An experience of scaling and intensifying the industrial production of the Gam-COVID-Vac vector adenovirus vaccine in the limiting conditions of the pandemic

The COVID-19 pandemic has presented a global challenge to the health system. More than 200 years of world epidemiological experience since the first mass use of vaccines have convincingly shown that effective vaccines are the key tools in the fight against dangerous infectious diseases, especially epidemic and pandemic ones. In the context of a rapidly spreading pandemic of a new infectious agent, it is crucial not only to develop fundamentally new vaccines, but also to be able to quickly organise their large-scale production. In the Russian Federation, in 2020, a team of the National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya developed an innovative vector vaccine, Gam-COVID-Vaс, for the prevention of coronavirus disease caused by the SARS-CoV-2 virus. A number of pharmaceutical companies faced the challenge of producing the vaccine. The aim of the study was to optimise the production technology of Gam-COVID-Vac for scaling and increasing the production capacity. In the course of the work, the authors established critical quality attributes of the product, optimised analytical methods for their control, identified poorly scalable technological stages, streamlined the technological process before its transfer to production, and modified non-scalable and technologically unfeasible stages. The work resulted in the launch of industrial-scale production of active pharmaceutical ingredients for both components of Gam-COVID-Vac, which made it possible not only to meet the critical need for COVID-19 immunoprophylaxis in the Russian Federation, but also to supply this vaccine to a number of foreign countries.

Global spread of carbapenem-resistant Enterobacteriaceae: Epidemiological features, resistance mechanisms, detection and therapy

Bacterial drug resistance has become a global public health threat, among which the infection of carbapenem-resistant Enterobacterales (CRE) is one of the top noticeable issues in the global anti-infection area due to limited therapy options. In recent years, the prevalence of CRE transmission around the world has increased, and the transmission of COVID-19 has intensified the situation to a certain extent. CRE resistance can be induced by carbapenemase, porin, efflux pump, penicillin-binding protein alteration, and biofilm production. Deletion, mutation, insertion, and post-transcriptional modification of corresponding coding genes may affect the sensitivity of Enterobacterales bacteria to carbapenems. Clinical and laboratory methods to detect CRE and explore its resistance mechanisms are being developed. Due to the limited options of antibiotics, the clinical treatment of CRE infection also faces severe challenges. The clinical therapies of CRE include single or combined use of antibiotics, and some new antibiotics and treatment methods are also being developed. Hence, this review summarizes the epidemiology, resistance mechanisms, screening and clinical treatments of CRE infection, to provide references for clinical prevention, control and treatment of CRE infection. © 2022 Elsevier GmbH

Anxiety Levels of People Living with HIV and Problems in Accessing Healthcare Services and Drugs During the COVID-19 Pandemic

Introduction: Since its emergence in December 2019, COVID-19 has caused severe morbidity and mortality. Access to healthcare services for individuals with chronic diseases including people living with HIV was disrupted due to many factors such as the density in hospitals and social closure strategies to stop the spread of the pandemic. The aim of this study was to determine whether HIV status and social and medical problems faced by people living with HIV caused anxiety during the COVID-19 pandemic. Materials and Methods: Between October 2021 and February 2022, the Beck anxiety scale and a 16-item questionnaire including questions on demographic information was completed by 100 people living with HIV who visited our Çukurova University Infectious Diseases and Clinical Microbiology outpatient clinic and gave consent to be included in the study. Results: Overall, 93 (93%) participants were male and seven (7%) were female, with a mean age of 36 ± 10 years. Among all participants, 44% reported a decrease in their general quality of life, 42.4% reported an increase in the level of anxiety, 33% reported a decrease in access to resources such as money and food, and 13% reported that they had difficulty in paying the rent of their own house. During the pandemic, 11.3% of the participants lost their jobs and 9.1% lost their health insurance;8.1% reported that they became homeless and moved to live with someone else. Access to antiretroviral treatment decreased in 7.2% of the participants, the number of hospital visits were reduced in 33.3%, and 26% reported a reduction in monitoring tests such as HIV RNA. The mean Beck anxiety score, which was used to evaluate the patients' anxiety level, was 12.32 ± 12.35 (min-max= 0-54) and suggested mild anxiety symptoms. Conclusion: The difficulties and problems in the daily lives of individuals living with HIV have deepened with the COVID-19 pandemic. The data we obtained in our study helps us understand the difficulties and anxiety levels of people living with HIV in receiving healthcare.

