Suzanne Pickering

• PhD
• King's College London

Evolution of SARS-CoV-2 in long-term persistent infections is hypothesised to be a major source of variants of concern (VOC). However, determination of viral subpopulations by linkage of intra-host variants into haplotypes has been limited by commonly used genomic sequencing techniques. We developed a sequencing and analysis methods for identifying...

The role of myeloid cells in the pathogenesis of SARS-CoV-2 is well established, in particular as drivers of cytokine production and systemic inflammation characteristic of severe COVID-19. However, the potential for myeloid cells to act as bona fide targets of productive SARS-CoV-2 infection, and the specifics of entry, remain unclear. Using a pan...

SARS-CoV-2 spreads predominantly through superspreading, with a minority of individuals responsible for the majority of transmission, though the drivers of this heterogeneity are unclear. Here, we assess the contribution of variation in viral load and daily contact rates to this heterogeneity by combining viral load and contact survey data in a mat...

Rapid and accessible testing was paramount in the management of the COVID-19 pandemic. Our university established KCL TEST: a SARS-CoV-2 asymptomatic testing programme that enabled sensitive and accessible PCR testing of SARS-CoV-2 RNA in saliva. Here, we describe our learnings and provide our blueprint for launching diagnostic laboratories, partic...

The HIV-1 Vpu protein is expressed late in the virus lifecycle to promote infectious virus production and avoid innate and adaptive immunity. This includes the inhibition of the NF-κB pathway which, when activated, leads to the induction of inflammatory responses and the promotion of antiviral immunity. Here we demonstrate that Vpu can inhibit both...

The HIV-1 Vpu protein is expressed late in the virus lifecycle to promote infectious virus production and avoid innate and adaptive immunity. This includes the inhibition of the NF-kB pathway which, when activated, leads to the induction of inflammatory responses and the promotion of antiviral immunity. Here we demonstrate that Vpu can inhibit both...

Accumulating evidence suggests that variants of concern (VOC) of SARS-CoV-2 evolve to evade the human immune response, with much interest focused on mutations in the spike protein that escape from antibodies. However, resistance to the innate immune response is essential for efficient viral replication and transmission.

The appearance of new dominant variants of concern (VOCs) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) threatens the global response to the COVID-19 pandemic. Of these, the alpha variant (also known as B.1.1.7) that appeared initially in the UK became the dominant variant in much of Europe and North America in the first half...

SARS-CoV-2 Spike is the target for neutralizing antibodies elicited following both infection and vaccination. Whilst extensive research has shown that the receptor binding domain (RBD) and to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these reg...

Although the antibody response to COVID-19 vaccination has been studied extensively at the polyclonal level using immune sera, little has been reported on the antibody response at the monoclonal level. Here we isolate a panel of 44 anti-SARS-CoV-2 monoclonal antibodies (mAbs) from an individual who received two doses of the ChAdOx1 nCoV-19 (AZD1222...

Confirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyer’s patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the...

Confirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyers patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the...

Variants of concern (VOCs) of severe acute respiratory syndrome coronavirus type-2 (SARS-CoV-2) threaten the global response to the COVID-19 pandemic. The alpha (B.1.1.7) variant appeared in the UK became dominant in Europe and North America in early 2021. The Spike glycoprotein of alpha has acquired a number mutations including the P681H mutation...

COVID-19 vaccine design and vaccination rollout need to take into account a detailed understanding of antibody durability and cross-neutralizing potential against SARS-CoV-2 and emerging variants of concern (VOCs). Analyses of convalescent sera provide unique insights into antibody longevity and cross-neutralizing activity induced by variant spike...

Background Point-of-care (POC) SARS-CoV-2 lateral-flow antigen detection (LFD) testing in the emergency department (ED) could inform rapid infection control decisions but requirements for safe deployment have not been fully defined Methods Review of LFD test results, laboratory and POC-RT-PCR results and ED-performance metrics during a two-week hi...

There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available...

