Curating a knowledge base for individuals with coinfection of HIV and SARS-CoV-2: a study protocol of EHR-based data mining and clinical implementation

Introduction
Despite a higher risk of severe COVID-19 disease in individuals with HIV, the interactions between SARS-CoV-2 and HIV infections remain unclear. To delineate these interactions, multicentre Electronic Health Records (EHR) hold existing promise to provide full-spectrum and longitudinal clinical data, demographics and sociobehavioural data at individual level. Presently, a comprehensive EHR-based cohort for the HIV/SARS-CoV-2 coinfection has not been established; EHR integration and data mining methods tailored for studying the coinfection are urgently needed yet remain underdeveloped.

Methods and analysis
The overarching goal of this exploratory/developmental study is to establish an EHR-based cohort for individuals with HIV/SARS-CoV-2 coinfection and perform large-scale EHR-based data mining to examine the interactions between HIV and SARS-CoV-2 infections and systematically identify and validate factors contributing to the severe clinical course of the coinfection. We will use a nationwide EHR database in the USA, namely, National COVID Cohort Collaborative (N3C). Ultimately, collected clinical evidence will be implemented and used to pilot test a clinical decision support prototype to assist providers in screening and referral of at-risk patients in real-world clinics.

Ethics and dissemination
The study was approved by the institutional review boards at the University of South Carolina (Pro00121828) as non-human subject study. Study findings will be presented at academic conferences and published in peer-reviewed journals. This study will disseminate urgently needed clinical evidence for guiding clinical practice for individuals with the coinfection at Prisma Health, a healthcare system in collaboration.

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Settembre 2022

SARS-CoV-2 chronological genomic evolution and epidemiology in the Middle East and North Africa (MENA) region as affected by vaccination, conflict and socioeconomical disparities: a population-based cohort study

Objective
To describe the chronological genomic evolution of SARS-CoV-2 and its impact on public health in the Middle East and North Africa (MENA) region.

Methods
This study analysed all available SARS-CoV-2 genomic sequences, metadata and rates of COVID-19 infection from the MENA region retrieved from the Global Initiative on Sharing All Influenza Data database from January 2020 to August 2021. Inferential and ‎descriptive statistics were conducted to describe the epidemiology of SARS-CoV-2.

Results
Genomic surveillance of SARS-CoV-2 in the MENA region indicated that the variants in January 2020 predominately belonged to the G, GR, GH or O clades and that the most common variant of concern was Alpha. By August 2021, however, the GK clade dominated (57.4% of all sequenced genomes), followed by the G clade (18.7%) and the GR clade (11.6%). In August, the most commonly sequenced variants of concern were Delta in the Middle East region (91%); Alpha (44.3%) followed by Delta (29.7%) and Beta (25.3%) in the North Africa region; and Alpha (88.9%), followed by Delta (10%) in the fragile and conflict-affected regions of MENA. The mean proportion of the variants of concern among the total sequenced samples differed significantly by country (F=1.93, P=0.0112) but not by major MENA region (F=0.14, P=0.27) or by vaccination coverage (F=1.84, P=0.176).

Conclusion
This analysis of the genomic surveillance of SARS-CoV-2 provides an essential description the virus evolution and its impact on public health safety in the MENA region. As of August 2021, the Delta variant showed a genomic advantage in the MENA region. The MENA region includes several fragile and conflict-affected countries with extremely low levels of vaccination coverage and little genomic surveillance, which may soon exacerbate the existing health crisis within those countries and globally.

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Settembre 2022

Cohort profile: Stop the Spread Ottawa (SSO)–a community-based prospective cohort study on antibody responses, antibody neutralisation efficiency and cellular immunity to SARS-CoV-2 infection and vaccination

Purpose
To investigate the robustness and longevity of SARS-CoV-2 immune responses conferred by natural infection and vaccination among priority populations such as immunocompromised individuals and people with post-acute sequelae of COVID-19 in a prospective cohort study (Stop the Spread Ottawa—SSO) in adults living in the Ottawa region. In this paper, we describe the study design, ongoing data collection and baseline characteristics of participants.