SARS-CoV-2 in Terms of Medical Microbiology Laboratory

Coronaviruses (CoV), which are in the Coronaviridae family, cause different severity of gastrointestinal, respiratory and systemic diseases in wild and domestic animals, and can lead to different clinical manifestations, ranging from colds to pneumonia, depending on immunity. To date, seven types of coronavirus have been identified as infectious agents in humans;of these, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43 typically cause cold symptoms in immunocompetent individuals, while SARS-CoV (Severe Acute Respiratory Syndrome Coronavirus) and MERS-CoV (Middle East Respiratory Syndrome Coronavirus) is zoonotic and cause severe respiratory diseases and deaths. SARS-CoV-2, the causative agent of COVID-19, is the seventh coronavirus identified as an infection agent in humans, which started in December 2019 in Wuhan, Hubei Province of China and was identified as a pandemic in a short time. Since the World Health Organization (WHO) defines SARS-CoV-2-sourced COVID-19 as a pandemic, and because of the increasing number of cases and deaths worldwide, structure of the novel virus and viral diagnosis methods gained importance respectively for vaccine studies and for controlling the outbreak caused by the virus.

Evaluation of Crimean-Congo Hemorrhagic Fever Cases During the COVID-19 Pandemic Period

Introduction: Crimean-Congo Hemorrhagic Fever (CCHF) is a zoonotic disease that progresses with fever and bleeding and is endemic in our region. In this study, we aimed to determine the symptoms, transmission routes and risk factors in CCHF patients who have similar clinical features with COVID-19, and to investigate the relationship between CCHF cases and COVID-19 restrictions in our region where CCHF is endemic. Materials and Methods: One hundred fifty-nine patients diagnosed with CCHF in the infectious diseases and clinical microbiology clinic between April 2021 and September 2021 were included in the study. A questionnaire consisting of a set of questions was filled in for patients diagnosed with CCHF, in which demographic data, admission complaints, risk factors and habits during the COVID-19 pandemic were evaluated. Results: The mean age of the 159 CCHF patients included in the study was 50.9 ± 18.5 years and 59.7% were male. The most frequently reported complaints by the patients were fatigue (94.5%), muscle-joint pain (79.9%) and fever (74.2%). During the disease period, COVID-19 was suspected in 62.3% of them, PCR test was applied to all of them, and the result was positive in only one patient. There was no change of residence of the patients during the illness period. There was no significant increase in the population of the residence area or the frequency of visits due to the pandemic. The number of patients who reported an increase in the number of ticks in their environment was 44 (27.8%). It was determined that there was no significant increase in the number of activities such as visiting rural areas or having a picnic due to the COVID-19 pandemic. Only 32.2% of patients engaged in animal husbandry or field work reported an increase in the frequency of these jobs compared to the pre-pandemic period. Conclusion: The reason for the increase in the number of CCHF cases in our center was not associated with the increase in the frequency of visits to rural areas or the change of residence during the COVID-19 pandemic period.

Undergraduate Teaching During COVID-19.