Objectives Analysis of nosocomial transmission in the early stages of the pandemic at a large multi-site healthcare institution. Nosocomial incidence is linked with infection control interventions.. Methods Viral genome sequence and epidemiological data were analysed for 574 consecutive SARS-CoV-2 PCR-positive patients including 86 nosocomial case...

Background Many countries require incoming air travellers to quarantine on arrival and/or undergo testing to limit importation of SARS-CoV-2. Methods We developed mathematical models of SARS-CoV-2 viral load trajectories over the course of infection to assess the effectiveness of quarantine and testing strategies. We consider the use of Polymerase...

As SARS–CoV–2 variants continue to emerge globally, a major challenge for COVID–19 vaccination is the generation of a durable antibody response with cross–neutralizing activity against both current and newly emerging viral variants. Cross–neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following...

Background Lateral flow devices (LFDs) for rapid antigen testing are set to become a cornerstone of SARS-CoV-2 mass community testing, although their reduced sensitivity compared with PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is, therefore, essential for successful implemen...

Containing the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been an unprecedented challenge due to high horizontal transmissivity and asymptomatic carriage rates. Lateral flow device (LFD) immunoassays were introduced in late 2020 to detect SARS-CoV-2 infection in asymptomatic or presymptomatic individuals rapidl...

The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein. The presence of a polybasic cleavage site in SARS-CoV-2 spike at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-Co...

During the first wave of the global COVID-19 pandemic the clinical utility and indications for SARS-CoV-2 serological testing were not clearly defined. The urgency to deploy serological assays required rapid evaluation of their performance characteristics. We undertook an internal validation of a CE marked lateral flow immunoassay (LFIA) (SureScree...

Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RB...

Containing the global SARS-CoV-2 pandemic has been an unprecedented challenge due to high horizontal transmissivity and asymptomatic carriage rates. Lateral Flow Device (LFD) immunoassays were introduced in late 2020 to detect SARS-CoV-2 infection in asymptomatic or pre-symptomatic individuals rapidly. Whilst LFD technologies have been used for ove...

Background: Rapid antigen lateral flow devices (LFDs) are set to become a cornerstone of SARS-CoV-2 mass community testing. However, their reduced sensitivity compared to PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is therefore essential for successful implementation. To addr...

The interaction of the SARS–CoV–2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS–CoV–2 variants has revealed mutations arising in th...

The cellular entry of severe acute respiratory syndrome-associated coronaviruses types 1 and 2 (SARS-CoV-1 and -2) requires sequential protease processing of the viral spike glycoprotein (S). The presence of a polybasic cleavage site in SARS-CoV-2 S at the S1/S2 boundary has been suggested to be a factor in the increased transmissibility of SARS-Co...

Antibody responses to SARS-CoV-2 can be detected in most infected individuals 10–15 d after the onset of COVID-19 symptoms. However, due to the recent emergence of SARS-CoV-2 in the human population, it is not known how long antibody responses will be maintained or whether they will provide protection from reinfection. Using sequential serum sample...

Many healthcare facilities report SARS-CoV-2 outbreaks but transmission analysis is complicated by the high prevalence of infection and limited viral genetic diversity. The contribution of different vectors to nosocomial infection or the effectiveness of interventions is therefore currently unclear. Detailed epidemiological and viral nanopore seque...

There is a clear requirement for an accurate SARS-CoV-2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential use as diagnostic tools. Highly specific in-house ELISAs were developed...

Objectives: Determine indications and clinical utility of SARS-CoV-2 serology testing in adults and children. Design: Prospective evaluation of initial three weeks of a daily Monday to Friday pilot SARS-CoV-2 serology service for patients. Setting: Early post 'first-wave' SARS-CoV-2 transmission period at single centre London teaching hospital that...

Antibody (Ab) responses to SARS-CoV-2 can be detected in most infected individuals 10-15 days following the onset of COVID-19 symptoms. However, due to the recent emergence of this virus in the human population it is not yet known how long these Ab responses will be maintained or whether they will provide protection from re-infection. Using sequent...

