The Need for Speed: How Operation Warp Speed Shifted the Pharma Industry

During the United States government's push for vaccine development and manufacturing (dubbed Operation Warp Speed)-and partly because of it-capital projects struggled to acquire adequate construction materials and equipment. Additionally, video production equipment was leveraged to offer an overview of progress in real time and even perform equipment testing. [...]startups are competing for a few outsourced manufacturing slots. The main solution to limited manufacturing opportunities is to work with a consulting partner who can help them accelerate the process of finding, prequalifying, and negotiating with appropriate and available contract manufacturers.

Synthesis and Analysis of the SARS-CoV-2 ORF7a Accessory Protein Transmembrane Domain and Determination of the Oligomerization State

The ongoing SARS-CoV-2 pandemic continues to sicken millions worldwide and fundamentally change the way people interact with each other. In order to better characterize the SARS-CoV-2 virus and potentially develop methods of inhibition for further spread of the disease, this research project focused on synthesizing and characterizing the trans-membrane region of the accessory protein ORF7a. ORF7a has been implicated in proper viral assembly, leading to the idea that inhibition of this protein could prevent viral copies from being produced and halt the spread of the virus. The goal of this project was to determine the oligomerization state of the protein through a fluorescence assay in order to better understand the quaternary structure of the ORF7a complex and how it folds. The fluorescence assay is performed using three different samples of the synthesized peptide: one labeled with a TAMRA fluorophore, one labeled with a NBD fluorophore, and the last is unlabeled. After determining the oligomerization state of the protein, potential inhibitors could be synthesized and tested for their efficacy at inhibiting the function of the protein. Further applications of these inhibitors on other viruses can be explored due to the highly conserved nature of transmembrane domains across multiple viral families. Synthesis of the protein was done using a Solid Phase Peptide Synthesis (SPPS) technique and multiple batches of all three samples of peptide have been generated. Characterization and purification were done using High Performance Liquid Chromatography (HPLC) as well as Liquid Chromatography Mass Spectrometry (LCMS). Current research focuses on the purification and quantification of purified ORF7a oligopeptide for implementation of the fluorescence assay. -Hampden-Sydney College Office of Undergraduate Research.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Surveillance of RNase P, PMMoV, and CrAssphage in wastewater as indicators of human fecal concentration across urban sewer neighborhoods, Kentucky.

Wastewater surveillance has been widely used as a supplemental method to track the community infection levels of severe acute respiratory syndrome coronavirus 2. A gap exists in standardized reporting for fecal indicator concentrations, which can be used to calibrate the primary outcome concentrations from wastewater monitoring for use in epidemiological models. To address this, measurements of fecal indicator concentration among wastewater samples collected from sewers and treatment centers in four counties of Kentucky (N = 650) were examined. Results from the untransformed wastewater data over 4 months of sampling indicated that the fecal indicator concentration of human ribonuclease P (RNase P) ranged from 5.1 × 101 to 1.15 × 106 copies/ml, pepper mild mottle virus (PMMoV) ranged from 7.23 × 103 to 3.53 × 107 copies/ml, and cross-assembly phage (CrAssphage) ranged from 9.69 × 103 to 1.85 × 108 copies/ml. The results showed both regional and temporal variability. If fecal indicators are used as normalization factors, knowing the daily sewer system flow of the sample location may matter more than rainfall. RNase P, while it may be suitable as an internal amplification and sample adequacy control, has less utility than PMMoV and CrAssphage as a fecal indicator in wastewater samples when working at different sizes of catchment area. The choice of fecal indicator will impact the results of surveillance studies using this indicator to represent fecal load. Our results contribute broadly to an applicable standard normalization factor and assist in interpreting wastewater data in epidemiological modeling and monitoring.

Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.

Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly.

SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.

Development of a spin-label model system for investigation of protein oligomerization states