Introduction: Universities were challenged during the COVID-19 pandemic to continue providing quality education for their students while navigating the uncertainties of the SARS-CoV-2 virus. Objectives: The goal of this article is to describe strategies used by Colorado State University (CSU) to mitigate SARS-CoV-2 transmission among faculty, staff, and students and to describe procedures used in microbiology teaching laboratories. Methods: Information concerning CSU's pandemic response was gathered via email communications to the CSU community, town hall meetings, and interviews with leaders, researchers, and staff who spearheaded public health initiatives. Results: To date, there have been no known cases of transmission of SARS-CoV-2 in the classroom. Early strategies that contributed to this success included social norming of safe public health behaviors, development of low-cost, rapid screening and surveillance methods, an online COVID-19 reporting system, contact tracing and quarantine, rearranging classrooms to reduce the capacity by 50%, increasing air flow, enhanced cleaning and production of sanitizer, and flexible instructors who quickly changed their courses for remote delivery or launched extra risk management procedures for face-to-face delivery of laboratory, performance, or studio classes. Conclusion: Intense collaboration among the CSU community, open and frequent communication, coordination of efforts, flexible instructors, and the willingness to follow safe public health behaviors allowed CSU to continue face-to-face teaching in courses that required hands-on learning or demanded in-person instruction. It is the hope of the authors that this information can provide both a historical account and useful information for others dealing with the COVID-19 pandemic.

Durability of neutralization against Omicron subvariants after vaccination and breakthrough infection.

Booster immunizations and breakthrough infections can elicit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariant neutralizing activity. However, the durability of the neutralization response is unknown. We characterize the sensitivity of BA.1, BA.2, BA.2.75, BA.4/BA.5, BF.7, BQ.1.1, and XBB against neutralizing antibodies from vaccination, hybrid immunity, and breakthrough infections 4-6 months after vaccination and infection. We show that a two-dose CoronaVac or a third-dose ZF2001 booster elicits limited neutralization against Omicron subvariants 6 months after vaccination. Hybrid immunity as well as Delta, BA.1, and BA.2 breakthrough infections induce long-term persistence of the antibody response, and over 70% of sera neutralize BA.1, BA.2, BA.4/BA.5, and BF.7. However, BQ.1.1 and XBB, followed by BA.2.75, are more resistant to neutralization, with neutralizing titer reductions of ∼9- to 41-fold, ∼16- to 63-fold, and ∼4- to 25-fold, respectively. These data highlight additional vaccination in CoronaVac- or ZF2001-vaccinated individuals and provide insight into the durability of neutralization against Omicron subvariants.

Avoiding culture shock with the SARS-CoV-2 spike protein.

When culturing SARS-CoV-2 in the laboratory it is vital to avoid deletions in the gene for the spike protein that could affect the interpretation of experiments.

COVID-19 Drug Discovery and Comparison Between Generative and Predictive Approach

The spread of the SARS-Cov-2 virus in the human race has caused 6.56M deaths worldwide as of Oct 2022 and has brought the economy to a standstill. It has also introduced several challenges worldwide. So, the need of finding a drug that would be able to dilute the symptoms of COVID-19 in the patients. The current methods for drug discovery via conventional methods are a tedious and time-consuming process. So here, the deep learning algorithms come to our rescue. Scientists and Doctors are diligently studying and analyzing the genome sequence of the virus and trying to understand the interaction between the coronavirus protease and a covalent inhibitor. Taking advantage of one such research work published by Shanghai Tech University, the research attempts in making research which is based on an approach to inhibit the protease of SARS-Cov-2(Or any virus) by a covalent inhibitor(also called Ligand). The research was done for some similar viruses to SARS-Cov-2, like SARS, MERS, and HIV. Protein target GI73745819 - SARS Protease, Protein target GI75593047 - HIV pol polyprotein, NS3 - Hep3 protease, and 3CL-Pro - Mers Protease. Bioactivities measured in these papers by medicinal chemists and biochemists are tracked by The National Center for Biotechnology Information (NCBI) which can be accessed by everyone. The goal of this research is to make efforts toward proposing a potentially highly active molecule against a target protein of the 2019 Novel Coronavirus. This research features training of the model in such a way that it predicts the binding power of the drug toward COVID-19 protease. Then compared and reported the inhibition score of ligand and protease to find out one of the best inhibitors. © 2022 IEEE.

Stick with the nose Saliva rapid antigen testing is not a viable method for testing children under 5 years old.

