Association between bacterial homoplastic variants and radiological pathology in tuberculosis.

Funder: Biotechnology and Biological Sciences Research Council; FundRef: http://dx.doi.org/10.13039/501100000268Funder: FP7 People: Marie-Curie Actions; FundRef: http://dx.doi.org/10.13039/100011264; Grant(s): EU FP7-PEOPLE-2013-IRSES - Marie Curie Action DEANBACKGROUND: Understanding how pathogen genetic factors contribute to pathology in TB could enable tailored treatments to the most pathogenic and infectious strains. New strategies are needed to control drug-resistant TB, which requires longer and costlier treatment. We hypothesised that the severity of radiological pathology on the chest radiograph in TB disease was associated with variants arising independently, multiple times (homoplasies) in the Mycobacterium tuberculosis genome. METHODS: We performed whole genome sequencing (Illumina HiSeq2000 platform) on M. tuberculosis isolates from 103 patients with drug-resistant TB in Lima between 2010 and 2013. Variables including age, sex, HIV status, previous TB disease and the percentage of lung involvement on the pretreatment chest radiograph were collected from health posts of the national TB programme. Genomic variants were identified using standard pipelines. RESULTS: Two mutations were significantly associated with more widespread radiological pathology in a multivariable regression model controlling for confounding variables (Rv2828c.141, RR 1.3, 95% CI 1.21 to 1.39, p<0.01; rpoC.1040 95% CI 1.77 to 2.16, RR 1.9, p<0.01). The rpoB.450 mutation was associated with less extensive radiological pathology (RR 0.81, 95% CI 0.69 to 0.94, p=0.03), suggestive of a bacterial fitness cost for this mutation in vivo. Patients with a previous episode of TB disease and those between 10 and 30 years of age also had significantly increased radiological pathology. CONCLUSIONS: This study is the first to compare the M. tuberculosis genome to radiological pathology on the chest radiograph. We identified two variants significantly positively associated with more widespread radiological pathology and one with reduced pathology. Prospective studies are warranted to determine whether mutations associated with increased pathology also predict the spread of drug-resistant TB

Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy

COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively. Mutations occur within the antibody epitopes and for casirivimab+imdevimab multiple mutations are present on contiguous raw reads, simultaneously affecting both components. Using surface plasmon resonance and pseudoviral neutralisation assays we demonstrate these mutations reduce or completely abrogate antibody affinity and neutralising activity, suggesting they are driven by immune evasion. In addition, we show that some mutations also reduce the neutralising activity of vaccine-induced serum

Association Between Bacterial Homoplastic Variants and Radiological Pathology in Tuberculosis

Background Understanding how pathogen genetic factors contribute to pathology in tuberculosis could enable tailored treatments to the most pathogenic and infectious strains. New strategies are needed to control drug-resistant tuberculosis which requires longer and costlier treatment. We hypothesized that the severity of radiological pathology on the chest radiograph in tuberculosis disease was associated with variants arising independently, multiple times (homoplasies) in the Mycobacterium tuberculosis genome. Methods We performed whole genome sequencing (Illumina HiSeq2000 platform) on M. tuberculosis isolates from 103 drug-resistant tuberculosis patients in Lima between 2010-2013. Variables including age, sex, HIV status, previous tuberculosis disease and the percentage of lung involvement on the pre-treatment chest radiograph were collected from health posts of the national tuberculosis program. Genomic variants were identified using standard pipelines. Results Two mutations were significantly associated with more widespread radiological pathology in a multivariable regression model controlling for confounding variables [Rv2828c.141, RR 1.3 95%CI 1.21-1.39, p<0.01; rpoC.1040 95%CI 1.77-2.16, RR 1.9, p<0.01]. The rpoB.450 mutation was associated with less extensive radiological pathology (RR 0.81 95%CI 0.69-0.94, p=0.03) suggestive of a bacterial fitness cost for this mutation in vivo. Patients with a previous episode of tuberculosis disease and those between 10-30 years of age also had significantly increased radiological pathology. Conclusions This study is the first to compare the M. tuberculosis genome to radiological pathology on the chest radiograph. We identified two variants significantly positively associated with more widespread radiological pathology, and one with reduced pathology. Prospective studies are warranted to determine whether mutations associated with increased pathology also predict the spread of drug-resistant tuberculosis

Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID‐19 cases treated with sotrovimab in the community in England

There are concerns that sotrovimab has reduced efficacy at reducing hospitalisation risk against the BA.2 sub-lineage of the Omicron SARS-CoV-2 variant. We performed a retrospective cohort (n = 8850) study of individuals treated with sotrovimab in the community, with the objective of assessing whether there were any differences in risk of hospitalisation of BA.2 cases compared with BA.1. We estimated that the hazard ratio of hospital admission with a length of stay of 2 days or more was 1.17 for BA.2 compared with BA.1 (95%CI 0.74–1.86). These results suggest that the risk of hospital admission was similar between the two sub-lineages

Impact of prior SARS-CoV-2 infection and COVID-19 vaccination on the subsequent incidence of COVID-19: a multicentre prospective cohort study among UK healthcare workers - the SIREN (Sarscov2 Immunity & REinfection EvaluatioN) study protocol.