The transmembrane domains of viral proteins are highly conserved and crucial to normal viral function. Oligomeric transmembrane domains present novel opportunities for drug development, as their disruption can prevent the assembly of the virus. The Reichart lab is particularly interested in developing retro-inverso peptide inhibitors. Retro-inverso peptides are peptides using D-amino acids mirroring a region of target protein, which allows the peptide to inhibit viral assembly, but they are also significantly less likely to be catabolized by natural metabolic or immunologic processes. The efficacy of these inhibitors is governed largely by the extent to which they mirror the target protein, making highly conserved regions, such as transmembrane domains, ideal target regions for these inhibitors. The primary technique in the literature for the investigation of oligomerization states uses fluorescence spectroscopy. We are now working on developing a novel alternative system to evaluate protein oligomerization using spin-labeled peptides that are directly incorporated into the peptide sequence. Direct incorporation of the spin-label into the peptide sequence is a more powerful technique than the standard procedures used in the literature. In particular, the ability to incorporate spin labels in various positions within the protein can give novel insights into the relative depth of the protein within a membrane, which is very difficult to study using other techniques and not possible using the fluorescence technique. The transmembrane domains of proteins with known and well-characterized monomer and trimer standard oligomerization states were synthesized using an Fmoc Solid- Phase Peptide Synthesis (SPPS) procedure incorporating an Fmoc-2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, (Fmoc-TOAC) instead of an alanine. Direct incorporation of stable N-oxide spin labels, which can be contrasted to labeling cysteine residues after the protein synthesis, has been used for the investigation of the secondary structure of proteins for decades, but the application of this spin labeling technique to study the oligomerization states of transmembrane domains of proteins is an understudied application. The products of SPPS were analyzed using a Liquid Chromatography Mass Spectroscopy instrument and purified using High Performance Liquid Chromatography. The spin-label was then deprotected and evaluated using Electron Spin Resonance (ESR) Spectroscopy. There are two primary future directions following this research project: first, the generation of viral proteins with spin labels incorporated in different positions to determine the relative depth of each position within the membrane;second, the incorporation of spin labels into SARS-CoV- 2 proteins to develop a model for in vitro evaluation of retro-inverso peptide assembly inhibitors. -Hampden-Sydney College Office of Undergraduate Research.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

TARGETING THE HOST-VIRUS INTERFACE TO BLOCK SARS-CoV-2 ASSEMBLY IN AIRWAY CELLS

Background: The rapid emergence of the SARS-CoV-2 Omicron variant that evades many therapies illustrates the need for antiviral treatments with high genetic barriers to resistance. The small molecule PAV-104, identified through a moderate-throughput screen involving cell-free protein synthesis, was recently shown to target a subset of host protein assembly machinery in a manner specific to viral assembly with minimal host toxicity. The chemotype shows broad activity against respiratory viral pathogens, including Orthomyxoviridae, Paramyxoviridae, Adenoviridae, Herpesviridae, and Picornaviridae, with low susceptibility to evolutionary escape. Here, we investigated the capacity of PAV-104 to inhibit SARS-CoV-2 replication in human airway epithelial cells (AECs). Method(s): Dose-dependent cytotoxicity of PAV-104 in Calu-3 cells was determined by MTT assay. Calu-3 cells were infected with SARS-CoV-2 isolate USA-WA1/2020 (MOI=0.01). Primary AECs were isolated from healthy donor lung transplant tissue, cultured at air liquid interface (ALI), and infected with SARS-CoV-2 Gamma, Delta, and Omicron variants (MOI=0.1). SARS-CoV-2 replication was assessed by RT-PCR quantitation of the N gene, immunofluorescence assay (IFA) of nucleocapsid (N) protein, and titration of supernatant (TCID50). Transient co-expression of four SARS-CoV-2 structural proteins (N, M, S, E) to produce virus-like particles (VLPs) was used to study the effect of PAV-104 on viral assembly. Drug resin affinity chromatography was performed to study the interaction between PAV-104 and N. Glycerol gradient sedimentation was used to assess N oligomerization. Total RNA-seq and the REACTOME database were used to evaluate PAV-104 effects on the host transcriptome. Result(s): PAV-104 reached 50% cytotoxicity in Calu-3 cells at 3732 nM (Fig.1A). 50 nM PAV-104 inhibited >99% of SARS-CoV-2 infection in Calu-3 cells (p< 0.01) and in primary AECs (p< 0.01) (Fig.1B-E). PAV-104 specifically inhibited SARS-CoV-2 post entry, and suppressed production of SARS-CoV-2 VLPs without affecting viral protein synthesis. PAV-104 interacted with SARS-CoV-2 N and interfered with N oligomerization. Transcriptome analysis revealed that PAV-104 treatment reversed SARS-CoV-2 induction of the interferon and maturation of nucleoprotein signaling pathways. Conclusion(s): PAV-104 is a pan-respiratory virus small molecule inhibitor with promising activity against SARS-CoV-2 in human airway epithelial cells that should be explored in animal models and clinical studies.

Entangling of Peptide Nanofibers Reduces the Invasiveness of SARS-CoV-2.

