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Competing Interests: The authors declare no conflicts of interest.

SARS-CoV-2 Omicron subvariants are still emerging and spreading worldwide. These variants contain a high number of polymorphisms in the spike (S) glycoprotein that could potentially impact their pathogenicity and transmission. We have previously shown that the S:655Y and P681H mutations enhance S protein cleavage and syncytia formation. Interestingly, these polymorphisms are present in Omicron S protein. Here, we characterized the cleavage efficiency and fusogenicity of the S protein of different Omicron sublineages. Our results showed that Omicron BA.1 subvariant is efficiently cleaved but it is poorly fusogenic compared to previous SARS-CoV-2 strains. To understand the basis of this phenotype, we generated chimeric S protein using combinations of the S1 and S2 domains from WA1, Delta and Omicron BA.1 variants. We found that the S2 domain of Omicron BA.1 hindered efficient cell-cell fusion. Interestingly, this domain only contains six unique polymorphisms never detected before in ancestral SARS-CoV-2 variants. WA1 614G S proteins containing the six individuals S2 Omicron mutations were assessed for their fusogenicity and S surface expression after transfection in cells. Results showed that the S:N856K and N969K substitutions decreased syncytia formation and impacted S protein cell surface levels. However, we observed that "first-generation" Omicron sublineages that emerged subsequently, had convergently evolved to an enhanced fusogenic activity and S expression on the surface of infected cells while "second-generation" Omicron variants have highly diverged and showed lineage-specific fusogenic properties. Importantly, our findings could have potential implications in the improvement and redesign of COVID-19 vaccines.

Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.

Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients., (© 2023. The Author(s).)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.

SARS-CoV-2 lineages have diverged into highly prevalent variants termed "variants of concern" (VOCs). Here, we characterized emerging SARS-CoV-2 spike polymorphisms in vitro and in vivo to understand their impact on transmissibility and virus pathogenicity and fitness. We demonstrate that the substitution S:655Y, represented in the gamma and omicron VOCs, enhances viral replication and spike protein cleavage. The S:655Y substitution was transmitted more efficiently than its ancestor S:655H in the hamster infection model and was able to outcompete S:655H in the hamster model and in a human primary airway system. Finally, we analyzed a set of emerging SARS-CoV-2 variants to investigate how different sets of mutations may impact spike processing. All VOCs tested exhibited increased spike cleavage and fusogenic capacity. Taken together, our study demonstrates that the spike mutations present in VOCs that become epidemiologically prevalent in humans are linked to an increase in spike processing and virus transmission., Competing Interests: Declaration of interests The A.G.-S. laboratory has received research support from Pfizer, Senhwa Biosciences, Kenall Manufacturing, Avimex, Johnson & Johnson, Dynavax, 7Hills Pharma, N-fold LLC, Pharmamar, ImmunityBio, Accurius, Nanocomposix, Hexamer, and Merck, outside of the reported work. A.G.-S. has consulting agreements for the following companies involving cash and/or stock: Vivaldi Biosciences, Contrafect, 7Hills Pharma, Avimex, Vaxalto, Pagoda, Accurius, Esperovax, Farmak, Applied Biological Laboratories, and Pfizer, outside of the reported work. A.G.-S. is inventor on patents and patent applications on the use of antivirals and vaccines for the treatment and prevention of virus infections, owned by the Icahn School of Medicine at Mount Sinai, New York. The Icahn School of Medicine at Mount Sinai has filed a patent application relating to SARS-CoV-2 serological assays, which lists Viviana Simon as co-inventor. Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2. The Krogan Laboratory has received research support from Vir Biotechnology and F. Hoffmann-La Roche. Nevan Krogan has consulting agreements with the Icahn School of Medicine at Mount Sinai, New York; Maze Therapeutics; and Interline Therapeutics. He is a shareholder in Tenaya Therapeutics, Maze Therapeutics, and Interline Therapeutics and is financially compensated by GEn1E Lifesciences, Inc. and Twist Bioscience Corp., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Introduction: COVID-19 has challenged healthcare systems worldwide. Some countries collapsed under surge conditions, while others (such as Malta) showed resilience. Public health measures in Malta quickly reined in COVID-19 spread. This review summarizes pandemic preparedness measures in Malta and the impact on routine services., Methods: A literature search was conducted using Google, Google Scholar and PubMed and by reviewing Maltese online newspapers. A comprehensive summary of internal operations conducted at Mater Dei Hospital (MDH) was made available., Results: A hospital 'Incident Command Group' was set up to plan an optimal COVID-19 response strategy. A 'rapid response team' was also created to cater for the logistics and management of supplies. A 'COVID-19 Emergency Operation Centre' simulated different COVID-19 scenarios. All elective services were suspended and all staff were mandatorily trained in wearing personal protective equipment. Staff were also retrained in the care of COVID-19 patients. In preparation for potential admission surges, MDH underwent rapid expansion of normal and intensive care beds. Swabbing was ramped up to one of the highest national rates worldwide. The cost for hospital COVID-19 preparedness exceeded €100 million for Malta's half a million population., Conclusion: Malta and its sole acute hospital coped well with the first wave with 680 cases and 9 deaths. The increased ability to deal with COVID-19 (a principally respiratory pathogen) will serve well for the anticipated combined annual influenza and the COVID-19 second wave this coming winter., (© The Author(s) 2020. Published by Oxford University Press on behalf of International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