An evaluation of a rapid portable gold- nanotechnology measuring SARS-CoV-2 IgM, IgA and IgG antibody concentrations against spike 1 (S1), spike 2 (S) and nucleocapsid (N) was conducted using serum samples from 74 patients tested for SARS-CoV-2 RNA on admission to hospital, and 47 historical control patients from March 2019. 59 patients were RNA(+)...

There is a clear requirement for an accurate SARS−CoV−2 antibody test, both as a complement to existing diagnostic capabilities and for determining community seroprevalence. We therefore evaluated the performance of a variety of antibody testing technologies and their potential as diagnostic tools. A highly specific in−house ELISA was developed for...

There is a worldwide shortage of reagents to perform detection of SARS-2. Many clinical diagnostic laboratories rely on commercial platforms that provide integrated end-to-end solutions. While this provides established robust pipelines, there is a clear bottleneck in the supply of reagents given the current situation of extraordinary high demand. S...

Along with other immune checkpoints, T cell i mmunoglobulin and m ucin domain-containing protein 3 (Tim-3) is expressed on exhausted CD4 ⁺ and CD8 ⁺ T cells and is upregulated on the surface of these cells upon infection by H uman I mmunodeficiency V irus Type 1 (HIV-1). Recent reports have suggested an antiviral role for Tim-3. However, the molecu...

The restriction factor BST-2 and the NK cell ligands NTB-A and PVR are among a growing list of membrane proteins found to be downregulated by HIV-1 Vpu. BST-2 antagonism enhances viral release, while NTB-A and PVR downmodulation contributes to NK cell evasion. However, it remains unclear how Vpu can target multiple cellular factors simultaneously....

Aim It was recently found that HIV can downregulate HLA-C on infected cells. This is mediated by the viral protein Vpu, and is in addition to the downregulation of HLA-A/B by Nef. The magnitude of HLA-C downregulation varies widely between primary HIV viruses, but the selection pressures resulting in either HLA-C downregulation or preservation are...

HIV-1 can downregulate HLA-C on infected cells, using the viral protein Vpu, and the magnitude of this downregulation varies widely between primary HIV-1 variants. The selection pressures that result in viral downregulation of HLA-C in some individuals, but preservation of surface HLA-C in others are not clear. To better understand viral immune eva...

Vpu sequence information for the longitudinally sampled individual studied in Fig 2E. (A) A phylogenetic tree of 87 Vpu sequences previously obtained from this individual [48]. Sequences are shown from samples taken 1 (light blue), 4 (dark blue), or 10 (magenta) years after seroconversion. The tree is rooted using NL4.3 and a consensus subtype B se...

Multiple linear regression model for viruses of each subtype. Using 191 primary Vpu clones from chronic infection a multiple linear regression model identified residues at 5 positions of Vpu affecting HLA-C downregulation (Fig 4B, shown on the left). This analysis was repeated separately for infections with viruses of different subtype (shown right...

Amino acid sequences of the 35 Vpu clones analyzed from 6 individuals in Fig 2. (DOCX)

HLA-C downregulation quantified for 14 primary viruses, comparing transfection of cloned Vpu molecules to in vitro infection of primary cells. (A) HeLa cells were transfected with Vpu cloned from NL4-3 or a primary virus that downregulates HLA-C. HeLa populations were then gated based on the expression of GFP, and the MFI of HLA-C staining compared...

HIV-1 subtypes differ in their frequency of HLA-C downregulation. Data is shown for 195 individuals from which HLA-C downregulation by a single Vpu clone from chronic untreated infection was measured by transfection of Molt-4 cells. HLA-C downregulation is observed more frequently for Vpu molecules from viral subtypes A and B, compared to subtypes...

Vpu sequence variation observed at positions identified as important in downregulation of HLA-C. 191 primary Vpu clones were analyzed in Fig 4 and identified residues at Vpu positions 3, 5, 15, 16 and 24 which associated independently with HLA-C downregulation. For each of these positions the frequency of all residues observed in this population of...

Residuals plot for predicted HLA-C downregulation. In Fig 4E a multiple linear regression model was used to predict downregulation of HLA-C based on Vpu sequence at 5 positions. The residuals between observed and predicted HLA-C downregulation are shown for all 191 Vpu clones in this analysis. (TIF)

Average expression level of HLA-C alleles. The average expression level for each 2-digit HLA-C allele is reported here, from previously described staining of peripheral blood CD3+ cells from healthy donors analyzed by flow cytometry using the monoclonal antibody DT9 [31]. MFI of DT9 staining was plotted twice for each donor, once for each 2-digit H...

Multiple linear regression model for viruses of each cohort. Using 191 primary Vpu clones from chronic infection a multiple linear regression model identified residues at 5 positions of Vpu affecting HLA-C downregulation (Fig 4B, shown on the left). This analysis was repeated separately for individuals of each of the two cohorts used (shown right)....

Stratification by cohort of analyses indicating HLA-C downregulation adapts to host HLA genotype. (A,B) Separately for BC HOMER and UARTO individuals, the proportion of Vpu clones that downregulate HLA-C strongly is shown for HLA-C alleles with n≥5 in both cohorts. The number of individuals in each group is shown above each plot. (C,D) HLA-C expres...

Correlations between viral sequence adaptation to host HLA-C and the observed downregulation of HLA-C by Vpu. For 72 individuals with subtype B virus the extent of HIV-1 adaptation to each HLA-C could be quantified from the proportion of Nef sequence variants which associate with that HLA-C allele, which are observed in individual viral sequences....

Sequences of HA-tagged HLA constructs. Black text indicates sequence from HLA-A, red indicates sequence from HLA-C, with green identifying the HA tag added at the N-terminus after the leader peptide. (TIF)

Multiple linear regression model including virus subtype as a covariate. Using 191 primary Vpu clones from chronic infection a multiple linear regression model identified residues at 5 positions of Vpu affecting HLA-C downregulation (Fig 4B, shown on the left). This analysis was repeated including viral subtype as a covariate (subtype A, B, C, or D...

Amino acid sequences of the single Vpu clones analyzed for 195 individuals in Figs 3 and 4 and S3 Fig. (DOCX)

Like all viruses, human immunodeficiency viruses (HIVs) and their primate lentivirus relatives must enter cells in order to replicate and, once produced, new virions need to exit to spread to new targets. These processes require the virus to cross the plasma membrane of the cell twice: once via fusion mediated by the envelope glycoprotein to delive...

Many pathogens evade cytotoxic T lymphocytes (CTLs) by downregulating HLA molecules on infected cells, but the loss of HLA can trigger NK cell-mediated lysis. HIV-1 is thought to subvert CTLs while preserving NK cell inhibition by Nef-mediated downregulation of HLA-A and -B but not HLA-C molecules. We find that HLA-C is downregulated by most primar...

HIV-1 Vpu prevents incorporation of tetherin (BST2/ CD317) into budding virions and targets it for ESCRT-dependent endosomal degradation via a clathrin-dependent process. This requires a variant acidic dileucine-sorting motif (ExxxLV) in Vpu. Structural studies demonstrate that recombinant Vpu/tetherin fusions can form a ternary complex with the cl...

Tetherin (BST2/CD317) restricts the release of enveloped viral particles from infected cells. Coupled to this virion retention, hominid tetherins induce proinflammatory gene expression via activating NF-κB. We investigated the events initiating this tetherin-induced signaling and show that physical retention of retroviral particles induces the phos...

The HIV-1 Vpu protein is expressed from a bi-cistronic message late in the viral life cycle. It functions during viral assembly to maximise infectious virus release by targeting CD4 for proteosomal degradation and counteracting the antiviral protein tetherin (BST2/CD317). Single genome analysis of vpu repertoires throughout infection in 14 individu...

