Non-Hodgkin's lymphoma complicated with human coronavirus HKU1 pneumonia: A case report and literature review.

Objective: To analyze the clinical manifestations, diagnostic methods and treatment process of the patients with non-Hodgkin's lymphoma complicated with human coronavirus(HCoV)-HKU1 pneumonia and improve the clinical medical staff's awareness of the disease, and to reduce the occurrence of clinical adverse events. Method(s): The clinical data of a patient with non-Hodgkin's lymphoma complicated with HCoV-HKU1 pneumonia with hot flashes and night sweats, dry cough and dry throat as the main clinical features who were hospitalized in the hospital in January 2021 were analyzed, and the relevant literatures were reviewed and the clinical manifestations and diagnosis of HCoV-HKU1 were analyzed. Result(s): The female patient was admitted to the hospital due to diagnosed non-Hodgkin's lymphoma for more than 2 months. The physical examination results showed Karnofsky score was 90 points;there was no palpable enlargement of systemic superfical lymph nodes;mild tenderness in the right lower abdomen, no rebound tenderness, and slightly thicker breath sounds in both lungs were found, and a few moist rales were heard in both lower lungs. The chest CT results showed diffuse exudative foci in both lungs, and the number of white blood cells in the urine analysis was 158 muL-1;next generation sequencing technique(NGS) was used the detect the bronchoalveolar lavage fluid, and HCoV-HKU1 pneumonia was diagnosed. At admission, the patient had symptoms such as dull pain in the right lower abdomen, nighttime cough, and night sweats;antiviral treatment with oseltamivir was ineffective. After treatment with Compound Sulfamethoxazole Tablets and Lianhua Qingwen Granules, the respiratory symptoms of the patient disappeared. The re-examination chest CT results showed the exudation was absorbed. Conclusion(s): The clinical symptoms of the patients with non-Hodgkin's lymphoma complicated with HCoV-HKU1 pneumonia are non-specific. When the diffuse shadow changes in the lungs are found in clinic, and the new coronavirus nucleic acid test is negative, attention should still be paid to the possibility of other HCoV infections. The NGS can efficiently screen the infectious pathogens, which is beneficial to guide the diagnosis and treatment of pulmonary infectious diseases more accurately.Copyright © 2023 Jilin University Press. All rights reserved.

Is there an increased incidence of bacteraemia among COVID-19 patients requiring critical care admission who have received IL-6 inhibitors?

Is there an increased incidence of bacteraemia among COVID-19 patients requiring critical care admission who have received IL-6 inhibitors? Introduction: Interleukin-6 (IL-6) inhibitors have been shown to reduce mortality in hospitalised COVID-19 patients. There is, however, concern that induced immunosuppression may increase the risk of secondary nosocomial infection. Objective(s): Our primary aim was to determine if there was increased incidence of bacteraemia in COVID-19 patients requiring critical care admission who had received IL-6 inhibitors compared to those who had not. Method(s): A retrospective review of all COVID-19 admissions to two critical care units in Liverpool from 4th March 2020 to 31st October 2021. Patients were divided into those who received an IL-6 inhibitor (sarilumab or tociluzimab) and those who did not. Hospital antimicrobial policy was to administer a five day prophylactic course of co-amoxiclav and clarithromycin for patients with severe COVID-19 during the study period. Blood culture results from 14 days before admission to critical care and 90 days after admission were included. The blood culture results comprised cultures taken in both critical care and on the wards. Data were linked and analysed using Stata V15.1 (StataCorp, Stata Statistical Software: Release 15, College Station, Texas, USA). Result(s): 894 patients were included in the study. 134 patients had at least one positive blood culture result. The most commonly identified pathogens were Coliforms (23/134, 17.2%), Enterobacter (22/134, 16.4%) and Escherichia coli (16/134, 11.9%). Of patients administered an IL-6 antagonist, 16.8% (114/565) developed a positive blood culture compared to 11.6% (20/172) who did not, p=0.096. We did not observe an increased frequency of antimicrobial resistant culture in the IL-6 administered group 22.8% (26/114) vs. 20.0% (4/20) in this cohort, p=0.781. Data have not been adjusted for demographic and clinical factors in this preliminary analysis. Conclusion(s): We observed a trend toward increased frequency of blood culture positivity in patients administered an IL-6 antagonist within this COVID-19 positive cohort but this was not statistically significant. Further analysis is required to adjust for relevant demographic and clinical factors.

