Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro , the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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Extensive global sampling and sequencing of the pandemic virus SARS-CoV-2 have enabled researchers to monitor its spread, and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals, and how likely they are to be transmitted. To characterize within-host diversity and transmission we deep-sequenced 1313 clinical samples from the UK. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high, and a narrow bottleneck at transmission. Most variants are either lost, or occasionally fixed, at the point of transmission, with minimal persistence of shared diversity - patterns which are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape variants are likely to arise infrequently, but could spread rapidly if successfully transmitted.

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 causing a global pandemic, with the United Kingdom (UK) one of the hardest hit countries. Rapid sequencing and publication of consensus genomes have enabled phylogenetic analysis of the virus, demonstrating SARS-CoV-2 evolves relatively slowly 1 , but with multiple sites in the genome that appear inconsistent with the overall consensus phylogeny 2 . To understand these discrepancies, we used veSEQ 3 , a targeted RNA-seq approach, to quantify minor allele frequencies in 413 clinical samples from two UK locations. We show that SARS-CoV-2 infections are characterised by extensive within-host diversity, which is frequently shared among infected individuals with patterns consistent with geographical structure. These results were reproducible in data from other sequencing locations around the UK, where we find evidence of mixed infection by major circulating lineages with patterns that cannot readily be explained by artefacts in the data. We conclude that SARS-CoV-2 diversity is transmissible, and propose that geographic patterns are generated by co-circulation of distinct viral populations. Co-transmission of mixed populations could open opportunities for resolving clusters of transmission and understanding pathogenesis. symptomatic individuals who tested positive for COVID-19 within two geographically-separate hospital trusts (Oxford University Hospitals and Basingstoke and North Hampshire Hospital, located 37 miles (60 km) apart; Supplementary Table 1) . Using veSEQ, a sequencing protocol based on a quantitative targeted enrichment strategy 3 , which we previously validated for other viruses 3 , 11 , 12 , we characterised the full spectrum of within-host diversity in SARS-CoV-2 and contextualised our findings within other high-quality, publicly available deep-sequencing datasets from the UK generated on the high-fidelity Illumina platform 13 , 14 . All genomic data has been made publicly available as part of the COVID-19 Genomics UK (COG-UK) Consortium [cogconsortium.uk] via GISAID 15 and the European Nucleotide Archive (ENA) study PRJEB37886. Within-host diversity is extensive and shared between individualsTo examine patterns of within-host diversity, we first considered the distribution of minor allele frequencies (MAFs) in the mapped reads at every position along the genome. This analysis was supported by data curation to ensure that only high-confidence variants were examined, which included analysis of in-batch quantification controls as well as a stringent computational clean-up to eliminate any residual cross-mapping 16 , previously validated for targeted metagenomics 11 (see Methods and Supplementary Text for a full description). In combination with unique dual indexing (UDI), these procedures generated highly robust minority variant calls, which were reproducible in independent replicates and distinguishable from methodological noise above a threshold of 2% of reads at a given position (Supplementary Figure 1). The distribution of MAFs was a...

This is a PDF file of a peer-reviewed paper that has been accepted for publication. Although unedited, the content has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text and figures will undergo copyediting and a proof review before the paper is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-g and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY 207-215 ; due to P13L, P13S, and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAP-RITF 9-17 ; and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK 361-369 . CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.

Context: Preterm birth accounts for significant neonatal mortality and morbidity as well as substantial health costs. As our understanding of aetiology and risk factors for preterm birth increases, predictive tools and prophylactic interventions have been developed to improve maternal and fetal outcomes. These are effective, but require surveillance of asymptomatic high-risk women, as well as ultrasound and surgical expertise. This has led to the development of preterm birth surveillance clinics (PSCs), which pool these resources together and have changed the focus of care from reactive to predictive and preventative management. Methods: A literature review of the evidence surrounding the predictive tests (cervical length, fetal fibronectin, Actim Partus, Partosure) and prophylactic interventions (cerclage, progesterone, Arabin pessary, antibiotics, and steroids) for preterm birth to understand what preterm birth surveillance clinics do and how effective they are. Results: Measuring cervical length and fetal fibronectin levels are two of the most accurate predictive tests preterm birth, especially when used in combination. Other predictive tools like Actim Partus and Partosure are effective for symptomatic women, but their role in surveillance of asymptomatic women is unclear. Cervical cerclage is effective in reducing preterm birth in women with previous losses, but the role of progesterone and pessaries remains debated. Steroids remain one of the most effective antenatal intervention, but they need to be administered within a tight timeframe in order to confer maximal benefit. The role of PSCs in predicting the timing of birth and targeting women at highest risk to appropriate interventions is therefore crucial in optimizing care and improving outcomes. Conclusions: Nearly every step of management is still debated although many have a strong evidence-base and effective interventions do exist. The challenge is finding the optimal management pathway, and details of which populations benefit from which interventions need to be evaluated. While evidence continues to be collated, the poor outcomes of preterm birth and the multiple options available to reduce them justify preterm birth surveillance clinics being resourced.Keywords: Preterm Birth, Predictive, Fetal Fibronectin, Cervical Length, Cervical Cerclage ContextDefined as spontaneous or induced birth before 37+ 0 weeks' gestation, preterm birth (PTB) is responsible for significant perinatal morbidity and mortality. Preterm labour affects 11.1% of live births worldwide (1) and 7.6% of live births in England and Wales (2), but incidence is rising globally (3). PTB causes more than 3 million perinatal deaths a year (1) and causes increased risks of neurodevelopmental impairment, behavioural problems and respiratory diseases, which constitute significant health costs and decreased quality of life (4-6). MethodsThe primary research question our review is addressing is "what predictive tests and prophylactic interventions to preterm birth surveillance clini...

AimsThere is a lack of biomarkers validated for assessing clinical deterioration in patients with COVID-19 on presentation to secondary or tertiary care. This evaluation looked at the potential clinical application of C reactive protein (CRP), procalcitonin, mid-regional proadrenomedullin (MR-proADM) and white cell count to support prediction of clinical outcomes.Methods135 patients presenting to Hampshire Hospitals NHS Foundation Trust between April and June 2020 confirmed to have COVID-19 via reverse-transcription-qPCR were included. Biomarkers from within 24 hours of presentation were used to predict disease progression by Cox regression and area under the receiver operating characteristic curves. The endpoints assessed were 30-day all-cause mortality, intubation and ventilation, critical care admission and non-invasive ventilation (NIV) use.ResultsElevated MR-proADM was shown to have the greatest ability to predict 30-day mortality adjusting for age, cardiovascular disease, renal disease and neurological disease. A significant association was also noted between raised MR-proADM and CRP concentrations and the requirement for critical care admission and NIV.ConclusionsThe measurement of MR-proADM and CRP in patients with confirmed COVID-19 infection on admission shows significant potential to support clinicians in identifying those at increased risk of disease progression and need for higher level care, subsequently enabling prompt escalation in clinical interventions.