Antiviral proteins that recognize pathogen-specific or aberrantly located molecular motifs are perfectly positioned to act as pattern-recognition receptors and signal to the immune system. Here we investigated whether the interferon-induced viral restriction factor tetherin (CD317/BST2), which is known to inhibit HIV-1 particle release by physicall...

Tetherin (BST2/CD317) has been recently recognized as a potent interferon-induced antiviral molecule that inhibits the release of diverse mammalian enveloped virus particles from infected cells. By targeting an immutable structure common to all these viruses, the virion membrane, evasion of this antiviral mechanism has necessitated the development...

Supplementary Figure 3. C'-ADE by monoclonal antibodies. The enhancing mAb 246-D and the neutralising mAb IgGb12 were serially diluted in NHS then incubated with C' or HIC' and virus, as per the standard enhancement assays. Fold enhancement is calculated relative to infection in the presence of NHS and C', as for other enhancement assays. Results a...

Supplementary Figure 1. Patient antibody profiles. (A) Anti-gp120 antibody levels were determined by a gp120 ELISA based on gp120 from IIIB. Antibody levels were standardised to pooled positive control serum from chronically-infected individuals, indicated on the graphs by the dashed horizontal line, to allow direct comparisons between individuals....

Supplementary Figure 2. The co-existence of C'-ADE and C'-MI activity in early serum samples from an infected individual. C'-MI, C'-ADE and neutralisation assays were carried out using early virus (MM26.62) and sequential autologous serum samples from MM26. Anti-gp120 antibody levels were measured in sequential serum samples from MM26 by ELISA. (A)...

Supplementary Figure 4. RT correlation and enhancement assay time course. In addition to % cells infected, fold enhancement was also measured using RT detected in the cell supernatant as a surrogate marker of virus production. (A) RT output was monitored in the cellular supernatant on days 1, 3 and 6 of enhancement assays for viruses showing high-l...

Non-neutralising antibodies to the envelope glycoprotein are elicited during acute HIV-1 infection and are abundant throughout the course of disease progression. Although these antibodies appear to have negligible effects on HIV-1 infection when assayed in standard neutralisation assays, they have the potential to exert either inhibitory or enhanci...

Expanded HIV-C-DC-CD8+ T cells exert an antiviral effect on autologous CD4+ TCs infected with HIV 3 days prior addition. An already on-going infection of CD4+ TCs (3 days pre-infected) was inhibited by addition of HIV-C-DC-primed CD8+ T cells as shown by determining p24 values from the supernatants 5 and 9 days post addition of CD8+ T cells. In con...

Figure S1A. Virus capture assay (VCA) of differentially opsonized HIV-preparations. HIV was opsonized with medium alone (HIV), normal human serum (NHS) as source of complement (HIV-C), or complement-inactivated NHS (HIV-hiC). Following opsonization the virus preparations were washed, centrifuged at 14000 rpm/90min/4°C, and the pellet was resuspende...

AT2-HIV-C-DCs exert an antiviral effect upon co-culture with infected, autologous CD4+ T cells. Expanded AT2-HIV-C-DC-primed CD8+ T cells proved to be functional upon addition to infected, autologous CD4+ T cells and significantly inhibited productive infection compared to CD8+ T cells primed/boosted with AT2-HIV-DCs (p = 0.02). Too, infection of C...

Author Summary Upon entering the body, HIV initiates immediate responses of the immune system. The complement system constitutes a first line of defense against HIV and bridges innate and adaptive immunity. Thus, in the acute phase of infection, HIV is coated with complement fragments. Following seroconversion, when HIV-specific antibodies appear,...

Several features of HIV have frustrated efforts to develop a vaccine able to induce broadly neutralising antibodies. The enormous genetic diversity of HIV is a major factor, accompanied by the camouflaged nature of the envelope spike, upon which HIV depends for cellular entry and to which antibodies must bind to neutralise. The picture is further c...