The viral spike (S) protein on the surface of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells, facilitating its entry and infection. Here, functionalized nanofibers targeting the S protein with peptide sequences of IRQFFKK, WVHFYHK and NSGGSVH, which are screened from a high-throughput one-bead one-compound screening strategy, are designed and prepared. The flexible nanofibers support multiple binding sites and efficiently entangle SARS-CoV-2, forming a nanofibrous network that blocks the interaction between the S protein of SARS-CoV-2 and the ACE2 on host cells, and efficiently reduce the invasiveness of SARS-CoV-2. In summary, nanofibers entangling represents a smart nanomedicine for the prevention of SARS-CoV-2.

A risk-averse two-stage stochastic programming model for a joint multi-item capacitated line balancing and lot-sizing problem

In this paper, a comprehensive production planning problem under uncertain demand is investigated. The problem intertwines two NP-hard optimization problems: an assembly line balancing problem and a capacitated lot-sizing problem. The problem is modelled as a two-stage stochastic program assuming a risk-averse decision maker. Efficient solution procedures are proposed for tackling the problem. A case study related to mask production is presented. Several insights are provided stemming from the COVID-19 pandemic. Finally, the results of a series of computational tests are reported. (c) 2021 Elsevier B.V. All rights reserved.

The Right to Freedom of Peaceful Assembly during the Covid-19 Pandemic in the Light of Echr Standards

The COVID-19 crisis confronted states with the challenge of finding an immediate balance between public health measures and the principles of the rule of law. The rapid spread of the virus associated with the severe consequences on human health and life required prompt action, without the necessary scientific evidence to assess the effectiveness of the measures taken. Being faced with such a situation, numerous countries opted for drastic measures, like lock down and the restriction of some fundamental human rights and freedoms. This paper analyses the freedom of peaceful assembly during the COVID-19 pandemic in Albania, addressing the research question of whether and to what extent the response of the Albanian government to the COVID-19 pandemic was in compliance with the European Convention of Human Rights (ECHR). In this attempt, it will briefly introduce the measures taken by the Albanian government in the face of the situation and their impact. Following, it will focus on the recent decision of the Constitutional Court of Albania (D-11/21) in relation to the constitutionality of Order 633/2020 of the Ministry of Health and Social Protection which restricted the right of assembly. It will also analyze the extensively-discussed Order 633/2020 in the light of the ECHR and EU standards. The paper concludes that the measures taken by the Ministry of Health and Social Protection of Albanian lacked clarity on ratio legis and most importantly, information on how these measures would be implemented and to what extent they would restrict human rights.

Challenges and Prospects for the Intergovernmental Negotiations to Develop a New Instrument on Pandemic Prevention, Preparedness, and Response.

As Member States of the World Health Organization (WHO) meet in an International Negotiating Body (INB) to negotiate a legally binding agreement on pandemic prevention, preparedness, and response for submission to the 77th World Health Assembly in May 2024, this column reflects on creative but pragmatic and complementary means that could be employed in the short timeframe allotted for this important global health law negotiation.

Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance

Featured ApplicationFast long-read assembly to reference in AWS cloud FPGA instances.In genomic analysis, long reads are an emerging type of data processed by assembly algorithms to recover the complete genome sample. They are, on average, one or two orders of magnitude longer than short reads from the previous generation, which provides important advantages in information quality. However, longer sequences bring new challenges to computer processing, undermining the performance of assembly algorithms developed for short reads. This issue is amplified by the exponential growth of genetic data generation and by the slowdown of transistor technology progress, illustrated by Moore's Law. Minimap2 is the current state-of-the-art long-read assembler and takes dozens of CPU hours to assemble a human genome with clinical standard coverage. One of its bottlenecks, the alignment stage, has not been successfully accelerated on FPGAs in the literature. GACT-X is an alignment algorithm developed for FPGA implementation, suitable for any size input sequence. In this work, GACT-X was adapted to work as the aligner of Minimap2, and these are integrated and implemented in an FPGA cloud platform. The measurements for accuracy and speed-up are presented for three different datasets in different combinations of numbers of kernels and threads. The integrated solution's performance limitations due to data transfer are also analyzed and discussed.

Russia's Utilization of the COVID-19 Pandemic: Lockdowns, Re-Sovereignization, and Disengagement from the West

This article discusses the challenges that the COVID-19 pandemic poses to the current concepts of globalization, universality of human rights, and the rules-based international order. This article discusses how Russia has used the COVID-19 pandemic to accelerate its move away from Western ideas and institutions so as to solidify the power of its executive branch. In particular, this article examines the Russian Constitutional Court in its dealings with both the 2020 Russian constitutional amendments and the government's lockdown measures. This article concludes that the Russian Constitutional Court-which is supposed to serve as a key guarantor of fundamental rights of citizens against the machinery of the state-is becoming increasingly politicized, which threatens the Court's independence. Russia's desire to strengthen the power of the executive branch, to retreat further into traditional notions of sovereignty, and to move away from international norms and institutions, is not unique. The COVID-19 pandemic has served as a powerful catalyst in magnifying and intensifying the existing divisions in the current international order.