PPP1R13L-Related Cardiomyopathy Stability Following IL1 Inhibition

Introduction: Variants in PPP1R13L are associated with severe childhood-onset cardiomyopathy resulting in rapid progression to death or cardiac transplantation. PPP1R13L is proposed to encode a protein that limits the transcriptional activity of the NFkappaB pathway leading to elevated IL-1, IL-6, and TNF-alpha production in murine models. Optimal medical management for PPP1R13L-related cardiomyopathy is unknown. Here we report usage of a targeted anti-IL-1 immuno-modulatory therapy resulting in cardiac stabilization in a pediatric patient with congenital cardiomyopathy secondary to PPP1R13L variants. Case Report: A 4-year-old boy presented acutely with fever in the setting of persistent abdominal pain, vomiting, fatigue, and decreased appetite for two months following a mild COVID-19 related illness. Echocardiogram revealed severely depressed biventricular systolic function with an ejection fraction of 30%. Due to acute decompensated heart failure symptoms with hemodynamic instability, he was intubated and placed on continuous inotropic infusions with aggressive diuresis. Cardiac MRI demonstrated extensive subepicardial to near transmural fibrosis by late gadolinium enhancement in right and left ventricles. An implantable cardioverter-defibrillator (ICD) was placed due to frequent runs of polymorphic non-sustained ventricular tachycardia. Testing for viral pathogens was positive for rhino/enterovirus. Initial genetic testing was non-diagnostic (82-gene cardiomyopathy panel) but given the patient's significant presentation whole genome sequencing was pursued that showed two separate PPP1R13L variants in trans (c.2167A>C,p.T723P and c.2179_2183del,p. G727Hfs*25, NM_006663.4). Patient serum cytokine testing revealed elevations in IL-10 (4.7 pg/mL) and IL-1beta (20.9 pg/mL). Given the patient's tenuous circumstances and concern for continued progression of his cardiac disease, a trial of IL-1 inhibition via anakinra dosed at 3 mg/kg or 45 mg daily was initiated following hospital discharge. With approximately 6 months of therapy, the patient's cardiac function is stable with normalization of IL-10 and IL-1beta serum levels. Notably, the ventricular arrhythmia decreased after initiation of anakinra with no ICD shocks given. Therapy overall has been well tolerated without infectious concerns. Conclusion(s): In patients with PPP1R13L-related cardiomyopathy, immuno-modulatory therapies should be considered in an attempt to slow cardiac disease progression.Copyright © 2023 Elsevier Inc.