INTRODUCTION: Understanding the effectiveness and durability of protection against SARS-CoV-2 infection conferred by previous infection and COVID-19 is essential to inform ongoing management of the pandemic. This study aims to determine whether prior SARS-CoV-2 infection or COVID-19 vaccination in healthcare workers protects against future infection. METHODS AND ANALYSIS: This is a prospective cohort study design in staff members working in hospitals in the UK. At enrolment, participants are allocated into cohorts, positive or naïve, dependent on their prior SARS-CoV-2 infection status, as measured by standardised SARS-CoV-2 antibody testing on all baseline serum samples and previous SARS-CoV-2 test results. Participants undergo monthly antibody testing and fortnightly viral RNA testing during follow-up and based on these results may move between cohorts. Any results from testing undertaken for other reasons (eg, symptoms, contact tracing) or prior to study entry will also be captured. Individuals complete enrolment and fortnightly questionnaires on exposures, symptoms and vaccination. Follow-up is 12 months from study entry, with an option to extend follow-up to 24 months.The primary outcome of interest is infection with SARS-CoV-2 after previous SARS-CoV-2 infection or COVID-19 vaccination during the study period. Secondary outcomes include incidence and prevalence (both RNA and antibody) of SARS-CoV-2, viral genomics, viral culture, symptom history and antibody/neutralising antibody titres. ETHICS AND DISSEMINATION: The study was approved by the Berkshire Research Ethics Committee, Health Research Authority (IRAS ID 284460, REC reference 20/SC/0230) on 22 May 2020; the vaccine amendment was approved on 12 January 2021. Participants gave informed consent before taking part in the study.Regular reports to national and international expert advisory groups and peer-reviewed publications ensure timely dissemination of findings to inform decision making. TRIAL REGISTRATION NUMBER: ISRCTN11041050

Do Antibody Positive Healthcare Workers Have Lower SARS-CoV-2 Infection Rates than Antibody Negative Healthcare Workers? Large Multi-Centre Prospective Cohort Study (The SIREN Study), England: June to November 2020

Background: There is an urgent need to better understand whether individuals who have recovered from COVID-19 are protected from future SARS-CoV-2 infection.Methods: A large multi-centre prospective cohort was recruited from publicly funded hospital staff in the UK. Participants attended regular SARS-CoV-2 PCR and antibody testing (every 2-4 weeks) and completed fortnightly questionnaires on symptoms and exposures. At enrolment, participants were assigned to either the positive cohort (antibody positive or prior PCR/antibody test positive) or negative cohort (antibody negative, not previously known to be PCR/antibody positive). Potential reinfections were clinically reviewed and classified according to case definitions (confirmed, probable, possible (subdivided by symptom-status)) depending on hierarchy of evidence. Individuals in the primary infection were excluded from this analysis if infection was confirmed by antibody only. Reinfection rates in the positive cohort were compared against new PCR positives in the negative cohort using a mixed effective multivariable logistic regression analysis.Findings: Between 18 June and 09 November 2020, 44 reinfections (2 probable, 42 possible) were detected in the baseline positive cohort of 6,614 participants, collectively contributing 1,339,078 days of follow-up. This compares with 318 new PCR positive infections and 94 antibody seroconversions in the negative cohort of 14,173 participants, contributing 1,868,646 days of follow-up. The incidence density per 100,000 person days between June and November 2020 was 3.2 reinfections in the positive cohort, compared with 22.4 new PCR confirmed infections in the negative cohort. The adjusted odds ratio was 0.17 for all reinfections (95% CI 0.13-0.24) compared to PCR confirmed primary infections. The median interval between primary infection and reinfection was over 160 days.Interpretation: A prior history of SARS-CoV-2 infection was associated with an 83% lower risk of infection, with median protective effect observed five months following primary infection. This is the minimum likely effect as seroconversions were not included.Trial Registration: Trial registered with ISRCTN, Trial ID: ISRCTN11041050. https://www.isrctn.com/ISRCTN11041050.Funding Statement: Department of Health and Social Care and Public Health England, with contributions from the Scottish, Welsh and Northern Irish governments.Declaration of Interests: No conflicts of interest declared.Ethics Approval Statement: IRAS ID 284460, Berkshire Research Ethics Committee, Health Research Authority and Health and Care Research Wales approval granted 22 May 2020