HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.

CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.

Retrospective spatial analysis of cases of COVID-19 in a single military accommodation block corridor, RMAS, January-March 21.

Shared ablutions and stairwells, corridor cross-ventilation and non-deliberate perflation (natural draft blowing through a space) are potential risk factors for COVID-19 transmission in corridor-based accommodation. This paper uses retrospective spatial analysis to identify potential built environmental risk factors during the January-March 2021 outbreak in Victory College, Royal Military Academy Sandhurst.Distance was measured in units of single room spacing. Odds, ORs and 95% CIs were calculated to identify and measure associations between distance from exposure and having COVID-19. Distance response trends were assessed using Pearson's χ2 for trend test. Linear relationships were tested using the t-test or rank-sum test.Stairwells and ablutions were not identified as likely sources of infection for all corridor occupants. Assuming occupants used their nearest ablutions, closer distance among those attributed to using ablutions 2 (one of four sets of ablutions), was identified as a risk factor (p=0.05). Testing distance response by χ2 linear trend testing showed a potential association between nearest adjacent positive room and COVID-19 (p=0.06), strongest if dominant air movement along the corridor length was from the left (p=0.10) compared with the right (p=0.24).Formal qualitative spatial analysis and environmental assessment of ventilation and air movement has a role in outbreak investigation in assessing factors related to the built environment. Environmental investigations would best inform outbreak investigations if undertaken contemporaneously. Pre-emptive and retrospective studies can help inform public health advice to military establishments in business continuity planning for isolation facilities, during outbreaks or in future development of the built environment.

Lessons learnt from an outbreak of COVID-19 in a workplace providing an essential service, Thames Valley, England 2020: Implications for investigation and control.

OBJECTIVES: Human behavioural factors are an important consideration in the response to COVID-19 outbreaks. Prior to the emergence of highly infectious variants of SARS-CoV-2 and implementation of vaccination programmes, we conducted a study to explore the role of behavioural factors influencing transmission at an essential services workplace during an outbreak of COVID-19. STUDY DESIGN: Observational cohort study. METHODS: In response to a COVID-19 outbreak in November 2020 at an office-based call centre workplace providing an essential service in Thames Valley, we designed and conducted an anonymous staff questionnaire to explore potential behavioural factors of staff behaviour that influence transmission. RESULTS: A total of 45 staff (27%) tested positive for SARS-CoV-2 over a six-week period between 26 October and 14 December 2020. The online questionnaire was cascaded to 168 staff members; the response rate was 41%. Self-reported use of hand sanitiser, face masks and cleaning of equipment in line with workplace guidance was 86%, 66% and 63% respectively. On the same behaviours, respondents reported that 33%, 31% and 14% of their colleagues followed the recommendations. Almost two thirds of respondents (63%) reported that they were unable to maintain social distancing at the workplace, primarily due to operational constraints. CONCLUSIONS: Prevention and control of COVID-19 outbreaks at workplaces providing an essential service is challenging. Operational requirements, often compounded by reduced staff availability, impede implementation of more robust control measures. Ongoing assessment of human behavioural factors in the control of COVID-19 outbreaks at workplaces in the post-vaccine era is essential.

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.

6 COVID-19 outbreak investigation in a London army barracks. Understanding prevalence, seroconversion, transmission risk factors and control measures for COVID-19

IntroductionMilitary Establishments are at increased risk of rapid spread of respiratory infections. Little was known in March 2020 about SARS-CoV-2 prevalence, serological conversion, asymptomatic transmission or risk factors for transmission, particularly in military populations. Early identification, swift implementation of control measures, and investigation of a potential outbreak with Public Health England in an Army barracks following one confirmed case and 11 symptomatic personnel, allowed exploration of these questions.MethodsAll adult personnel, including civilians working or living at the Barracks were invited to participate at initial visit and day-36 follow-up. Participants completed a symptom and transmission risk factor questionnaire;gave nasal and throat swabs for SARS-CoV-2 RT-PCR, infectious virus isolation, whole genome sequencing (WGS);and blood samples to detect SARS-CoV-2 and neutralising antibodies. Risk factors were statistically analysed using STATA v15.0, described in univariate analysis by relative risks and assessed using Fisher’s Exact test.ResultsAt first visit, 24/304 (8%) participants were RT-PCR positive and infectious virus recovered from 7/24 (29%). Seropositivity was 7% (19/285). 64% of all positive participants were asymptomatic. WGS identified more than three separate introductions, and evidence of asymptomatic transmission through genetically indistinguishable samples. Significant transmission risk factors included contact with a confirmed case, female gender, and two-person shared bathrooms. After 36 days, there were no new cases, all previously RT-PCR positive participants seroconverted, but not all developed neutralising antibodies;seropositivity was 13% (25/193).ConclusionsMost positive military personnel were asymptomatic, but those with symptoms reported ageusia or anosmia. Some RT-PCR positive participants, but none who were simultaneously positive for neutralising antibodies, had infectious virus. Initial infection rates were five times general London estimates, but effective implementation of control measures including enhanced cleaning, social distancing, and prompt isolation mitigated on-site spread. 36 days later seropositivity was below London’s rate. Ongoing risks include new COVID-19 introduction into the barracks from off-site personnel, asymptomatic transmission between cases and contacts, and use of two-person bathrooms.