Burden of respiratory coinfections in haematology patients with COVID-19

Introduction: Following the lifting of generalised restrictions and universal masking, severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2)- infected patients, especially the clinically extremely vulnerable (CEV) haematology patients, are at an increased risk for other respiratory viral coinfections;therefore, physicians need to be cognizant about excluding other treatable respiratory pathogens. Here, we report coinfection with SARS-CoV- 2 and other respiratory pathogens in patients with haematological cancers presenting to a large tertiary care hospital. Method(s): From July 2022-December 2022, patients with haematological disorders were screened for SARS-CoV- 2 and other 10 common respiratory pathogens by PCR. We performed a retrospective analysis of patients with concurrent respiratory viruses and will prospectively evaluate the same from Jan 2023 to March 2023. Result(s): During this period a total of 322 inpatients had routine screening and additional 6213 swabs were done in the outpatient/ambulatory setting, of which 294 were positive in 221 patients. We excluded all patients who had a single positive PCR swab result and specifically analysed only patients with coinfections. We identified 30 patients (14%) who had respiratory coinfections with 73 viral infections/reactivations over 6 months period, which represented 25% of all positive swabs: 25 inpatients (19 symptomatic/6 asymptomatic) and 48 in outpatients (32 symptomatic/16 asymptomatic). The median age of the cohort was 47.3 years (21-77). Patients were post allograft (n = 15), autograft (n = 7), post CART (n = 5) and postchemotherapy (n = 4). Of the 30 cases, 13 patients had concurrent infections: 5 SARS-CoV2, 10 Respiratory syncytial virus (RSV), 7 Rhino and 4 Influenza A, with all patients having dual viral infection. The remaining 17 patients had multiple viral infections but separated by a median of 54 days (range 27-137 days): 16 SARS-CoV2, 5 RSV, 6 Rhino, 2 Parainfluenza, 2 Adeno and one each of Influenza A, Influenza B, and metapneumovirus. Of the treatable infections (n = 46), 22% were detected on routine asymptomatic swabbing, with 50% of SARS-CoV2 detected on routine swabs. All 8 patients with Influenza were treated with oseltamivir, of 16 RSV cases one was treated with oral ribavirin and of the 22 SARS-CoV2 patients, 5 were treated (4 Paxlovid and 1 Remdesivir). No patients needed intensive care support and no deaths were reported. Conclusion(s): The burden of respiratory coinfections in CEV cohort has a significant impact on respiratory isolation and management, including appropriate & timely initiation of therapy for treatable viral infections. Although mortality was not increased secondary to respiratory coinfections and none needed intensive care, larger prospective cohorts are needed to assess the exact impact.

COVID-19 associated severe mucocutaneous blistering eruptions: A case series

Introduction: Mucocutaneous eruptions are associated with many viral processes and present as erythema multiforme (EM), reactive infectious mucocutaneous eruption (RIME), Stevens Johnson syndrome (SJS) or toxic epidermal necrosis (TEN). Limited reports have described the association of COVID-19 and mucocutaneous eruptions in children and adults to date. Method(s): This was a multicenter descriptive case series performed at six tertiary medical centers. Inclusion required a clinical diagnosis of EM, RIME, SJS or TEN and a positive COVID-19 test (rapid antigen or PCR) less than 4 weeks prior to onset of dermatologic manifestation. Data was collected at time of each patient encounter. Result(s): A total of 7 patients met criteria and had a median age of 15 years for pediatric patients (<18 years of age) and 36 years for adult patients (>18 years of age). Patients were found to have a diagnosis of RIME in 85.7% of cases. Oral mucosal involvement was the most common clinical finding (100%), followed by ocular (57.1%), urogenital (57.1%) and skin (42.9%) involvement. 71.4% of cases required hospitalization for their cutaneous eruption. No patients died from their inflammatory condition. Discussion(s): This case series highlights the development of mucocutaneous eruptions in association with COVID-19 infection. Within our cohort, RIME was the most commonly identified COVID-associated eruption. These findings provide additional evidence that abnormalities in host immune response to viral pathogens play a role in severe mucocutaneous blistering conditions. Further investigation will aid our understanding of this disease to improve diagnostics and advance targeted treatments for patients in the future.

Viruses and the risk of lung cancer: prevention and treatment

Lung cancer is the most common cancer in males and the second most common among females both in Europe and worldwide. Moreover, lung cancer is the leading cause of death due to cancer in males. The European region accounts for 23% of total cancer cases and 20% of cancer-related deaths. Relationships have been described between a number of infectious agents and cancers, but our knowledge of the role of viruses, both respiratory and systemic, in the pathogenesis of lung cancer is still rudimentary and has been poorly disseminated. In this chapter, we review the available evidence on the involvement of HPV, Epstein-Barr virus, HIV, cytomegalovirus and measles virus in the epidemiology and pathogenesis of lung cancer.Copyright © ERS 2021.