AIM: Respiratory testing with rapid antigen tests (RATs) in children under 5 years of age may be uncomfortable and presents specific challenges to testing due to compliance and procedural distress. The aim of this study was to investigate sensitivity and feasibility of self-collected nasal and saliva RAT tests compared with a combined nose and throat (CTN) swab PCR in children under 5. METHODS: Children aged between 1 month and 5 years, with confirmed COVID-19 or who were a household contact within 7 days were included. A saliva RAT, nasal RAT and CTN swab were collected by the parent. SARS-CoV-2 cycle threshold (Ct) values for CTN tested by PCR were compared with saliva and nasal RAT results. Parent preference for method of sample was recorded. RESULTS: Forty-one children were recruited with median age of 1.5 (interquartile range 0.7-4.0) years. Only 22/41 (54%) of parents were able to successfully collect a saliva RAT from their child. Sensitivity of the nasal RAT and saliva RAT was 0.889 (95% confidence interval (CI) 0.739-0.969) and 0.158 (95% CI 0.034-0.396), respectively. Upper limit of nasal RAT detection by CTN Ct value was higher than saliva (36.05 vs. 27.29). While saliva RAT was rated most comfortable, nasal RAT was rated the preferred specimen by parents for future testing, due to saliva collection difficulties and time taken. CONCLUSIONS: Rapid antigen testing with nasal RAT is a more feasible and sensitive method for SARS-CoV-2 detection in young children compared with saliva RAT.

Innovative COVID-19 point-of-care diagnostics suitable for tuberculosis diagnosis: a scoping review protocol.

INTRODUCTION: In 2014, the WHO published high-priority target product profiles (TPPs) for new tuberculosis (TB) diagnostics to align end-user needs with test targets and specifications; nevertheless, no TB test meets these targets to date. The COVID-19-driven momentum in the diagnostics world offers an opportunity to address the long-standing lack of innovation in the field of TB diagnostics. This scoping review aims to summarise point-of-care (POC) molecular and antigen tests for COVID-19 diagnosis that, when applied to TB, potentially meet WHO TPPs. This summary of currently available innovative diagnostic tools will guide the development of novel TB diagnostics toward the WHO-set targets. METHODS AND ANALYSIS: We will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension Scoping Reviews recommendations. MEDLINE (via PubMed), bioRxiv, MedRxiv and other publicly available in vitro diagnostic test databases were searched on 23 November 2022. POC antigen or molecular tests developed for SARS-CoV-2 detection that meet the eligibility criteria will be included in the review. Developer description, test description, operation characteristics, pricing information, performance and commercialisation status of diagnostic tests identified will be extracted using a predefined standardised data extraction form. Two reviewers will independently perform the screening and data extraction. A narrative synthesis of the final data will be provided. ETHICS AND DISSEMINATION: No ethical approval is required because individual patient data will not be included. The findings will be published in open-access scientific journals.

Human influenza virus infection elicits distinct patterns of monocyte and dendritic cell mobilization in blood and the nasopharynx.

During respiratory viral infections, the precise roles of monocytes and dendritic cells (DCs) in the nasopharynx in limiting infection and influencing disease severity are incompletely described. We studied circulating and nasopharyngeal monocytes and DCs in healthy controls (HCs) and in patients with mild to moderate infections (primarily influenza A virus [IAV]). As compared to HCs, patients with acute IAV infection displayed reduced DC but increased intermediate monocytes frequencies in blood, and an accumulation of most monocyte and DC subsets in the nasopharynx. IAV patients had more mature monocytes and DCs in the nasopharynx, and higher levels of TNFα, IL-6, and IFNα in plasma and the nasopharynx than HCs. In blood, monocytes were the most frequent cellular source of TNFα during IAV infection and remained responsive to additional stimulation with TLR7/8L. Immune responses in older patients skewed towards increased monocyte frequencies rather than DCs, suggesting a contributory role for monocytes in disease severity. In patients with other respiratory virus infections, we observed changes in monocyte and DC frequencies in the nasopharynx distinct from IAV patients, while differences in blood were more similar across infection groups. Using SomaScan, a high-throughput aptamer-based assay to study proteomic changes between patients and HCs, we found differential expression of innate immunity-related proteins in plasma and nasopharyngeal secretions of IAV and SARS-CoV-2 patients. Together, our findings demonstrate tissue-specific and pathogen-specific patterns of monocyte and DC function during human respiratory viral infections and highlight the importance of comparative investigations in blood and the nasopharynx.