As an important technique for the detection of fingermarks on porous surfaces, 1,2-indanedione is widely used due to its excellent detection performance. In order to optimize the effectiveness of 1,2-indanedione, several institutions have modified the original formulation. In this study, four different 1,2-indanedione formulations were used to treat fingermarks deposited on different porous substrates to determine the most suitable formulation and whether Solstice-PF can be an alternative carrier solvent for the currently used HFE7100. It was found that the Solstice-PF-based formulation performed similarly to the HFE7100-based formulation on copy paper, but when treating fingermarks deposited on brown paper and newspaper, Solstice-PF was superior to HFE7100 by developing up to 10% more marks graded 3 and 4 regardless of the ageing period. The results confirm that Solstice-PF can be used as an alternative carrier solvent for 1,2-indanedione formulations with good detection rates and lower costs., Competing Interests: Declaration of Competing Interest We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled, “Effect of carrier solvent in 1,2-indanedione formulation on the development of fingermarks on porous substrates”., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Background: Plantar pressure reduction with the use of cushioning materials play an important role in the clinical management of the diabetic foot. Previous studies in people without diabetes have shown that appropriate selection of the stiffness of such materials can significantly enhance their capacity to reduce pressure. However the significance of optimised cushioning has not been yet assessed for people with diabetic foot syndrome., Research Question: What is the potential benefit of using footwear with optimised cushioning, with regards to plantar pressure reduction, in people with diabetes and peripheral neuropathy?, Methods: Plantar pressure distribution was measured during walking for fifteen people with diabetic foot syndrome in a cohort observational study. The participants were asked to walk in the same type of footwear that was fitted with 3D-printed footbeds. These footbeds were used to change the stiffness of the entire sole-complex of the shoe; from very soft to very stiff. The stiffness that achieved the highest pressure reduction relative to a no-footbed condition was identified as the patient-specific optimum one., Results: The use of the patient-specific optimum stiffness reduced, on average, peak pressure by 46% (±14%). Using the same stiffness across all participants lowered the footwears' capacity for pressure reduction by at least nine percentile points (37% ± 17%); a statistically significant difference (paired samples t-test, t(13) = -3.733, p = 0.003, d = 0.997). Pearson correlation analysis indicated that patient-specific optimum stiffness was significantly correlated with the participants' body mass index (BMI), with stiffer materials needed for people with higher BMI (rs(14) = 0.609, p = 0.021)., Significance: This study offers the first quantitative evidence in support of optimising cushioning in diabetic footwear as part of standard clinical practice. Further research is needed to develop a clinically applicable method to help professionals working with diabetic feet identify the optimum cushioning stiffness on a patient-specific basis., Competing Interests: Declaration of Competing Interest Authors P. Chatzistergos and N. Chockalingam are named co-inventors in a relevant patent (International Application No. PCT/GB2018/052944)., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Solstice ® Performance Fluid (PF), trans-1-chloro-3,3,3-trifluoropropene, is presented as an alternative to HFE7100, methoxy-nonafluorobutane, as a carrier solvent in a number of chemical formulations used for the visualisation of latent fingermarks. The supply of HFE7100 may be at risk due to a recent European Union regulation to control global warming. Laboratory trials using split depletions and a pseudo-operational trial of 1000 porous samples have shown that Solstice ® PF is a viable alternative to HFE7100 for the chemical formulations of ninhydrin and 1,2-indanedione. Other preliminary trials have also indicated that Solstice ® PF can be used as a carrier solvent for the zinc toning of marks found using ninhydrin as well as the α-naphtholflavone fixative solution for iodine developed marks. Results from the pseudo-operational trial demonstrate that the number of marks detected by ninhydrin and 1,2-indanedione formulations for each carrier solvent is comparable. When compared to HFE7100, advantages of Solstice ® PF include a very low global warming potential and atmospheric lifetime in addition to a higher wetting index and lower costs. This study also provides a validation study that supports the potential replacement of DFO with 1,2-indanedione., (Copyright © 2017 Elsevier B.V. All rights reserved.)