Antibiotic therapy of Acinetobacter baumannii bloodstream infection in COVID-19 patients

Secondary bacterial infection is one of the important risk factors for the development of severe course and death in COVID-19. The rational choice of antibacterial therapy is based on the data of microbiological monitoring of pathogens of healthcare-associated infections. The aim of the study is to determine the main options for antibiotic therapy of Acinetobacter baumannii bloodstream infection in COVID-19 patients. Material and methods. A retrospective, single-centre, uncontrolled study of the incidence of A. baumannii bacteremia in COVID-19 patients treated at the City Clinical Hospital No. 52 in Moscow from October 2020 to September 2021 was performed. For each strain of A. baumannii sensitivity to the main antibacterial agents was determined. Genetic determinants of antibiotic resistance were studied by real-time multiplex polymerase chain reaction. The main therapeutic options for A. baumannii bloodstream infection were analyzed. Results and discussion. Bloodstream infections were diagnosed in 4.7% of hospitalized patients with COVID-19 (758/16 047). Gram-negative bacteria were the causative agents of bloodstream infections in 76% of cases. A. baumannii were isolated from the blood of 143 patients (0.89%). Detection of the pathogen in the blood of COVID-19 patients was associated with severe and extremely severe course of the disease. Most of the strains (93%) were isolated in the intensive care unit. The A. baumannii strains studied were carbapenem-resistant (CRAb) and phenotypically belonged to the XDR class. According to a PCR study, A. baumannii strains were producers of oxacillinases OXA-23, OXA-40, and OXA-51. Conclusion. The circulation of A. baumannii CRAb in intensive care units makes empiric therapy based on carbapenems irrational and ineffective. For the etiotropic therapy of A. baumannii bloodstream infection it is recommended to use combined antibiotic therapy regimens with the inclusion of polymyxin B and sulbactam.Copyright © Eco-Vector, 2022.

Probability of Infectious Disease in Humans during Epidemic

Popular SIR models and their modifications used to generate predictions about epidemics and, specifically, the COVID-19 pandemic, are inadequate. The aim of this study was to find the laws describing the probability of infection in a biological object. Using theoretical methods of research based on the probability theory, we constructed the laws describing the probability of infection in a human depending on the infective dose and considering the temporal characteristics of a given infection. The so-called generalized time-factor law, which factors in the time of onset and the duration of an infectious disease, was found to be the most general. Among its special cases are the law describing the probability of infection developing by some point in time t, depending on the infective dose, and the law that does not factor in the time of onset. The study produced a full list of quantitative characteristics of pathogen virulence. The laws described in the study help to solve practical tasks and should lie at the core of mathematical epidemiological modeling.Copyright © 2022 Obstetrics, Gynecology and Reproduction. All rights reserved.

Pan-Respiratory Disease Surveillance in Southeast Asia: Past, Present and Future

The Global Influenza Surveillance and Response System (GISRS) was established by WHO in 1952 to conduct surveillance for influenza to inform strain selection for seasonal vaccines and to monitor for influenza pandemics. In 2016 WHO initiated a pilot project to add RSV to influenza surveillance platforms;this was disrupted by the SARS CoV-2 pandemic, and SARS CoV-2 was the first pathogen to be incorporated into influenza sentinel surveillance on a wide scale. This resulted in a "GISRS-plus" surveillance network for influenza and SARS CoV-2 that is now being standardized by WHO. In the wake of the SARS CoV-2 pandemic, there is global interest and funding to support pan-respiratory disease surveillance, which could result in expanding influenza/SARS CoV-2 surveillance platforms to include other pathogens and enhancing event- and indicator-based surveillance. Challenges with expanding sentinel surveillance include overburdening sentinel surveillance systems, reduced number of samples collected and loss of data quality for influenza and SARS CoV-2;thus, other types of surveillance for respiratory diseases might also be considered. This talk describes CDC-supported influenza surveillance platforms in Southeast Asia and recent successes and challenges in adding SARS CoV-2 to this surveillance. It discusses potential risks and benefits to GISRS-plus surveillance created by including other pathogens. Finally, it discusses decision-making steps on which methods to use for collecting data on respiratory viruses.Copyright © 2023

Concomitant Infection of Sars-Cov-2, Influenza a/B Virus and Respiratory Syncytial Virus

