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.

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.

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.

Although often referred to as “the forgotten chamber”, compared with left ventricle (LV), especially in the past years, the left atrium (LA) plays a critical role in the clinical expression and prognosis of patients with heart and cerebrovascular disease, as demonstrated by several studies. Echocardiographers initially focused on early detection of atrial geometrical abnormalities through monodimensional atrial diameter quantification and then bidimensional (2D) areas and volume estimation. Now, together with conventional echocardiographic parameters, new echocardiographic techniques, such as strain Doppler, 2D speckle tracking and three-dimensional (3D) echocardiography, allow assessing early LA dysfunction and they all play a fundamental role to detect early functional remodelling before anatomical alterations occur. LA dysfunction and its important prognostic implications may be detected sooner by LA strain than by volumetric measurements.

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<b><i>Background:</i></b> Point-of-care lung ultrasound (LUS) score is a semiquantitative score of lung damage severity. High-resolution computed tomography (HRCT) is the gold standard method to evaluate the severity of lung involvement from the novel coronavirus disease (COVID-19). Few studies have investigated the clinical significance of LUS and HRCT scores in patients with COVID-19. Therefore, the aim of this study was to evaluate the prognostic yield of LUS and of HRCT in COVID-19 patients. <b><i>Methods:</i></b> We carried out a multicenter, retrospective study aimed at evaluating the prognostic yield of LUS and HRCT by exploring the survival curve of COVID-19 inpatients. LUS and chest CT scores were calculated retrospectively by 2 radiologists with &#x3e;10 years of experience in chest imaging, and the decisions were reached in consensus. LUS score was calculated on the basis of the presence or not of pleural line abnormalities, B-lines, and lung consolidations. The total score (range 0–36) was obtained from the sum of the highest scores obtained in each region. CT score was calculated for each of the 5 lobes considering the anatomical extension according to the percentage parenchymal involvement. The resulting overall global semiquantitative CT score was the sum of each single lobar score and ranged from 0 (no involvement) to 25 (maximum involvement). <b><i>Results:</i></b> One hundred fifty-three COVID-19 inpatients (mean age 65 ± 15 years; 65% M), including 23 (15%) in-hospital deaths for any cause over a mean follow-up of 14 days were included. Mean LUS and CT scores were 19 ± 12 and 10 ± 7, respectively. A strong positive linear correlation between LUS and CT scores (Pearson correlation <i>r</i> = 0.754; <i>R</i>² = 0.568; <i>p</i> &#x3c; 0.001) was observed. By ROC curve analysis, the optimal cut-point for mortality prediction was 20 for LUS score and 4.5 for chest CT score. According to Kaplan-Meier survival analysis, in-hospital mortality significantly increased among COVID-19 patients presenting with an LUS score ≥20 (log-rank 0.003; HR 9.87, 95% CI: 2.22–43.83) or a chest CT score ≥4.5 (HR 4.34, 95% CI: 0.97–19.41). At multivariate Cox regression analysis, LUS score was the sole independent predictor of in-hospital mortality yielding an adjusted HR of 7.42 (95% CI: 1.59–34.5). <b><i>Conclusion:</i></b> LUS score is useful to stratify the risk in COVID-19 patients, predicting those that are at high risk of mortality.

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Chromosome deletions in the mouse have proven invaluable in the dissection of gene function. The brown deletion complex comprises >28 independent genome rearrangements, which have been used to identify several functional loci on chromosome 4 required for normal embryonic and postnatal development. We have constructed a 172-bacterial artificial chromosome contig that spans this 22-megabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones. The deletion complex is strikingly gene-poor, containing only 52 protein-coding genes (of which only 39 are supported by human homologues) and has several further notable genomic features, including several segments of >1 Mb, apparently devoid of a coding sequence. We have used sequence polymorphisms to finely map the deletion breakpoints and identify strong candidate genes for the known phenotypes that map to this region, including three lethal loci (l4Rn1, l4Rn2, and l4Rn3) and the fitness mutant brown-associated fitness (baf). We have also characterized misexpression of the basonuclin homologue, Bnc2, associated with the inversion-mediated coat color mutant white-based brown (B w ).This study provides a molecular insight into the basis of several characterized mouse mutants, which will allow further dissection of this region by targeted or chemical mutagenesis.brown locus ͉ chromosome deletion ͉ mouse genome sequence T he mouse brown (b) mutation is one of the oldest known loci and was one of the first to be cloned. The mutation is in the tyrosinase-related protein 1 (Tyrp1) gene, encoding a melanocyte enzyme required for the production of dark eumelanin (1). Homozygous loss of Tyrp1 results in a brown coat; because it was a simply scored phenotype, brown was used as part the mousespecific locus test carried out at the Oak Ridge National Laboratories and elsewhere (reviewed in ref.2). Wild-type mice were exposed to chemical or radiological mutagens and crossed with a tester stock homozygous for seven recessive visible mutations. The efficacy of the mutagenic treatments is assessed in the resulting F 1 progeny. These experiments generated many chromosomal deletions that inactivated Tyrp1, particularly in the progeny of animals exposed to radiation or clastogenic chemical mutagens such as chlorambucil or melphalan.Deletions around the seven specific loci have provided a unique opportunity to study gene function within these intervals. Individual deletions are hemizygous viable but when homozygous or in combination with others give lethal or visible phenotypes, which indicate the presence of essential genes neighboring the specific loci. Intercrossing deletions of different extents provided an avenue to map the resulting phenotypes. The deletions also provided the means to produce physical maps of genetic markers. Studies of this kind have been published for several loci, including albino (Tyr), piebald (Ednrb), pink-eyed dilution (p), and the brown deletion complex (2-6).Studies of the brown deletions established genetic ...