Neutralizing immunity in vaccine breakthrough infections from the SARS-CoV-2 Omicron and Delta variants.

Virus-like particle (VLP) and live virus assays were used to investigate neutralizing immunity against Delta and Omicron SARS-CoV-2 variants in 259 samples from 128 vaccinated individuals. Following Delta breakthrough infection, titers against WT rose 57-fold and 3.1-fold compared with uninfected boosted and unboosted individuals, respectively, versus only a 5.8-fold increase and 3.1-fold decrease for Omicron breakthrough infection. Among immunocompetent, unboosted patients, Delta breakthrough infections induced 10.8-fold higher titers against WT compared with Omicron (p = 0.037). Decreased antibody responses in Omicron breakthrough infections relative to Delta were potentially related to a higher proportion of asymptomatic or mild breakthrough infections (55.0% versus 28.6%, respectively), which exhibited 12.3-fold lower titers against WT compared with moderate to severe infections (p = 0.020). Following either Delta or Omicron breakthrough infection, limited variant-specific cross-neutralizing immunity was observed. These results suggest that Omicron breakthrough infections are less immunogenic than Delta, thus providing reduced protection against reinfection or infection from future variants.

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/µL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant.

We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.

Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination.

SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals1,2. The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.

Nuclear accumulation of host transcripts during Zika Virus Infection.

Zika virus (ZIKV) infects fetal neural progenitor cells (NPCs) causing severe neurodevelopmental disorders in utero. Multiple pathways involved in normal brain development are dysfunctional in infected NPCs but how ZIKV centrally reprograms these pathways remains unknown. Here we show that ZIKV infection disrupts subcellular partitioning of host transcripts critical for neurodevelopment in NPCs and functionally link this process to the up-frameshift protein 1 (UPF1). UPF1 is an RNA-binding protein known to regulate decay of cellular and viral RNAs and is less expressed in ZIKV-infected cells. Using infrared crosslinking immunoprecipitation and RNA sequencing (irCLIP-Seq), we show that a subset of mRNAs loses UPF1 binding in ZIKV-infected NPCs, consistent with UPF1's diminished expression. UPF1 target transcripts, however, are not altered in abundance but in subcellular localization, with mRNAs accumulating in the nucleus of infected or UPF1 knockdown cells. This leads to diminished protein expression of FREM2, a protein required for maintenance of NPC identity. Our results newly link UPF1 to the regulation of mRNA transport in NPCs, a process perturbed during ZIKV infection.

Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant contains extensive sequence changes relative to the earlier-arising B.1, B.1.1, and Delta SARS-CoV-2 variants that have unknown effects on viral infectivity and response to existing vaccines. Using SARS-CoV-2 virus-like particles (VLPs), we examined mutations in all four structural proteins and found that Omicron and Delta showed 4.6-fold higher luciferase delivery overall relative to the ancestral B.1 lineage, a property conferred mostly by enhancements in the S and N proteins, while mutations in M and E were mostly detrimental to assembly. Thirty-eight antisera samples from individuals vaccinated with Pfizer/BioNTech, Moderna, or Johnson & Johnson vaccines and convalescent sera from unvaccinated COVID-19 survivors had 15-fold lower efficacy to prevent cell transduction by VLPs containing the Omicron mutations relative to the ancestral B.1 spike protein. A third dose of Pfizer vaccine elicited substantially higher neutralization titers against Omicron, resulting in detectable neutralizing antibodies in eight out of eight subjects compared to one out of eight preboosting. Furthermore, the monoclonal antibody therapeutics casirivimab and imdevimab had robust neutralization activity against B.1 and Delta VLPs but no detectable neutralization of Omicron VLPs, while newly authorized bebtelovimab maintained robust neutralization across variants. Our results suggest that Omicron has similar assembly efficiency and cell entry compared to Delta and that its rapid spread is due mostly to reduced neutralization in sera from previously vaccinated subjects. In addition, most currently available monoclonal antibodies will not be useful in treating Omicron-infected patients with the exception of bebtelovimab.