Intro: In the first year of SARS-CoV-2 (CoV-2) pandemic, prevalence of common respiratory viruses, like influenza A/B (Flu A/B) and respiratory syncytial virus (RSV), had a temporary decrease in worldwide circulation, Portugal being no exception. Since this type of viruses share similar routes of transmission with CoV-2, the preventive social measures implemented to avert the spread of the new virus had a significant impact in their transmission as well. With the evolution of pandemic in association with the application of different levels of lockdown restrictions and the reopening of society across several countries, a boost of the circulation of Flu A/B and RVS and/or a change in their seasonal epidemiology can occur and co-infection with CoV-2 may be a possibility. The aim of this work was the evaluation of the Flu A/B and RSV circulation during the last year in COVID-19 samples. Method(s): Between May 2021 and January 2022, about 104 205 human clinical samples for routine CoV-2 diagnostic were tested using Alinity M (Abbott) Resp- 4-Plex assay which simultaneously detected targets from CoV-2, Flu A/ B and RSV. Finding(s): A total of 6627 (6.36%) CoV-2, 483 (0.46%) Flu A, 42(0.04%) Flu B and 2606 (2.50%) RSV positive cases were detected, point out the presence of 75 co-infections: 57 RSV/CoV-2, 17 Flu A/ CoV-2 and 1 Flu B/CoV-2. In accordance with the increase of cases of both viruses, RSV/CoV-2 co-infection occurred mainly between August and December 2021 and Flu A/ CoV-2 between December 2021 and January 2022. It was observed a high RSV season atypically early (August) with only 15.8% of the concomitant cases occurring in children. Conclusion(s): In conclusion, this study reports that co-infection arose between these viruses highlighting the importance of a continuous respiratory pathogen surveillance during pandemics, as well as atypically peaks in atypical periods can emerge when restrictions change.Copyright © 2023

Preparing Long-term care facilities for future pandemics-A systematic review of non-pharmacological interventions

Background Due to climate change, the likelihood of an extreme infectious disease events-similar to the COVID-19 pandemic-is very likely to increase. Anticipating and preparing for such events Is therefore essential. A setting of high risk in such an event are long-term care facilities (LTCF), which accounted for 30-60 % of all COVID-19 related deaths in most high-income countries (HIC). To prevent, mitigate, and avoid potential adverse consequences of future outbreaks of viral respiratory pathogens with pandemic potential (e.g., SARSCoV-2, SARS, MERS, influenza) in LTCFs, a systematic review will analyze which non-pharmacological interventions (NPI) are effective in LTCFs. Methods We conducted literature searches in Medline, Embase, CINAHL, and two comprehensive specialized registries focused on COVID-19-related literature. We included experimental, quasi-experimental, and specific observational studies assessing the effect of NPIs implemented in LTCFs regarding the outcomes: infections, outbreaks, hospitalizations and deaths due to the viral pathogens of interest and adverse consequences. Screening for eligibility and risk-of-bias (RoB) assessment was done in duplicate. For RoB assessment, we used the RoB2 and ROBINS-I tool. We synthesized findings narratively, focusing on the direction of effect. The certainty of evidence was evaluated using GRADE. Results We included 16 observational studies, 14 of which focused on intervention effectiveness. All were conducted in HIC and most focused on SARSCoV-2 (n = 14). There were serious concerns regarding RoB in almost all studies. We found low/very low certainty of evidence for the effectiveness of entry regulation measures (n = 1), regular testing of residents/staff (n = 5), combined outbreak control measures (n = 2), and for combinations of multiple NPIs (n = 3) in preventing outbreaks or mitigating their consequences. The evidence on the effectiveness of hand and surface hygiene interventions showed mixed results (n = 4). We found mixed results regarding adverse mental health outcomes due to visiting restrictions. Conclusion This review indicates a number of measures which could be effective in protecting residents and staff in LTCFs in upcoming extreme infectious disease epidemics, which are expected to become more likely in the future. Furthermore, we can point out several gaps in the evidence which require further research and specific study designs to improve pandemic preparedness in LTCFs.