There are numerous enhancement techniques (physical and chemical) which have been developed for the successful visualisation of latent fingermarks. Nonetheless, problems arise when latent fingermarks require enhancement on difficult surfaces such as human skin, food stuffs, fabric and animals. The ability to develop latent fingermarks on the surface of bird of prey feathers and that of their eggs was investigated. Red and green magnetic fluorescent powders proved to be most suitable on the surface of bird of prey feathers whereas black magnetic powder was the most suitable technique on the eggs. These powders produced the highest quality of visible ridge-detailed developments over a controlled period of time., (Copyright © 2014 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.)

Fingermarks, footwear marks, blood and semen are amongst the most commonly encountered types of evidence at crime scenes. Previous work has extensively investigated fingermark and blood enhancement techniques and a sequence developed to maximise evidence recovery; however, there is limited research as to the effect of these techniques on the subsequent detection of body fluids such as semen. In this study, seven fingermark and blood enhancement techniques (e.g. powder suspension, cyanoacrylate fuming and acid violet 17) were employed followed by the subsequent detection of semen/spermatozoa. Other variables included in the study were the use of two substrates (white ceramic tiles and grey laminate flooring), a depletion series and ageing periods of 1, 7, 14 and 28 days. The effect these techniques had on the subsequent detection of semen was assessed by visual and fluorescence examination followed by presumptive and confirmatory testing for semen and spermatozoa. The results found that protein stains (acid violet 17 and acid yellow 7) caused a loss in presumptive test reactivity; however, sperm heads were still observed using microscopic examination after extraction and staining. The use of black magnetic powder, Bluestar(®) Forensic Magnum luminol, Lumicyano™ 4% and cyanoacrylate fuming followed by basic yellow 40 staining did not hinder subsequent presumptive and confirmatory tests for semen and sperm heads. Powder suspension caused a loss in both presumptive test reactivity and sperm heads from the substrate. In general, the enhancement techniques resulted in the improved visualisation of the semen stains under white and violet/blue light. The results from this study aim to provide a strategy to maximise evidence recovery and improve efficiency in an integrated forensic approach., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)

The abilities of two natural products, genipin and lawsone, to enhance blood contaminated fingermarks on papers of various porosities and colour were investigated and compared to the routinely used amino acid reagents, ninhydrin and 1,8-diazafluoren-9-one (DFO). Fingermarks in blood were deposited as a split depletion series on various paper types and colours for ageing periods of 6 weeks, 4 weeks, 2 weeks and 1 week before enhancement. The developed marks were observed under different lighting conditions, recorded and graded by way of attributing quantitative data to each series. Results indicated that while genipin showed some potential as a reagent for the enhancement of latent fingermarks, it displayed no suitability for the enhancement of fingermarks in blood on paper. Lawsone also failed to successfully enhance either type of fingermark. Upon comparison of the results with those of ninhydrin and DFO it was found that ninhydrin displayed the highest success rate of development of these marks., (Copyright © 2013 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.)

The potential for enhancement and recovery of latent fingerprints on a variety of foodstuffs has been investigated. In general, black magnetic powder and black powder suspensions appear to be the most successful enhancement techniques with a high number of ridge detail-developed prints over a selected time scale. Banana, apple and tomato surfaces showed enhancement of latent prints but potato and egg surfaces proved to be less successful., (Copyright © 2012 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.)