Tropism of SARS-CoV-2 for human cortical astrocytes.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) readily infects a variety of cell types impacting the function of vital organ systems, with particularly severe impact on respiratory function. Neurological symptoms, which range in severity, accompany as many as one-third of COVID-19 cases, indicating a potential vulnerability of neural cell types. To assess whether human cortical cells can be directly infected by SARS-CoV-2, we utilized stem-cell-derived cortical organoids as well as primary human cortical tissue, both from developmental and adult stages. We find significant and predominant infection in cortical astrocytes in both primary tissue and organoid cultures, with minimal infection of other cortical populations. Infected and bystander astrocytes have a corresponding increase in inflammatory gene expression, reactivity characteristics, increased cytokine and growth factor signaling, and cellular stress. Although human cortical cells, particularly astrocytes, have no observable ACE2 expression, we find high levels of coronavirus coreceptors in infected astrocytes, including CD147 and DPP4. Decreasing coreceptor abundance and activity reduces overall infection rate, and increasing expression is sufficient to promote infection. Thus, we find tropism of SARS-CoV-2 for human astrocytes resulting in inflammatory gliosis-type injury that is dependent on coronavirus coreceptors.

Changes in high-order interaction measures of synergy and redundancy during non-ordinary states of consciousness induced by meditation, hypnosis, and auto-induced cognitive trance.

High-order interactions are required across brain regions to accomplish specific cognitive functions. These functional interdependencies are reflected by synergistic information that can be obtained by combining the information from all the sources considered and redundant information (i.e., common information provided by all the sources). However, electroencephalogram (EEG) functional connectivity is limited to pairwise interactions thereby precluding the estimation of high-order interactions. In this multicentric study, we used measures of synergistic and redundant information to study in parallel the high-order interactions between five EEG electrodes during three non-ordinary states of consciousness (NSCs): Rajyoga meditation (RM), hypnosis, and auto-induced cognitive trance (AICT). We analyzed EEG data from 22 long-term Rajyoga meditators, nine volunteers undergoing hypnosis, and 21 practitioners of AICT. We here report the within-group changes in synergy and redundancy for each NSC in comparison with their respective baseline. During RM, synergy increased at the whole brain level in the delta and theta bands. Redundancy decreased in frontal, right central, and posterior electrodes in delta, and frontal, central, and posterior electrodes in beta1 and beta2 bands. During hypnosis, synergy decreased in mid-frontal, temporal, and mid-centro-parietal electrodes in the delta band. The decrease was also observed in the beta2 band in the left frontal and right parietal electrodes. During AICT, synergy decreased in delta and theta bands in left-frontal, right-frontocentral, and posterior electrodes. The decrease was also observed at the whole brain level in the alpha band. However, redundancy changes during hypnosis and AICT were not significant. The subjective reports of absorption and dissociation during hypnosis and AICT, as well as the mystical experience questionnaires during AICT, showed no correlation with the high-order measures. The proposed study is the first exploratory attempt to utilize the concepts of synergy and redundancy in NSCs. The differences in synergy and redundancy during different NSCs warrant further studies to relate the extracted measures with the phenomenology of the NSCs.

Simultaneous mapping of cathodoluminescence spectra and backscatter diffraction patterns in a scanning electron microscope.

Electron backscatter diffraction and cathodoluminescence are complementary scanning electron microscopy modes widely used in the characterisation of semiconductor films, respectively revealing the strain state of a crystalline material and the effect of this strain on the light emission from the sample. Conflicting beam, sample and detector geometries have meant it is not generally possible to acquire the two signals together during the same scan. Here, we present a method of achieving this simultaneous acquisition, by collecting the light emission through a transparent sample substrate. We apply this combination of techniques to investigate the strain field and resultant emission wavelength variation in a deep-ultraviolet micro-LED. For such compatible samples, this approach has the benefits of avoiding image alignment issues and minimising beam damage effects.

Evaluation of selected tropical marine microalgal cultures for use in biophotovoltaic platforms.