Metavirome in Sewage and Fecally-Tainted River Waters in the Philippines: Highlighting the Role of Environmental Surveillance in the Covid-19 Pandemic

Intro: The COVID-19 pandemic has triggered global collaborative efforts on response and research to detect SARS-CoV-2 particles not just in the human population but also in wastewater. While the examination of clinical samples from COVID-19 patients links SARS-CoV-2 to specific individuals, the analysis of an amalgam of human feces through environmental surveillance (ES) links SARSCoV-2 to populations and communities served by the wastewater system. Studies on SARS-CoV-2 in the environment were already done in high-resource countries. However, its epidemiology in wastewater bodies in the Philippines is limited. In this study, we used the National ES for Polio and Other Pathogens Network to investigate the molecular epidemiology and transmission dynamics of SARS-CoV-2 at the outset of the pandemic. Method(s): This is a retrospective study of 250 wastewater samples collected from May 2020 to July 2021. Samples were processed using the two-phase concentration technique. Pepper mild mottle virus RNAs were quantified as the internal control. Real-time PCR was used to detect the N-gene of the SARS-CoV-2. Whole genomes were sequenced using the COVID-19 ARTIC v4.0. Phylogenetic and mutation analysis were done and lineage assignments were established using the PANGOLIN software. Finding(s): Forty-two percent (107/250) of the environmental samples detected SARS-CoV-2 particles. Fifty-nine samples with Ct values <=38 were sequenced and the whole genome analysis revealed B.1.1 and B.6. lineages of SARS-CoV-2. When viral load were plotted with the weekly cases in the respective site, we observed that SARS-CoV2 can be detected in wastewater weeks before the spike of cases in the community. Conclusion(s): This is the first report on the detection of B.1.1 and B.6 SARS-CoV-2 particles in waste/surface waters in the Philippines. With the declining incidence of COVID-19 cases, this study provided data regarding the feasibility of establishing environmental surveillance for SARS-CoV-2 as a supplemental tool for human or case monitoring especially in resource-limited settings.Copyright © 2023

Antibiotic Stewardship Strategies to Limit Inappropriate Antibiotic Use and Reduce Multi-Drug Resistant Pathogens during Covid-19 Pandemic

Antibiotics have been extensively used in COVID-19 patients without a clear indication. COVID-19 pneumonia is associated with a mortality up to 20% varying by country with the number of global deaths over 5 million. Antibiotics have been extensively used in COVID-19 patients in intensive care units (ICUs) without a clear indication. According to a previous study, the frequency of bacterial pneumonia in COVID-19 patients was 6.9%, while >70% of patients received antibiotics. This is likely due to the clinical findings of COVID-19 pneumonia overlapping with those of bacterial pneumonia and the lack of reliable indicators of bacterial infection. Strategies that distinguish bacterial from viral pneumonia are desirable. In this session, I will discuss the impact of inappropriate antibiotic use during pandemic as well as the strategy to limit inappropriate antibiotic use as well as multi-drug resistant pathogen during COVID-19 pandemic among COVID-19 and non-COVID-19 populations.Copyright © 2023

Bacterial Infectious Diseases in the Covid-19 Era

The outbreak of SARS-CoV-2 in December 2019 in China quickly spread to the rest of the world. By March 2020, the World Health Organization declared the COVID-19 pandemic, and several mitigation strategies were implemented worldwide, highlighting social distancing, quarantine and the use of face masks. Since then, many studies have reported the impact of these interventions on the occurrence of other infectious diseases, especially bacterial infectious diseases disseminated through airborne. Invasive infections with respiratory bacterial pathogens, such as Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, Bordetella pertussis, Chlamydia pneumoniae and Mycoplasma pneumoniae have had a marked decline in several countries of the world. Low- and middle-income (LMIC) and high-income countries (HIC) were at different seasons of the year when COVID-19 started and interventions were implemented, but long-lasting consequences of seasonal differences are yet to be elucidated. In this session, we aim to describe the impact of COVID-19 and related intervention strategies in bacterial infectious diseases between LMIC and HIC;determine whether and how the onset of COVID-19 pandemic has changed the broader scenario of infectious diseases;and envision future and emerging infectious diseases in the post-pandemic world.Copyright © 2023

