Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation.

SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. 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 by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma 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 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 and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against ΔH69/ΔV70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.

A single amino acid substitution in the murine norovirus capsid protein is sufficient for attenuation in vivo.

Murine norovirus (MNV), a prevalent pathogen of laboratory mice, shares many characteristics with human noroviruses. Previous results indicated that passage of MNV1 in the macrophage cell line RAW 264.7 results in attenuation in STAT1-deficient mice (C. E. Wobus, S. M. Karst, L. B. Thackray, K. O. Chang, S. V. Sosnovtsev, G. Belliot, A. Krug, J. M. Mackenzie, K. Y. Green, and H. W. Virgin, PLoS. Biol. 2:e432, 2004). Sequence analysis revealed two amino acid differences between the virulent and attenuated viruses. Using an infectious cDNA clone of the attenuated virus, we demonstrated that a glutamate-to-lysine substitution at position 296 in the capsid protein (VP1) is sufficient to restore virulence in vivo, identifying, for the first time, a virus-encoded molecular determinant of norovirus virulence.

Cloning of the fliI gene from Rhodobacter sphaeroides WS8 by analysis of a transposon mutant with impaired motility.

A transposon mutant of Rhodobacter sphaeroides WS8 was isolated that showed reduced swarming on soft agar plates. Liquid cultures of this mutant (M18) showed a low percentage of motile swimming cells in mid-exponential phase and a low level of extracellular flagellin protein by Western blotting. M18 was complemented by a clone from a library of R. sphaeroides WS8 DNA, and restriction mapping of the site of TnphoA insertion in the mutant, coupled with DNA sequencing, showed that it had a defect in the fliI gene. To determine if a partly functional fliI gene was giving the low-motility phenotype of M18, a drug resistance omega cartridge was inserted into the gene to give a complete null mutant. This null strain also produced a low percentage of motile cells. Possible reasons for this apparent fliI-independent flagellar formation are discussed.

Echoviruses bind heparan sulfate at the cell surface.

Some echoviruses (EV) that bind decay-accelerating factor (DAF) also bind cells of human and murine origins in a DAF-independent manner. Pretreatment of cells with heparinase 1 or heparin blocks the binding of radiolabeled virus to the cell surface, and heparin prevents infection of rhabdomyosarcoma cells by certain EV, including several low-passage clinical isolates of EV 6 and some EV that do not bind DAF. These studies suggest that heparan sulfate may be of in vivo relevance as an attachment molecule for EV.

Echovirus infection of rhabdomyosarcoma cells is inhibited by antiserum to the complement control protein CD59.

A number of echoviruses use decay accelerating factor (DAF) as a cellular receptor or attachment protein for cell infection. Binding of echovirus 7 to DAF at the cell surface, but not to soluble DAF in solution, triggers the formation of virus particles exhibiting an altered sedimentation coefficient ('A' particles) which are considered indicative of the particle uncoating process. We have previously demonstrated that antibodies to beta(2)-microglobulin block cell infection at a stage prior to 'A' particle formation and suggested that this reflects the involvement of beta(2)-microglobulin (or the associated MHC-I) in a virus-receptor complex that forms at the cell surface. We demonstrate here that antiserum to CD59 specifically blocks infection of rhabdomyosarcoma cells by a range of echoviruses, including viruses that bind DAF (e. g. echovirus 7) and those that use currently unidentified receptors other than DAF. The block occurs prior to 'A' particle formation and is cell-type specific. The potential role of CD59 as an active member, or passive participant, in the virus-receptor complex is discussed.

Echoviruses and coxsackie B viruses that use human decay-accelerating factor (DAF) as a receptor do not bind the rodent analogues of DAF.

Many serotypes of echovirus (EV) and Coxsackie B virus (CBV) bind human decay-accelerating factor (DAF) and use it as a receptor for infection. Analogues for DAF have been isolated from mice and rats and characterized; these analogues have amino acid identities to human DAF of approximately 60%. EV serotypes 3, 6', 7, 11-13, and 29 and CBV serotypes 1, 3, and 5 caused hemagglutination of human erythrocytes but not rat or mouse erythrocytes, suggesting failure to bind rodent DAF. To confirm this evidence, radiolabeled viruses were incubated with transfected Chinese hamster ovary (CHO) cells that were abundantly expressing each type of DAF. Only cells that expressed human DAF bound virus. Although binding of EV and CBV was specific for human DAF, complement inhibition by DAF expressed in CHO cells was similar for each analogue.

Purification and characterization of the flagellar basal body of Rhodobacter sphaeroides.

Flagellar hook-basal body (HBB) complexes were purified from Rhodobacter sphaeroides. The HBB was more acid labile but more heat stable than that of Salmonella species, and protein identification revealed that HBB components were expressed only from one of the two sets of flagellar gene clusters on the R. sphaeroides genome, under the heterotrophic growth conditions tested here.