well-being through healthy eating and exercise, and leaving alcoholic beverages and salty snacks. * The privacy imperative: consumers are more careful about sharing data and firms are learning how to handle this imperative, becoming a point of differentiation and competitive advantage.

Novel SARS-CoV-2 encoded small RNAs in the passage to humans.

MOTIVATION: The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease 2019. This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored. RESULTS: We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprograming of the new host upon infection. AVAILABILITY AND IMPLEMENTATION: https://github.com/sinc-lab/sarscov2-mirna-discovery. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Structural and Functional Comparison of SARS-CoV-2-Spike Receptor Binding Domain Produced in Pichia pastoris and Mammalian Cells (preprint)

The yeast Pichia pastoris is a cost-effective and easily scalable system for recombinant protein production. In this work we compared the conformation of the receptor binding domain (RBD) from SARS-CoV-2 Spike protein expressed in P. pastoris and in the well established HEK-293T mammalian cell system. RBD obtained from both yeast and mammalian cells was properly folded, as indicated by UV-absorption, circular dichroism and tryptophan fluorescence. They also had similar stability, as indicated by temperature-induced unfolding (observed Tm were 50 {degrees}C and 52 {degrees}C for RBD produced in P. pastoris and HEK-293T cells, respectively). Moreover, the stability of both variants was similarly reduced when the ionic strength was increased, in agreement with a computational analysis predicting that a set of ionic interactions may stabilize RBD structure. Further characterization by HPLC, size-exclusion chromatography and mass spectrometry revealed a higher heterogeneity of RBD expressed in P. pastoris relative to that produced in HEK-293T cells, which disappeared after enzymatic removal of glycans. The production of RBD in P. pastoris was scaled-up in a bioreactor, with yields above 45 mg/L of 90% pure protein, thus potentially allowing large scale immunizations to produce neutralizing antibodies, as well as the large scale production of serological tests for SARS-CoV-2.

Fixed single-cell RNA sequencing for understanding virus infection and host response (preprint)

Single-cell RNA sequencing studies requiring intracellular protein staining, rare-cell sorting, or pathogen inactivation are severely limited because current high-throughput methods are incompatible with paraformaldehyde treatment, a very common and simple tissue/cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single-cells. We used FD-seq to address two important questions in virology. First, by analyzing a rare population of cells supporting lytic reactivation of the human tumor virus KSHV, we identified TMEM119 as a host factor that mediates reactivation. Second, we studied the transcriptome of lung cells infected with the 2 coronavirus OC43, which causes the common cold and also serves as a safer model pathogen for SARS-CoV-2. We found that pro-inflammatory pathways are primarily upregulated in abortively-infected or uninfected bystander cells, which are exposed to the virus but fail to express high level of viral genes. FD-seq is suitable for characterizing rare cell populations of interest, for studying high-containment biological samples after inactivation, and for integrating intracellular phenotypic with transcriptomic information.

Mutational signatures in countries affected by SARS-CoV-2: Implications in host-pathogen interactome (preprint)

We are in the midst of the third severe coronavirus outbreak caused by SARS-CoV-2 with unprecedented health and socio-economic consequences due to the COVID-19. Globally, the major thrust of scientific efforts has shifted to the design of potent vaccine and anti-viral candidates. Earlier genome analyses have shown global dominance of some mutations purportedly indicative of similar infectivity and transmissibility of SARS-CoV-2 worldwide. Using high-quality large dataset of 25k whole-genome sequences, we show emergence of new cluster of mutations as result of geographic evolution of SARS-CoV-2 in local population ({greater than or equal to}10%) of different nations. Using statistical analysis, we observe that these mutations have either significantly co-occurred in globally dominant strains or have shown mutual exclusivity in other cases. These mutations potentially modulate structural stability of proteins, some of which forms part of SARS-CoV-2-human interactome. The high confidence druggable host proteins are also up-regulated during SARS-CoV-2 infection. Mutations occurring in potential hot-spot regions within likely T-cell and B-cell epitopes or in proteins as part of host-viral interactome, could hamper vaccine or drug efficacy in local population. Overall, our study provides comprehensive view of emerging geo-clonal mutations which would aid researchers to understand and develop effective countermeasures in the current crisis.