Lipid-dependent assembly and budding of emerging viral pathogens

Lipid enveloped viruses replicate and bud from the host cell where they acquire their lipid coat. Lipid-enveloped viruses include dangerous pathogens such as coronaviruses (SARSCoV-2, etc.), filoviruses (Ebola virus and Marburg virus) and paramyxoviruses (Nipah virus, Hendra virus, etc.). Despite understanding some of the basics of how these viruses cause disease and enter host cells, not much is known on how these dangerous pathogens interact with host cell lipids to achieve new virion formation. The viral matrix or membrane protein regulates assembly and budding from the host cell membrane, connecting the viral lipid envelope to the viral nucleocapsid. Depending on the virus family, this assembly and budding may occur at the plasma membrane or the ER-Golgi intermediate compartment. This presentation will detail the biophysical and biochemical basis of how these emerging pathogens hijack host lipid membrane and metabolic networks to form new virus particles that undergo release from the host cell. These studies were funded in part by the National Institute of Allergy and Infectious Diseases (R01AI081077, AI158220, AI169896).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Alternative structures of RNA control gene expression and offer therapeutic strategies

RNA viruses are diverse and abundant pathogens responsible for numerous human ailments, from common colds to AIDS, SARS, Ebola, and other dangerous diseases. RNA viruses possess relatively compact genomes and have therefore evolved multiple mechanisms to maximize their coding capacities, often using overlapping reading frames. In this way, one RNA sequence can encode multiple proteins via mechanisms including alternative splicing and ribosomal frameshifting. Many such processes in gene expression involve the RNA folding into three-dimensional structures that can recruit ribosomes without initiation factors, hijack host proteins, cause ribosomes to frameshift, and expose or occlude regulatory protein binding motifs to ultimately control each key process in the viral life cycle. I will discuss the RNA structure of HIV-1 and SARS-CoV-2 and the importance of alternative conformations assumed by the same RNA sequence in controlling gene expression of viruses and bacteria.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Highly synergistic combinations of nanobodies that target SARS-CoV-2 reduce viral load in hACE2 transgenic mice

The ongoing emergence of SARS-CoV-2 variants threatens current vaccines and renders current therapeutic antibodies obsolete, demanding powerful new treatments that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against past and present emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind dissimilar sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies. All mouse involved experiments were performed in compliance with the Institutional Animal Care and Use Committee and mice were housed and maintained in a specific pathogen-free conditions at Seattle Children's Research Institute. Infected mice with SARSCoV- 2 were housed in a Biosafety Level 3 facility in an Animal Biohazard Containment Suite. Prophylactic intranasal application of a synergistic pair of unmodified nanobodies in 10-12 week-old female K18-hACE2 transgenic mice, a mouse model of SARS-CoV-2 infection, showed significant reduction in viral load after 3 days post-challenge with SARS-CoV-2, the first demonstration of synergy in vivo. In summary, our results show that our diverse repertoire of nanobodies can neutralize current variants of live SARS-CoV-2, pairs of nanobodies that bind distinct sites on spike show tremendous synergy in neutralizing efficacy in vitro, and the application of synergizing pair of nanobodies translates to an in vivo mouse model of SARSCoV- 2. Research funded by the Mathers Foundation, Robertson Foundation, NIH P41GM109824.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Targeting virus-induced vulnerabilities using synthetic lethality as a new class of host-based antivirals