Tissue Engineering Challenges for Cultivated Meat to Meet the Real Demand of a Global Market.

Cultivated meat (CM) technology has the potential to disrupt the food industry-indeed, it is already an inevitable reality. This new technology is an alternative to solve the environmental, health and ethical issues associated with the demand for meat products. The global market longs for biotechnological improvements for the CM production chain. CM, also known as cultured, cell-based, lab-grown, in vitro or clean meat, is obtained through cellular agriculture, which is based on applying tissue engineering principles. In practice, it is first necessary to choose the best cell source and type, and then to furnish the necessary nutrients, growth factors and signalling molecules via cultivation media. This procedure occurs in a controlled environment that provides the surfaces necessary for anchor-dependent cells and offers microcarriers and scaffolds that favour the three-dimensional (3D) organisation of multiple cell types. In this review, we discuss relevant information to CM production, including the cultivation process, cell sources, medium requirements, the main obstacles to CM production (consumer acceptance, scalability, safety and reproducibility), the technological aspects of 3D models (biomaterials, microcarriers and scaffolds) and assembly methods (cell layering, spinning and 3D bioprinting). We also provide an outlook on the global CM market. Our review brings a broad overview of the CM field, providing an update for everyone interested in the topic, which is especially important because CM is a multidisciplinary technology.

QUASI-MILITANT DEMOCRACY AS A NEW FORM OF SACRED IN POLAND DURING THE CORONA CRISIS

This article aims to explore the political mythology created by the Polish government and its subservient organizations with an aim to legitimize quasi-militant democracy as a new form of sacred in the populist discourse during the pandemic. Drawing on theories of political myths and on intertextual qualitative document analysis, the research shows that the sacred appeared in political myths which proved to be an efficient means of gaining public support for all sorts of efforts that undermine democracy. The conspiracy myth established social divisions and produced effects along with the interrelated myths of the savior, unity, and the golden age. The government took on the role of a savior whose mission was to deliver Poles "the people" from the hostile "others" that put their lives and health at risk. Those who desire social and economic help and do not want to be excluded from the community, must submit to the yoke of the savior. The unity myth rested on the vision of Poles as the government's followers who exposed and reported transgressions for the good of the community. All the limitations to which Poles complied and the denunciatory actions they took were oriented towards the golden age of a strong state, providing social and economic security unique in the post-pandemic world.

Organizational actions to tackle distrust: Building Trust Italy

According to the Italian Code of Medical Deontology, mutual trust and mutual respect for values and rights are the care relationship foundation. To establish reciprocal trust and respect, the communication between care providers and patients must be skilled and appropriate, and the time devoted to communication must be considered time of care. But in Italy, in the last decades costs containment policy in the organizations of the National Health Service critically shortened the time available for care. Today, doctors and other healthcare professionals literally do not have the time to establish appropriate care relationships, and this causes a widespread and increasing distrust of patients and their families in the care system. During COVID-19 pandemic also vaccine hesitancy, defined by experts as a delay in acceptance or refusal of vaccination despite availability of vaccination services, was mainly due to a lack of confidence in care system and in scientific research. Slow Medicine ETS, an Italian proactive movement of healthcare professionals and citizens, following the example of the initiative 'Building Trust' recently activated by the ABIM Foundation in the USA, launched a national initiative aimed to promote and plan concrete actions to restore and consolidate people's trust in healthcare professionals and organizations, in researchers, in scientific and rational approach to knowledge and in its use for the improvement of health and quality of life. Slow Medicine ETS, still successfully leading and supporting the 'Choosing Wisely Italy' project, will be engaged in assembling the national network of the new project 'Building Trust Italy'.Copyright © the Author(s), 2022.

Practical Implementation of Lean Management Techniques and Ergonomic Consideration to Improve Manual Assembly Process During the COVID-19 Crisis

This research focused on the cycle time reduction of the automotive audio monitor base frame assembly process in a small electronic parts manufacturing company through the application of the Lean and ergonomics approaches. In recent years, the company has faced the problem of not being able to assemble products to meet customers' orders due to the need to lay off some skilled workers to survive during the COVID-19 crisis. This resulted in a severe loss in customer goodwill and confidence. The improvement process began with a review of the current assembly workflow as well as the detailed hand and arm movements of workers. Then, to determine the as-is operational procedure and average cycle time of the assembly process, a series of videos were recorded and playback in slow motion. Lean management techniques, such as 7 wastes and 5 Whys, were employed to identify the potential root causes of the problems. In addition, the ECRS (eliminate, combine, rearrange and simplify) techniques of Lean management in combination with the ergonomics principles were applied to modify the operational procedure and the postures and movements of the workers. The workspace and environmental conditions were also adjusted to enable more efficient workers' operations. The result demonstrated that such an approach could help reduce the cycle time of the assembly process to achieve the predefined target. © 2023, Chulalongkorn University, Faculty of Fine and Applied Arts. All rights reserved.