In this study, the bioelectrical power generation potential of four tropical marine microalgal strains native to Malaysia was investigated using BPV platforms. Chlorella UMACC 258 produced the highest power density (0.108 mW m-2), followed by Halamphora subtropica UMACC 370 (0.090 mW m-2), Synechococcus UMACC 371 (0.065 mW m-2) and Parachlorella UMACC 245 (0.017 mW m-2). The chlorophyll-a (chl-a) content was examined to have a linear positive relationship with the power density (p < 0.05). The photosynthetic performance of strains was studied using the pulse-amplitude modulation (PAM) fluorometer; parameters measured include the following: maximum quantum efficiency (Fv/Fm), alpha (α), maximum relative electron transport rate (rETRmax), photo-adaptive index (Ek) and non-photochemical quenching (NPQ). The Fv/Fm values of all strains, except Synechococcus UMACC 371, ranged between 0.37 and 0.50 during exponential and stationary growth phases, suggesting their general health during those periods. The low Fv/Fm value of Synechococcus UMACC 371 was possibly caused by the presence of background fluorescence from phycobilisomes or phycobiliproteins. Electrochemical studies via cyclic voltammetry (CV) suggest the presence of electrochemically active proteins on the cellular surface of strains on the carbon anode of the BPV platform, while morphological studies via field emission scanning electron microscope (FESEM) imaging verify the biocompatibility of the biofilms on the carbon anode. KEY POINTS: • Maximum power output of 0.108 mW m-2 is recorded by Chlorella UMACC 258 • There is a positive correlation between chl-a content and power output • Proven biocompatibility between biofilms and carbon anode sans exogenous mediators.

Microbiota and Gut-Liver Axis: An Unbreakable Bond?

The gut microbiota, amounting to approximately 100 trillion (1014) microbes represents a genetic repertoire that is bigger than the human genome itself. Evidence on bidirectional interplay between human and microbial genes is mounting. Microbiota probably play vital roles in diverse aspects of normal human metabolism, such as digestion, immune modulation, and gut endocrine function, as well as in the genesis and progression of many human diseases. Indeed, the gut microbiota has been most closely linked to various chronic ailments affecting the liver, although concrete scientific data are sparse. In this narrative review, we initially discuss the basic epidemiology of gut microbiota and the factors influencing their initial formation in the gut. Subsequently, we delve into the gut-liver axis and the evidence regarding the link between gut microbiota and the genesis or progression of various liver diseases. Finally, we summarise the recent research on plausible ways to modulate the gut microbiota to alter the natural history of liver disease.

Safety Assessment of Ultra High Dilutions of Camphora officinarum: A Preclinical Investigation.

Background: Camphora officinarum (CO) is a commonly used homeopathic remedy for treating colds, collapse, and recurrent eruptive illnesses. Objective: Due to the non-availability of safety data on CO, the current study intended to determine the oral toxicity of CO in its ethanol-potentized dilutions 6C, 30C, and 200C in Wistar albino rats as per OECD guidelines. Materials and methods: A single oral dose of CO-6C, 30C, and 200C (2000 µl/kg) was administered, and the animals were monitored for behavior and mortality for up to 14 days in an acute toxicity study. In the subacute study, the effects of daily oral administration of CO-6C, 30C, and 200C (200 µl/kg) for 28 days were observed for clinical signs, change in body weight, and mortality. Hematological, biochemical, and histopathological analyses were assessed and organ weights were determined. Results: Results indicate no mortality of CO in its potencies in the acute toxicity study and was found to be safe at 2000 µl/kg dosage in the subacute toxicity study. CO (200 µl/kg/day) did not show any signs of toxicity in the hematological, biochemical, and histopathological analyses, along with organ weights. Conclusion: In conclusion, the findings suggest that CO in potencies of 6C, 30C, and 200C is safe up to a single oral dose of 2000 µl/kg body weight, and the No Observed Adverse Effect Level (NOAEL) was determined to be greater than 200 µl/kg/day.

Characterizing genetic diversity of Sclerotium rolfsii isolates by biomapping of mycelial compatibility groupings and multilocus sequence analysis.

Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing targeted strategies for disease management in affected crops. In our study, a comprehensive genetic analysis was conducted on 50 isolates of S. rolfsii, collected from various geographic regions and host plants. Two specific genes, TEF1α and RPB2, were utilized to assess the genetic diversity and relationships among these isolates. Notably, out of 1225 pairings examined, only 154 exhibited a compatible reaction, while the majority displayed antagonistic reactions, resulting in the formation of a barrier zone. The isolates were grouped into 10 distinct MCGs. These MCGs were further characterized using genetic sequencing. TEF1α sequences distinguished the isolates into 17 distinct clusters, and RPB2 sequences classified them into 20 clusters. Some MCGs shared identical gene sequences within each gene, while others exhibited unique sequences. Intriguingly, when both TEF1α and RPB2 sequences were combined, all 10 MCGs were effectively differentiated, even those that appeared identical with single-gene analysis. This combined approach provided a comprehensive understanding of the genetic diversity and relationships among the S. rolfsii isolates, allowing for precise discrimination between different MCGs. The results shed light on the population structure and genetic variability within this plant pathogenic fungus, providing valuable insights for disease management and control strategies. This study highlights the significance of comprehending the varied virulence characteristics within S. rolfsii isolates, categorizing them into specific virulence groups based on disease severity index (DSI) values. The association with MCGs provides additional insights into the genetic underpinnings of virulence in this pathogen. Furthermore, the identification of geographical patterns in virulence implies the influence of region-specific factors, with potential implications for disease control and crop protection strategies.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [G. M. Sandeep] Last name [Kumar]. Author 2 Given name: [Praveen Kumar] Last name [Singh]. Also, kindly confirm the details in the metadata are correct.I confirm that the given names are accurate and presented in the correct sequence.

Peripheral nerve blocks for analgesia following cesarean delivery A narrative review.

Spinal and epidural blocks are commonly employed for pain relief during and following cesarean section. Intrathecal morphine (ITM) has been the gold standard for the same for many years. In recent times, many peripheral nerve blocks (PNBs) have been tried for postoperative analgesia following cesarean delivery (PACD). This article has reviewed the common PNBs used for PACD. The role of PNBs along with ITM has been studied and the current best strategy for PACD has also been explored. Currently, Ilio-inguinal nerve and anterior transversus abdominis plane block in conjunction with intrathecal morphine have been found to be the most effective strategy, providing lower rest pain at 6 hours as compared to ITM alone. In patients not receiving intrathecal morphine, recommended PNBs are lateral transversus abdominis plane block, single shot local anesthetic wound infiltration, or continuous wound infiltration with catheter below rectus fascia. PNBs are recommended for PACD. They have an opioid-sparing effect and are devoid of adverse effects associated with central neuraxial blocks such as hypotension, bradycardia, and urine retention. However, caution must be observed with PNBs for possible local anesthetic toxicity due to the large volumes of drug required.

Late endosomal/lysosomal accumulation of a neurotransmitter receptor in a cellular model of Smith-Lemli-Opitz syndrome.

Smith-Lemli-Opitz syndrome (SLOS) is a congenital and developmental malformation syndrome associated with defective cholesterol biosynthesis. It is characterized by accumulation of 7-dehydrocholesterol (the immediate biosynthetic precursor of cholesterol in the Kandutsch-Russell pathway) and an altered cholesterol to total sterol ratio. Because SLOS is associated with neurological malfunction, exploring the function and trafficking of neuronal receptors and their interaction with membrane lipids under these conditions assume significance. In this work, we generated a cellular model of SLOS in HEK-293 cells stably expressing the human serotonin1A receptor (an important neurotransmitter G-protein coupled receptor) using AY 9944, an inhibitor for the enzyme 3ß-hydroxy-steroid-∆7 -reductase (7-DHCR). Using a quantitative flow cytometry based assay, we show that the plasma membrane population of serotonin1A receptors was considerably reduced under these conditions without any change in total cellular expression of the receptor. Interestingly, the receptors were trafficked to sterol-enriched LysoTracker positive compartments, which accumulated under these conditions. To the best of our knowledge, our results constitute one of the first reports demonstrating intracellular accumulation and misregulated traffic of a neurotransmitter GPCR in SLOS-like conditions. We believe these results assume relevance in our overall understanding of the molecular basis underlying the functional relevance of neurotransmitter receptors in SLOS.

Opto-thermoelectric trapping of fluorescent nanodiamonds on plasmonic nanostructures.

