Molecular architecture of the SARS-CoV-2 virus

Abstract

<jats:title>Abstract</jats:title><jats:p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins and the complexes of the spike (S) proteins with the cellular receptor ACE2 or neutralizing antibodies, detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in both pre- and postfusion conformations were determined to average resolutions of 9-11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed highly similar overall processing states of the native glycans to that of the recombinant glycoprotein glycans. The <jats:italic>in situ</jats:italic> architecture of the ribonucleoproteins (RNP) and its higher-order assemblies were revealed. These characterizations have revealed the architecture of the SARS-CoV-2 virus to an unprecedented resolution, and shed lights on how the virus packs its ~30 Kb long single-segmented RNA in the ~80 nm diameter lumen. Overall, the results unveiled the molecular architecture and assembly of the SARS-CoV-2 in native context.</jats:p>

Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures

“…The size values measured for SARS-CoV in our study (∼100 nm, without peplomers) differ from the values measured by cryo-EM (SARS-CoV: 86.5 nm 31 ; SARS-CoV-2: 90-97 nm 11,13,14 ). As already menNoned above, it is highly likely that the plasNc embedding changed the size of the virus parNcles.…”

“…Peplomer density of SARS-CoV-2 was determined recently by cryo-EM for different virus isolates than the virus isolate used in our study. The reported mean values vary from 25 to 40 peplomers per virus parNcle with significant variaNon among parNcles [11][12][13][14] . Our measurements of 9 peplomers per virus segment, represenNng roughly a third of the enNre virus, falls in the same range.…”

“…Biosafety sNll requires inacNvaNon of the virus preparaNon before conducNng the sample preparaNon for cryo-EM, and the effects on the ultrastructure must be carefully controlled. The recently published work on isolated SARS-CoV-2 [11][12][13] only parNally addressed those aspects 11 .…”

“…For instance, it is known that the tannic acid and bloc-contrasNng scheme which we have used increases membrane thickness 32 and that tannic acid binds to glycoproteins 33 such as the Sprotein, which could account for the observed differences in size. Other reasons to explain the difference could be the different virus strains which we have used in comparison to the strains used in the cryo-EM studies 11,13,14,31 S3) which are pracNcally idenNcal to the values measured by cryo-EM (∼90 nm 11,14 ).…”

“…Very recently, morphometric data on isolated SARS-CoV-2 parNcles [10][11][12][13] and virus parNcles in cells 14 , obtained by cryo-EM, were published or became available as a preprint. While cryo-EM is definitely the best method to study virus ultrastructure and structural biology, convenNonal EM, using plasNc embedding, sNll is of relevance, especially for the study of samples, which cannot be easily analyzed by cryo-EM, such as complex mulNcellular objects or pathological material obtained from paNents.…”