Dynamics of Microbial Community and Potential Microbial Pollutants in Shopping Malls.

Shopping malls offer various niches for microbial populations, potentially serving as sources and reservoirs for the spread of microorganisms of public health concern. However, knowledge about the microbiome and the distribution of human pathogens in malls is largely unknown. Here, we examine the microbial community dynamics and genotypes of potential pathogens from floor and escalator surfaces in shopping malls and adjacent road dusts and greenbelt soils. The distribution pattern of microbial communities is driven primarily by habitats and seasons. A significant enrichment of human-associated microbiota in the indoor environment indicates that human interactions with surfaces might be another strong driver for mall microbiomes. Neutral community models suggest that the microbial community assembly is strongly driven by stochastic processes. Distinct performances of microbial taxonomic signatures for environmental classifications indicate the consistent differences of microbial communities of different seasons/habitats and the strong anthropogenic effect on homogenizing microbial communities of shopping malls. Indoor environments harbored higher concentrations of human pathogens than outdoor samples, also carrying a high proportion of antimicrobial resistance-associated multidrug efflux genes and virulence genes. These findings enhanced the understanding of the microbiome in the built environment and the interactions between humans and the built environment, providing a basis for tracking biothreats and communicable diseases and developing sophisticated early warning systems. IMPORTANCE Shopping malls are distinct microbial environments which can facilitate a constant transmission of microorganisms of public health concern between humans and the built environment or between human and human. Despite extensive investigation of the natural environmental microbiome, no comprehensive profile of microbial ecology has been reported in malls. Characterizing microbial distribution, potential pathogens, and antimicrobial resistance will enhance our understanding of how these microbial communities are formed, maintained, and transferred and help establish a baseline for biosurveillance of potential public health threats in malls.

New Biocompatible Nanohydrogels of Predefined Sizes for Complexing Nucleic Acids.

The advent of protein expression using m-RNA applied lately for treating the COVID pandemic, and gene editing using CRISPR/Cas9 technology for introducing DNA sequences at a specific site in the genome, are milestones for the urgent need of developing new nucleic acid delivery systems with improved delivery properties especially for in vivo applications. We have designed, synthesized, and characterized novel cross-linked monodispersed nanohydrogels (NHG's) with well-defined sizes ranging between 50-400 nm. The synthesis exploits the formation of self-assemblies generated upon heating a thermo-responsive mixture of monomers. Self-assemblies are formed and polymerized at high temperatures resulting in NHGs with sizes that are predetermined by the sizes of the intermediate self-assemblies. The obtained NHGs were chemically reduced to lead particles with highly positive zeta potential and low cell toxicity. The NHGs form complexes with DNA, and at optimal charge ratio the size of the complexes is concomitant with the size of the NHG's. Thus, the DNA is fully embedded inside the NHGs. The new NHGs and their DNA complexes are devoid of cell toxicity which together with their tunned sizes, make them potential tools for gene delivery and foreign protein expression.

Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data.

The massive amount of genomic data appearing for SARS-CoV-2 since the beginning of the COVID-19 pandemic has challenged traditional methods for studying its dynamics. As a result, new methods such as Pangolin, which can scale to the millions of samples of SARS-CoV-2 currently available, have appeared. Such a tool is tailored to take as input assembled, aligned, and curated full-length sequences, such as those found in the GISAID database. As high-throughput sequencing technologies continue to advance, such assembly, alignment, and curation may become a bottleneck, creating a need for methods that can process raw sequencing reads directly. In this article, we propose Reads2Vec, an alignment-free embedding approach that can generate a fixed-length feature vector representation directly from the raw sequencing reads without requiring assembly. Furthermore, since such an embedding is a numerical representation, it may be applied to highly optimized classification and clustering algorithms. Experiments on simulated data show that our proposed embedding obtains better classification results and better clustering properties contrary to existing alignment-free baselines. In a study on real data, we show that alignment-free embeddings have better clustering properties than the Pangolin tool and that the spike region of the SARS-CoV-2 genome heavily informs the alignment-free clusterings, which is consistent with current biological knowledge of SARS-CoV-2.