Deterministic optical manipulation of fluorescent nanodiamonds (FNDs) in fluids has emerged as an experimental challenge in multimodal biological imaging. Designing and developing nano-optical trapping strategies to serve this purpose is an important task. In this Letter, we show how chemically prepared gold nanoparticles and silver nanowires can facilitate an opto-thermoelectric force to trap individual entities of FNDs using a long working distance lens, low power-density illumination (532-nm laser, 12 µW/µm2). Our trapping configuration combines the thermoplasmonic fields generated by individual plasmonic nanoparticles and the opto-thermoelectric effect facilitated by the surfactant to realize a nano-optical trap down to a single FND that is 120 nm in diameter. We use the same trapping excitation source to capture the spectral signatures of single FNDs and track their position. By tracking the FND, we observe the differences in the dynamics of the FND around different plasmonic structures. We envisage that our drop-casting platform can be extrapolated to perform targeted, low-power trapping, manipulation, and multimodal imaging of FNDs inside biological systems such as cells.

Stillbirth undercount in the sample registration system and national family health survey, India.

Objective: To assess the extent of under-reporting of stillbirths in India by comparing stillbirth and neonatal mortality rates from two national data sources and to review possible reasons for undercounting of stillbirths. Methods: We extracted data on stillbirth and neonatal mortality rates from the annual reports for 2016-2020 of the sample registration system, the Indian government's main source of vital statistics. We compared the data with estimates of stillbirth and neonatal mortality rates from the fifth round of the Indian national family health survey covering events from 2016-2021. We reviewed the questionnaires and manuals from both surveys and compared the sample registration system's verbal autopsy tool with other international tools. Findings: The stillbirth rate for India from the national family health survey (9.7 stillbirths per 1000 births; 95% confidence interval: 9.2-10.1) was 2.6 times higher than the average rate reported in the sample registration system over 2016-2020 (3.8 stillbirths per 1000 births). However, neonatal mortality rates in the two data sources were similar. We identified issues with the definition of stillbirth, documentation of gestation period, and categorization of miscarriages and abortions that could result in undercounting stillbirths in the sample registration system. In the national family health survey only one adverse pregnancy outcome is documented, irrespective of the number of adverse pregnancy outcomes in the given period. Conclusion: For India to attain its 2030 target of single-digit stillbirth rate and to monitor actions to end preventable stillbirths, efforts are needed to improve the documentation of stillbirths in its data collection systems.

Accelerated RNA detection using tandem CRISPR nucleases.

Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (Ct) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.

Improving the optoelectronic properties of monolayer MoS2field effect transistor through dielectric engineering.

The reduced dielectric screening in atomically thin two-dimensional materials makes them very sensitive to the surrounding environment, which can be modulated to tune their optoelectronic properties. In this study, we significantly improved the optoelectronic properties of monolayer MoS2by varying the surrounding environment using different liquid dielectrics, each with a specific dielectric constant ranging from 1.89 to 18. Liquid mediums offer the possibility of environment tunability on the same device. For a back-gated field effect transistor, the field effect mobility exhibited more than two-order enhancement when exposed to a high dielectric constant medium. Further investigation into the effect of the dielectric environment on the optoelectronic properties demonstrated a variation in photoresponse relaxation time with the dielectric medium. The rise and decay times were observed to increase and decrease, respectively, with an increase in the dielectric constant of the medium. These results can be attributed to the dielectric screening provided by the surrounding medium, which strongly modifies the charged impurity scattering, the band gap, and defect levels of monolayer MoS2. These findings have important implications for the design of biological and chemical sensors, particularly those operating in a liquid environment. By leveraging the tunability of the dielectric medium, we can optimize the performance of such sensors and enhance their detection capabilities.

Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts.

The replication of SARS-CoV-2 and other coronaviruses depends on transcription of negative-sense RNA intermediates that serve as the templates for the synthesis of positive-sense genomic RNA (gRNA) and multiple different subgenomic mRNAs (sgRNAs) encompassing fragments arising from discontinuous transcription. Recent studies have aimed to characterize the expression of subgenomic SARS-CoV-2 transcripts in order to investigate their clinical significance. Here, we describe a novel panel of reverse transcription droplet digital PCR (RT-ddPCR) assays designed to specifically quantify multiple different subgenomic SARS-CoV-2 transcripts and distinguish them from transcripts that do not arise from discontinuous transcription at each locus. These assays can be applied to samples from SARS-CoV-2 infected patients to better understand the regulation of SARS-CoV-2 transcription and how different sgRNAs may contribute to viral pathogenesis and clinical disease severity.