CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.The sequencing costs were funded by the COVID-19 Genomics UK (COG-UK) Consortium which is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute

Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.

The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.The sequencing costs were funded by the COVID-19 Genomics UK (COG-UK) Consortium which is supported by funding from the Medical Research Council (MRC) part of UK Research and Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

The role of obesity in the immune response during sepsis

Background/objectives: Sepsis is one of the most important causes of mortality in the developed world, where almost two thirds of the population suffer from obesity. Therefore, the coexistence of both conditions has become frequent in clinical practice and a growing number of clinical studies attempts to examine the potential effect of obesity on sepsis with controversial results up to now. The present study investigates how obesity influences the immune response of septic patients, by assessing the number and activation state of adipose tissue macrophages, serum and adipose tissue tumor necrosis factor-alpha (TNFα) levels and plasma oxidative stress markers.Subjects/methods: The study included 106 patients, divided into four groups (control n = 26, obesity n = 27, sepsis n = 27 and sepsis and obesity n = 26). The number of macrophages in subcutaneous and visceral adipose tissue (SAT and VAT) and their subtypes (M1 and M2) were defined with immunohistochemical staining techniques under light microscopy. TNFα mRNA levels were determined in SAT and VAT using real-time reverse transcription-PCR. Serum levels of TNFα were determined with sandwich enzyme-linked immunosorbent assay. Plasma oxidative stress was evaluated using selective biomarkers [thiobarbituric acid-reactive substances (TBARS), protein carbonyls and total antioxidant capacity (TAC)].Results: Sepsis increased the total number of macrophages and their M2 subtype in VAT, whereas obesity did not seem to affect the concentration of macrophages in fat. Obesity increased TNFα mRNA levels (P < 0.05) in VAT as well as the plasma TBARS (P < 0.001) and protein carbonyls (P < 0.001) in septic patients. The plasma TAC levels were decreased and the serum TNFα levels were increased in sepsis although they were not influenced by obesity.Conclusions: Obesity is associated with elevated TNFα adipose tissue production and increased oxidative stress biomarkers, promoting the proinflammatory response in septic patients.Σκοπός: Η σήψη αποτελεί μια από τις σημαντικότερες αιτίες νοσηλείας και θνησιμότητας στον ανεπτυγμένο κόσμο, όπου σχεδόν τα δύο - τρίτα του πληθυσμού υποφέρουν από παχυσαρκία. Σαν αποτέλεσμα, η συνύπαρξη των δύο αυτών καταστάσεων έχει γίνει όλο και συχνότερη στην κλινική πράξη και ένας συνεχώς αυξανόμενος αριθμός κλινικών μελετών προσπαθεί να προσεγγίσει την πιθανή επίδραση της παχυσαρκίας στην νοσηρότητα και θνησιμότητα των ασθενών με σήψη, με έως τώρα αντιφατικά αποτελέσματα. Σκοπός της παρούσας μελέτης είναι να διερευνήσει τον τρόπο με τον οποίο η παχυσαρκία επηρεάζει την ανοσιακή απάντηση των σηπτικών ασθενών, εκτιμώντας τον αριθμό και την κατάσταση ενεργοποίησης των μακροφάγων του λιπώδους ιστού, τα επίπεδα του TNFα στον ορό και στον λιπώδη ιστό και δείκτες οξειδωτικού stress στο πλάσμα.Ασθενείς και Μέθοδοι: Μελετήθηκαν 106 ασθενείς, οι οποίοι χωρίστηκαν σε τέσσερις ομάδες (Ελέγχου n=26, Παχυσαρκίας n=27, Σήψης n=27, Σήψης & Παχυσαρκίας n=26). Ο αριθμός των μακροφάγων στο υποδόριο και ενδοκοιλιακό λίπος και οι υπότυποί τους (M1 και M2) αναγνωρίστηκαν με ανοσοϊστοχημική τεχνική υπό μικροσκόπηση. Τα επίπεδα του TNFα mRNA στο υποδόριο και ενδοκοιλιακό λίπος μετρήθηκαν με real-time reverse transcription-PCR. Στον ορό τα επίπεδα του TNFα μετρήθηκαν με sandwich enzyme-linked immunosorbent assay (ELISA). Το οξειδωτικό stress στο πλάσμα εκτιμήθηκε χρησιμοποιώντας επιλεγμένους βιοδείκτες [TBARS (thiobarbituric acid-reactive substances), Πρωτεϊνικά Καρβονύλια, TAC (total antioxidant capacity)].Αποτελέσματα: Παρατηρήθηκε ότι η σήψη αυξάνει τον ολικό αριθμό και τον Μ2 υπότυπο των μακροφάγων στο ενδοκοιλιακό λίπος, ενώ η παχυσαρκία δεν φάνηκε να επηρεάζει τη συγκέντρωση των μακροφάγων στο λίπος. Η παχυσαρκία βρέθηκε ότι αυξάνει τα επίπεδα του TNFα mRNA (P<0.05) στο ενδοκοιλιακό λίπος καθώς επίσης και τα επίπεδα των TBARS (P<0.001) και Πρωτεϊνικών Καρβονυλίων (P<0.001) στο πλάσμα των σηπτικών ασθενών. Τα επίπεδα της TAC στο πλάσμα βρέθηκε ότι μειώνονται και τα επίπεδα TNFα στον ορό ότι αυξάνονται με τη σήψη, ενώ δεν επηρεάζονταν από την παχυσαρκία. Συμπεράσματα: Η παχυσαρκία σχετίζεται με αυξημένη παραγωγή TNFα στον λιπώδη ιστό και αύξηση του οξειδωτικού stress, προάγοντας την προ-φλεγμονώδη απάντηση στους σηπτικούς ασθενείς

Effectiveness of filtering or decontaminating air to reduce or prevent respiratory infections: A systematic review

Installation of technologies to remove or deactivate respiratory pathogens from indoor air is a plausible non-pharmaceutical infectious disease control strategy. OBJECTIVE: We undertook a systematic review of worldwide observational and experimental studies, published 1970-2022, to synthesise evidence about the effectiveness of suitable indoor air treatment technologies to prevent respiratory or gastrointestinal infections. METHODS: We searched for data about infection and symptom outcomes for persons who spent minimum 20 hours/week in shared indoor spaces subjected to air treatment strategies hypothesised to change risk of respiratory or gastrointestinal infections or symptoms. RESULTS: Pooled data from 32 included studies suggested no net benefits of air treatment technologies for symptom severity or symptom presence, in absence of confirmed infection. Infection incidence was lower in three cohort studies for persons exposed to high efficiency particulate air filtration (RR 0.4, 95%CI 0.28-0.58, p<0.001) and in one cohort study that combined ionisers with electrostatic nano filtration (RR 0.08, 95%CI 0.01-0.60, p=0.01); other types of air treatment technologies and air treatment in other study designs were not strongly linked to fewer infections. The infection outcome data exhibited strong publication bias. CONCLUSIONS: Although environmental and surface samples are reduced after air treatment by several air treatment strategies, especially germicidal lights and high efficiency particulate air filtration, robust evidence has yet to emerge that these technologies are effective at reducing respiratory or gastrointestinal infections in real world settings. Data from several randomised trials have yet to report and will be welcome to the evidence base

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant