Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections.

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Clinical features and outcome of COVID-19 positive children from a tertiary healthcare hospital in Karachi.

: As the coronavirus disease 2019 (COVID-19) pandemic continues to evolve, differences in epidemiological and clinical features among pediatrics have been noticed across different countries. We describe the spectrum of COVID-19 in pediatric patients treated in tertiary health care. We conducted a retrospective chart review of pediatric patients admitted to Indus Hospital & Health care network, Korangi campus, Karachi; from April 1st, 2020 to July 31st, 2020. A total of 141 COVID-19 cases were reported, males were 81 (57%) and the median age was 8 (0.3-17) years. Moderate and severe infections were noted in 36(26%), and 17(12%) children respectively. Fever (50%) was the most common clinical feature. The SF ratio less than 264 was significantly associated with severe disease (p < .05). Lab investigations that differed significantly across disease severity groups included IL-6 levels (p < .01) and Prothrombin time (p < .05). Majority of children were advised home isolation 89 (63%), 29 (20.5%) were admitted while mortality was observed in 10 (7%) children. No significant difference was observed between children with and without malignancy. Pre-existing comorbidities are significantly associated with COVID-19 infections among children. Reduced SF ratio, elevated Prothrombin time, and interleukin-6 levels are associated with greater disease severity.

Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing.

LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals. The limit of detection of LamPORE was 10 genome copies/µl of extracted RNA, which is above the limit achievable by RT-PCR, but was not associated with a significant reduction of sensitivity in clinical samples. Positive clinical specimens came mostly from patients with acute symptomatic infection, and among them, LamPORE had a diagnostic sensitivity of 99.1% (226/228; 95% confidence interval [CI], 96.9% to 99.9%). Among negative clinical specimens, including 153 with other respiratory pathogens detected, LamPORE had a diagnostic specificity of 99.6% (278/279; 98.0% to 100.0%). Overall, 1.4% (7/514; 0.5% to 2.9%) of samples produced an indeterminate result on first testing, and repeat LamPORE testing on the same RNA extract had a reproducibility of 96.8% (478/494; 94.8% to 98.1%). LamPORE has a similar performance as RT-PCR for the diagnosis of SARS-CoV-2 infection in symptomatic patients and offers a promising approach to high-throughput testing.

Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.

The COVID-19 Sequelae: A Cross-Sectional Evaluation of Post-recovery Symptoms and the Need for Rehabilitation of COVID-19 Survivors.

Background  As of January 19, 2021, around two million fatalities and 68 million recoveries from coronavirus disease 2019 (COVID-19) have been reported around the globe. The past pandemics of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) hint toward a risk of occurrence of "Long-COVID" syndrome, i.e., the persistence of post-discharge symptoms among COVID-19 survivors. With the scarcity of literature addressing post-COVID-19 manifestations and little regard for the stigma associated with this disease, survivors' rehabilitation remains widely neglected. The current study aims to assess the prevalence and characteristics of post-COVID-19 manifestations and their effect on the quality of life (QoL) of COVID-19 recovered individuals. We have also analyzed the relationship of time since the recovery of COVID-19 and its severity with the post-discharge symptoms. The stigma affiliated with the infection of SARS coronavirus-2 (SARS-CoV-2) has also been highlighted. Methodology A descriptive, cross-sectional, questionnaire-based study was conducted from September 2020 to December 2020 among 158 COVID-19 recovered patients, whose information was obtained from Dow Diagnostic Laboratory, Ojha Campus, Karachi, Pakistan. The questionnaire consisted of four sections: sociodemographic data, post-COVID-19 manifestations, questions relating to the stigma, and the QoL of the recovered COVID-19 patients. We used the EuroQol five-dimension five-level questionnaire to assess the QoL, while the modified BG Prasad Socioeconomic Classification updated for 2019 was employed to determine the socioeconomic status of the participants. Data were analyzed using SPSS version 24.0 (IBM Corp., Armonk, NY, USA). Data were presented in the form of frequencies and percentages. Results An overwhelming majority (94.9%) experienced at least one post-COVID-19 symptom, with fatigue (82.9%) being the most prevalent post-discharge manifestation. We observed a significant correlation of post-COVID-19 symptoms with gender, age, and time since recovery. COVID-19 severity was found to be significantly related to the five dimensions of the QoL. A significant difference in EuroQol Visual Analog Scale health score was observed between the participants with mild, moderate, and severe COVID-19 infection (p < 0.001). Besides, the associated stigma with SARS-CoV-2 infection was found to be more prevalent in the participants belonging to the upper class as compared to the other classes (p < 0.05). Nonetheless, we also observed a significant association of disease severity with post-COVID-19 manifestations and pre-existing comorbidities. Conclusions The long-COVID syndrome is similar to the post-discharge manifestations of the survivors of prior pandemics of SARS and MERS. Multi-disciplinary rehabilitation teams, healthcare workers, and the general population should recognize the need for systematic assessment of their recovery and further rehabilitation.

Roll-out of SARS-CoV-2 testing for healthcare workers at a large NHS Foundation Trust in the United Kingdom, March 2020.

Healthcare workers (HCW) are potentially at increased risk of infection with coronavirus disease (COVID-19) and may transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to vulnerable patients. We present results from staff testing at Sheffield Teaching Hospitals NHS Foundation Trust, United Kingdom. Between 16 and 29 March 2020, 1,533 symptomatic HCW were tested, of whom 282 (18%) were positive for SARS-CoV-2. Testing HCW is a crucial strategy to optimise staffing levels during this outbreak.