Microbiological Profile of Infectious Keratitis During Covid-19 Pandemic.

Purpose: The Covid-19 pandemic introduced significant changes in our daily life, including the widespread use of face masks. The purpose of this study was to assess if significant changes occurred in the microbiological profile of infectious keratitis. Patients and Methods: A retrospective study was performed, based on a survey review of the electronic medical records of all patients with presumed infectious keratitis, between March 2020 and October 2021. The microbiological isolates in this sample (pandemic group) were compared with those obtained in our center between 2009 and 2018 (pre-pandemic group). Results: A total of 194 samples were included in the pandemic group. We obtained a culture-positivity rate of 43.3%, which was significantly higher when compared with the pre-pandemic data (35.15%, p = 0.033). Several further significant differences were found between the pandemic and the pre-pandemic groups: the proportion of bacteria, including gram-positive and gram-negative groups, was higher in our sample (pre-pandemic vs pandemic: 76.78% vs 83.33%, p = 0.010; 53.35% vs 60.71%, p = 0.016; 23.43% vs 34.52%, p = 0.005, respectively); two populations of Gram-positive bacteria found in this study were not isolated in the pre-pandemic sample - Dolosigranulum pigrum and Propionibacterium spp.; and two bacterial isolates were significantly increased in our sample - Corynebacterium spp. (18.41% vs 29.76%, p = 0.003) and Pseudomonas aeruginosa (9.00% vs 16.66%, p = 0.012). Conclusion: In conclusion, significant changes were found in the microbiological profile of infectious keratitis in our center during the Covid-19 pandemic. While these changes could be related to face mask use, more observational and experimental studies are needed to explore this possible association.

Antibiotic de-escalation in pneumonia with pharmacist education and ordering of methicillin-resistant Staphylococcus aureus nasal swabs.

INTRODUCTION: When methicillin-resistant Staphylococcus aureus (MRSA) is the causative pathogen in pneumonia, in-hospital mortality rate is approximately 31.2%. However, the occurrence of MRSA pneumonia is uncommon, with a reported incidence of approximately 4.2%. Vancomycin is often empirically used for MRSA pneumonia coverage, but can lead to serious harm. The purpose of this study was to measure the impact of a pharmacy-driven MRSA nares testing protocol on vancomycin and linezolid prescribing patterns and clinical outcomes in patients diagnosed with pneumonia after removal of immediate educational intervention. METHODS: This single-centre, quasi-experimental study evaluated the use of a MRSA nasal swab on patients diagnosed with community-acquired pneumonia, hospital-acquired pneumonia and ventilator-associated pneumonia. This study consisted of three phases, the preimplementation phase, the active/educational phase and the postimplementation phase. The primary outcome was intravenous anti-MRSA antibiotic duration of therapy. Secondary outcomes included the occurrence of acute kidney injury, duration of hospital stay, number of vancomycin levels obtained, the number of MRSA nares swabs ordered and time points in the MRSA nares collection process. RESULTS: The preimplementation phase (n=39), the active phase (n=45) and the postimplementation phase (n=26) demonstrated similar baseline characteristics. The primary outcome for duration of anti-MRSA therapy 0-72 hours was 61.5% vs 77.8% vs 76.9% (p=0.19). Acute kidney injury was decreased throughout the study at 25.6%, 24.4% and 16.7% (p=0.32). The number of MRSA nares swabs ordered were 23.1%, 60% and 30.8% in each of the phases, respectively (p=0.49). DISCUSSION: Our novel approach to measuring the impact of pharmacist education and ordering of MRSA nasal swabs has demonstrated benefits that were sustained for a short period after the intervention was removed. Additional study is required to determine the long-term impact. CONCLUSION: The implementation of a hospital-wide anti-MRSA protocol in patients with confirmed or suspected pneumonia indicated sustained changes for at least 3 months after direct intervention.

