Stability and expression of SARS-CoV-2 spike-protein mutations.

Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen between stability and ACE2 binding effects. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.

The contribution of population age-sex structure to the excess mortality estimates of 2020-2021 in Denmark, Finland, Iceland, Norway, and Sweden.

The Nordic countries offer an ideal case study of the COVID-19 pandemic due to their comparability, high data quality, and variable mitigations. We investigated the age- and sex-specific mortality patterns during 2020-2021 for the five Nordic countries and analysed the total age- and sex-adjusted excess deaths, ratios of actual to expected death rates, and age-standardized excess death estimates. We assessed excess deaths using several time periods and sensitivity tests, and 42 sex and age groups. Declining pre-pandemic age-specific death rates reflected improving health demographics. These affect the expected death estimates and should be accounted for in excess mortality models. Denmark had the highest death rates both before and during the pandemic, whereas in 2020 Sweden had the largest mortality increase. The age-standardized mortality of Denmark, Iceland and Norway was lowest in 2020. 2021 was one of the lowest mortality years for all Nordic countries. The total excess deaths in 2020-2021 were dominated by 70-89-year-olds, were not identified in children, and were more pronounced among men than women. Sweden had more excess deaths in 2020 than in 2021, whereas Finland, Norway and Denmark had the opposite. Our study provides new details on Nordic sex- and age-specific mortality during the first two years of the pandemic and shows that several metrics are important to enable a full understanding and comparison of the pandemic mortality.

Estimates of excess mortality for the five Nordic countries during the COVID-19 pandemic 2020-2021.

BACKGROUND: Excess mortality during the COVID-19 pandemic is of major scientific and political interest. METHODS: We critically reviewed different estimates of all-cause excess mortality for the five Nordic countries (Denmark, Finland, Iceland, Norway and Sweden), which have been much studied during the COVID-19 pandemic, using the latest register data to discuss uncertainties and implications. RESULTS: We show using back-calculation of expected deaths from Nordic all-cause deaths that the Institute for Health Metrics and Evaluation model is a clear outlier in the compared estimates and likely substantially overestimates excess mortality of Finland and Denmark, and probably Sweden. Our review suggests a range of total Nordic excess deaths of perhaps 15 000-20 000, but results are sensitive to assumptions in the models as shown. CONCLUSIONS: We document substantial heterogeneity and uncertainty in estimates of excess mortality. All estimates should be taken with caution in their interpretation as they miss detailed account of demographics, such as changes in the age group populations over the study period.

Structural heterogeneity and precision of implications drawn from cryo-electron microscopy structures: SARS-CoV-2 spike-protein mutations as a test case.

Protein structures may be used to draw functional implications at the residue level, but how sensitive are these implications to the exact structure used? Calculation of the effects of SARS-CoV-2 S-protein mutations based on experimental cryo-electron microscopy structures have been abundant during the pandemic. To understand the precision of such estimates, we studied three distinct methods to estimate stability changes for all possible mutations in 23 different S-protein structures (3.69 million ΔΔG values in total) and explored how random and systematic errors can be remedied by structure-averaged mutation group comparisons. We show that computational estimates have low precision, due to method and structure heterogeneity making results for single mutations uninformative. However, structure-averaged differences in mean effects for groups of substitutions can yield significant results. Illustrating this protocol, functionally important natural mutations, despite individual variations, average to a smaller stability impact compared to other possible mutations, independent of conformational state (open, closed). In summary, we document substantial issues with precision in structure-based protein modeling and recommend sensitivity tests to quantify these effects, but also suggest partial solutions to the problem in the form of structure-averaged "ensemble" estimates for groups of residues when multiple structures are available.

Structure and Mutations of SARS-CoV-2 Spike Protein: A Focused Overview.

The spike protein (S-protein) of SARS-CoV-2, the protein that enables the virus to infect human cells, is the basis for many vaccines and a hotspot of concerning virus evolution. Here, we discuss the outstanding progress in structural characterization of the S-protein and how these structures facilitate analysis of virus function and evolution. We emphasize the differences in reported structures and that analysis of structure-function relationships is sensitive to the structure used. We show that the average residue solvent exposure in nearly complete structures is a good descriptor of open vs closed conformation states. Because of structural heterogeneity of functionally important surface-exposed residues, we recommend using averages of a group of high-quality protein structures rather than a single structure before reaching conclusions on specific structure-function relationships. To illustrate these points, we analyze some significant chemical tendencies of prominent S-protein mutations in the context of the available structures. In the discussion of new variants, we emphasize the selectivity of binding to ACE2 vs prominent antibodies rather than simply the antibody escape or ACE2 affinity separately. We note that larger chemical changes, in particular increased electrostatic charge or side-chain volume of exposed surface residues, are recurring in mutations of concern, plausibly related to adaptation to the negative surface potential of human ACE2. We also find indications that the fixated mutations of the S-protein in the main variants are less destabilizing than would be expected on average, possibly pointing toward a selection pressure on the S-protein. The richness of available structures for all of these situations provides an enormously valuable basis for future research into these structure-function relationships.