Lisbon's COVID 19 response: harm reduction interventions for people who use alcohol and other drugs in emergency shelters.

Four emergency shelters were instituted in Lisbon during COVID-19, and are still in operation. Between March and August 2020, they served over 600 people. The shelters host a diverse population, including people experiencing homelessness, foreigners, LGBTI + people, those with reduced mobility, couples, those with pets, and People Who Use Drugs, including alcohol (henceforth PWUD). Individuals are provided care regardless of their immigration or residence status. In order to ensure continuity of care in the shelters and to bring in clients who usually refuse to be sheltered, a range of social and health interventions are integrated into the shelters. Harm reduction services ensure that the most vulnerable populations, PWUD and people experiencing homelessness, have access to the services they need. Innovations in service provision maximize the services impacts and pave the way for the future inclusion and development of these services.

Cross sectional investigation of a COVID-19 outbreak at a London Army barracks: Neutralising antibodies and virus isolation.

BACKGROUND: Military personnel in enclosed societies are at increased risk of respiratory infections. We investigated an outbreak of Coronavirus Disease 2019 in a London Army barracks early in the pandemic. METHODS: Army personnel, their families and civilians had nasal and throat swabs for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcriptase -polymerase chain reaction (RT-PCR), virus isolation and whole genome sequencing, along with blood samples for SARS-CoV-2 antibodies. All tests were repeated 36 days later. FINDINGS: During the first visit, 304 (254 Army personnel, 10 family members, 36 civilians, 4 not stated) participated and 24/304 (8%) were SARS-CoV-2 RT-PCR positive. Infectious virus was isolated from 7/24 (29%). Of the 285 who provided a blood sample, 7% (19/285) were antibody positive and 63% (12/19) had neutralising antibodies. Twenty-two (22/34, 64%) individuals with laboratory-confirmed infection were asymptomatic. Nine SARS-CoV-2 RT-PCR positive participants were also antibody positive but those who had neutralising antibodies did not have infectious virus. At the second visit, no new infections were detected, and 13% (25/193) were seropositive, including 52% (13/25) with neutralising antibodies. Risk factors for SARS-CoV-2 antibody positivity included contact with a confirmed case (RR 25.2; 95% CI 14-45), being female (RR 2.5; 95% CI 1.0-6.0) and two-person shared bathroom (RR 2.6; 95% CI 1.1-6.4). INTERPRETATION: We identified high rates of asymptomatic SARS-CoV-2 infection. Public Health control measures can mitigate spread but virus re-introduction from asymptomatic individuals remains a risk. Most seropositive individuals had neutralising antibodies and infectious virus was not recovered from anyone with neutralising antibodies. FUNDING: PHE.

Recovery of individual Service personnel in the COVID-19 recovery phase.

To deny the SARS-CoV-2 virus easy options for sustained transmission, commanders should model adherence to, and ensure implementation of, social mitigation measures. While some measures can be achieved at the organisational level through policy, every Service person's experience of the COVID-19 pandemic will have differed, affected by a range of personal, occupational and geographical factors. A successful recovery phase for each Service personnel (SP) therefore relies on localised assessments and individualised support plans. The return of SP to the physical environment must be safe, and the financial needs of their whole family must be considered. Commanders must understand the need for balance in supporting social reconnection both personally and in the workplace. Commanders have an important role in the development of SPs' mental resilience; supporting mental well-being, early recognition of deteriorating mental health and signposting, and compassionate understanding of the needs of SP deployed or bereaved. Disruptions to healthcare service provision will impact the duration of medical downgrading, workforce capacity and operational effectiveness according to extant parameters, which must be understood by commanders. Likewise, functional fitness may have been adversely affected. Physical health and fitness recovery can be supported by time-based extensions to occupational health policy and graduated return to work physical training programmes.

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.

T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.