Preclinical evaluation of a COVID-19 vaccine candidate based on a recombinant RBD fusion heterodimer of SARS-CoV-2.

Current COVID-19 vaccines have been associated with a decline in infection rates, prevention of severe disease, and a decrease in mortality rates. However, SARS-CoV-2 variants are continuously evolving, and development of new accessible COVID-19 vaccines is essential to mitigate the pandemic. Here, we present data on preclinical studies in mice of a receptor-binding domain (RBD)-based recombinant protein vaccine (PHH-1V) consisting of an RBD fusion heterodimer comprising the B.1.351 and B.1.1.7 SARS-CoV-2 variants formulated in SQBA adjuvant, an oil-in-water emulsion. A prime-boost immunisation with PHH-1V in BALB/c and K18-hACE2 mice induced a CD4+ and CD8+ T cell response and RBD-binding antibodies with neutralizing activity against several variants, and also showed a good tolerability profile. Significantly, RBD fusion heterodimer vaccination conferred 100% efficacy, preventing mortality in SARS-CoV-2 infected K18-hACE2 mice, but also reducing Beta, Delta and Omicron infection in lower respiratory airways. These findings demonstrate the feasibility of this recombinant vaccine strategy.

Antibiotic Guidance for OMFS inpatients

Introduction/Aims: Implementation of local antimicrobial guidelines is essential for optimal use of antibiotics and reduction of antibiotic resistance. The aims are: * To assess current antibiotic use for inpatients. * To assess which antibiotics are commonly prescribed in OMFS. * To assess dose/duration of antibiotics. * To assess second line antibiotic options for allergies. Material(s) and Method(s): Retrospective data was collected for elective and emergency admissions from October 2018 - October 2019. Data collection included: Antibiotic prescribed, clinical reason for antibiotics, dose, duration, administration method, discharge antibiotics, alternatives for penicillin allergic patients and microbiology swab results if applicable. Results/Statistics: Elective procedures included osteotomies, salivary gland surgery, TMJ surgery, cysts and major resections. 92% of osteotomies received prophylactic IV co-amoxiclav. 26% of salivary gland patients received antibiotics, majority co-amoxiclav. 58% of cyst patients received IV co-amoxiclav (43%), amoxicillin (43%) or amoxicillin and metronidazole (14%) and all major resection patients received IV antibiotics, majority amoxicillin and metronidazole (45%) 70 dental abscesses received IV antibiotics. 30% received amoxicillin and meronidazole, 22% received benzylpenicillin and metronidazole and the remaining 48% were prescribed a variety of combinations. 65% of abscesses had a microbiology pus swab taken. 48% were sensitive to penicillin, metronidazole or both. 33% had no growth. 91% of fractured mandibles received IV antibiotics, with co-amoxiclav and metronidazole the most common (30%). Conclusions/Clinical Relevance: Current practice was extremely varied. A guidance document was created for the department by a multidisciplinary team. A further round of data collection will be completed in due course following lifting covid restrictions to assess compliance. Copyright © 2022

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. Results: A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. Conclusions: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. Clinical trial number: NCT04405934.

Nonstructural protein 1 widespread RNA decay phenotype varies among coronaviruses.