RNA viruses are the major class of human pathogens responsible for many global health crises, including the COVID-19 pandemic. However, the current repertoire of U.S. Food and Drug Administration (FDA)-approved antivirals is limited to only nine out of the known 214 human-infecting RNAviruses, and almost all these antivirals target viral proteins. Traditional antiviral development generally proceeds in a virus-centric fashion, and successful therapies tend to be only marginally effective as monotherapies, due to dose-limiting toxicity and the rapid emergence of drug resistance. Host-based antivirals have potential to alleviate these shortcomings, but do not typically discriminate between infected and uninfected cells, thus eliciting unintended effects. In infected cells where host proteins are repurposed by a virus, normal host protein functions are compromised;a situation analogous to a loss-of-function mutation, and cells harboring the hypomorph have unique vulnerabilities. As well-established in model systems and in cancer therapeutics, these uniquely vulnerable cells can be selectively killed by a drug that inhibits a functionally redundant protein. This is the foundation of synthetic lethality (SL). To test if viral induced vulnerabilities can be exploited for viral therapeutics, we selectively targeted synthetic lethal partners of GBF1, a Golgi membrane protein and a critical host factor for many RNA viruses including poliovirus, Coxsackievirus, Dengue, Hepatitis C and E virus, and Ebola virus. GBF1 becomes a hypomorph upon interaction with the poliovirus protein 3A. A genome-wide chemogenomic CRISPR screen identified synthetic lethal partners of GBF1 and revealed ARF1 as the top hit. Disruption of ARF1, selectively killed cells that synthesize poliovirus 3A alone or in the context of a poliovirus replicon. Combining 3A expression with sub-lethal amounts of GCA - a specific inhibitor of GBF1 further exacerbated the GBF1-ARF1 SL effect. Together our data demonstrate proof of concept for host-based SL targeting of viral infection. We are currently testing all druggable synthetic lethal partners of GBF1 from our chemogenomic CRISPR-screen, in the context of dengue virus infection for their abilities to selectively kill infected cells and inhibit viral replication and infection. Importantly, these SL gene partners of viral-induced hypomorphs only become essential in infected cells and in principle, targeting them will have minimal effects on uninfected cells. Our strategy to target SL interactions of the viral-induced hypomorph has the potential to change the current paradigm for host-based therapeutics that can lead to broad-spectrum antivirals and can be applied to other intracellular pathogens. This work is supported by National Institutes of Health grants R01 GM112108 and P41 GM109824, R21 AI151344 and foundation grant FDN-167277 from the Canadian Institutes of Health Research.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Emerging membrane technologies and disinfection methods for efficient removal of waterborne pathogens during the COVID-19 pandemic and post-pandemic

Viruses and other microorganisms can enter water sources from different routes and cause pollution and irreparable damage. So, cost-effective and efficient systems for providing safe water are necessary. Efficient filtration systems based on antimicrobial materials have received a lot of attention in this regard. A wide range of materials play an important role in the production of efficient water filtration systems. Metal and metal oxide particles with anti-viral and antimicrobial properties comprising Cu, Cu2O, Ag, TiO2, and ZnO play a valuable role in the preparation of water filtration systems. Biopolymers such as cellulose or carbon nanomaterials like graphene or its derivatives have been reported to provide safe water. In this review, we summarize the use of diverse materials in the preparation of efficient filtration-based systems like membranes and paper filters for water treatment. Pathogen-containing water samples were effectively disinfected using the prepared water disinfection systems.Copyright © 2023 The Royal Society of Chemistry.

FROM PROMISE TO REALIZATION: SEQUENCING AND SURVEILLANCE FROM HIV-1 TO SARS-CoV-2

The advent of cheaper viral sequencing and opportunity to offer customized treatment through identification of resistance mutations in patients with HIV-1, also offered the first large-scale opportunity to use sequencing to generate insights into a global infectious disease pandemic. Using HIV-1 sequences, scientists were able to track mutations globally and within countries and use them to gain groundbreaking understanding of virus transmission and the evolution of resistance. Though invaluable in contributing to our knowledge of virus dynamics, much of what was feasible with HIV-1 was difficult to extend to other viruses due to the challenges and expense of full-genome sequences and the difficulty of obtaining samples from acute infections. More recent advances have made next-generation sequencing (NGS) possible and affordable, and growing realization of the insights sequencing can contribute has increased interest in generating sequences for an increasing variety of viruses. Against this backdrop of an advent of a new age of genomics in viral research, the SARSCoV- 2 pandemic has thrown sequencing and phylogenetics into the limelight, allowing the collection and sequencing of more samples than could even be conceived prior to 2020. It's a opportune time to consider not only where we've come from, but how the promise of 14 million sequences has been realized, and what the future holds for sequence-enabled pathogen research.