Extensive remodeling of host gene expression by nonstructural protein 1 (nsp1) of coronaviruses is a well-documented and conserved aspect of coronavirus-host takeover. Using comparative transcriptomics we investigated the diversity of transcriptional targets between various nsp1 proteins. Additionally, affinity purification followed by mass spectrometry was implemented to identify common interactors between the different nsp1 proteins. Although we detected widespread RNA destabilization, closely related nsp1 showed little similarities in clustering of targeted genes. We observed a partial overlap in transcriptional targeting between α-CoV 229E and MERS nsp1, which may suggest a common targeting mechanism, as MERS nsp1 preferentially targets nuclear transcripts. Our interactome data show great variability between nsp1 interactions, with 229E nsp1, the smallest nsp1 tested here, interacting with the most number of host proteins. Although nsp1 is a rather well-conserved protein with conserved functions across different coronaviruses, our data indicate that its precise effects on the host cell are virus specific.

CRISPR screening reveals a dependency on ribosome recycling for efficient SARS-CoV-2 programmed ribosomal frameshifting and viral replication.

During translation of the genomic RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus in the COVID-19 pandemic, host ribosomes undergo programmed ribosomal frameshifting (PRF) at a conserved structural element. Although PRF is essential for coronavirus replication, host factors that regulate this process have not yet been identified. Here we perform genome-wide CRISPR-Cas9 knockout screens to identify regulators of SARS-CoV-2 PRF. These screens reveal that loss of ribosome recycling factors markedly decreases frameshifting efficiency and impairs SARS-CoV-2 viral replication. Mutational studies support a model wherein efficient removal of ribosomal subunits at the ORF1a stop codon is required for frameshifting of trailing ribosomes. This dependency upon ribosome recycling is not observed with other non-pathogenic human betacoronaviruses and is likely due to the unique position of the ORF1a stop codon in the SARS clade of coronaviruses. These findings therefore uncover host factors that support efficient SARS-CoV-2 translation and replication.

Changes in Clinical Presentation of TB due to the COVID-19 pandemic

Background. In 2020/21, deaths due to active tuberculosis (TB) increased globally for the first time in decades with concomitant global decline in TB detection rates, suggesting that delay in TB diagnosis during the COVID-19 pandemic is associated with increased mortality. In the US and New York City, 20% decline in TB cases was reported in 2020/21. We aimed to compare symptom duration, sputum microscopy and radiographic findings in patients with newly diagnosed TB at Montefiore Medical Center (MMC) in the Bronx, New York, before and during the COVID-19 pandemic. We hypothesized that patients during the COVID-19 pandemic present with signs of more advanced TB than before. Methods. Using a cross-sectional study design, we retrospectively reviewed medical records of TB patients identified through microbiology lab records from 11/1/ 2018 to 3/11/2022 and stratified by admission before (11/1/2018-2/29/2020) and during (3/1/2020-3/11/2022) the COVID-19 pandemic. Inclusion criteria were age >=18 years, admission to an MMC hospital, and new diagnosis of culture-confirmed TB. Results. We identified 24 TB patients who presented before and 24 during the pandemic. About 1.7 new TB cases were diagnosed monthly before vs 1.0 during the pandemic, an >40% decline. Patients had both pulmonary and/or extrapulmonary manifestations without differences between groups. There were no significant differences in demographics and comorbidities between the two groups aside from diabetes, which was higher in the pre-COVID group (p = 0.03). Two TB patients had a prior history of COVID and one developed nosocomial COVID during the admission. There was no difference in mortality between groups. Patients with pulmonary manifestations had higher sputum AFB smear positivity (p=0.14) and significantly higher occurrence of multilobar or miliary infiltrates on chest X-ray during compared to before COVID (p = 0.01;Table 1). Table 1. Symptoms and diagnostics on initial presentation of patients with pulmonary TB before and during the COVID-19 pandemic Depending on distribution, t-tests or Mann Whitney U tests were used for continuous and Chi-square tests or Fisher's exact tests for categorical variables. Sputum AFB smears results are reported for the initial 3 smears. Conclusion. Our findings show >40% decline in patients presenting with TB in the Bronx during vs before the COVID-19 pandemic and suggests patients presented with more advanced disease than before the pandemic. Whether COVID-19 could have contributed to this remains to be investigated. Our results have implications for public health and emphasizes the need for earlier identification of TB.