Participants
Since October 2020, participants who tested positive for COVID-19 (convalescents) or at high risk of exposure to the virus (under surveillance) have provided monthly blood and saliva samples over a 10-month period. As of 2 November 2021, 1026 adults had completed the baseline survey and 976 had attended baseline bloodwork. 300 participants will continue to provide bimonthly blood samples for 24 additional months (ie, total follow-up of 34 months).

Findings to date
The median age of the baseline sample was 44 (IQR 23, range: 18–79) and just over two-thirds (n=688; 67.1%) were female. 255 participants (24.9%) had a history of COVID-19 infection confirmed by PCR and/or serology. Over 600 participants (60.0%) work in high-risk occupations (eg, healthcare, teaching and transportation). 108 participants (10.5%) reported immunocompromising conditions or treatments at baseline (eg, cancer, HIV, other immune deficiency, and/or use of immunosuppressants).

Future plans
SSO continues to yield rich research potential, given the collection of pre-vaccine baseline data and samples from the majority of participants, recruitment of diverse subgroups of interest, and a high level of participant retention and compliance with monthly sampling. The 24-month study extension will maximise opportunities to track SARS-CoV-2 immunity and vaccine efficacy, detect and characterise emerging variants, and compare subgroup humoral and cellular response robustness and persistence.

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Settembre 2022

Pre-COVID-19 pandemic health-related behaviours in children (2018-2020) and association with being tested for SARS-CoV-2 and testing positive for SARS-CoV-2 (2020-2021): a retrospective cohort study using survey data linked with routine health data in Wales, UK

Objectives
Examine if pre-COVID-19 pandemic (prior March 2020) health-related behaviours during primary school are associated with (1) being tested for SARS-CoV-2 and (2) testing positive between 1 March 2020 and 31 August 2021.

Design
Retrospective cohort study using an online cohort survey (January 2018 to February 2020) linked with routine PCR SARS-CoV-2 test results.

Setting
Children attending primary schools in Wales (2018–2020), UK, who were part of the Health and Attainment of Pupils in a Primary Education Network (HAPPEN)_school network.

Participants
Complete linked records of eligible participants were obtained for n=7062 individuals. 39.1% (n=2764) were tested (age 10.6±0.9; 48.9% girls) and 8.1% (n=569) tested positive for SARS-CoV-2 (age 10.6±1.0; 54.5% girls).

Main outcome measures
Logistic regression of health-related behaviours and demographics were used to determine the ORs of factors associated with (1) being tested for SARS-CoV-2 and (2) testing positive for SARS-CoV-2.

Results
Consuming sugary snacks (1–2 days/week OR=1.24, 95% CI 1.04 to 1.49; 5–6 days/week OR=1.31, 95% CI 1.07 to 1.61; reference 0 days), can swim 25 m (OR=1.21, 95% CI 1.06 to 1.39) and age (OR=1.25, 95% CI 1.16 to 1.35) were associated with an increased likelihood of being tested for SARS-CoV-2. Eating breakfast (OR=1.52, 95% CI 1.01 to 2.27), weekly physical activity ≥60 min (1–2 days OR=1.69, 95% CI 1.04 to 2.74; 3–4 days OR=1.76, 95% CI 1.10 to 2.82; reference 0 days), out-of-school club participation (OR=1.06, 95% CI 1.02 to 1.10), can ride a bike (OR=1.39, 95% CI 1.00 to 1.93), age (OR=1.16, 95% CI 1.05 to 1.28) and girls (OR=1.21, 95% CI 1.00 to 1.46) were associated with an increased likelihood of testing positive for SARS-CoV-2. Living in least deprived areas (quintile 4 OR=0.64, 95% CI 0.46 to 0.90; quintile 5 OR=0.64, 95% CI 0.46 to 0.89) compared with the most deprived (quintile 1) was associated with a decreased likelihood.

Conclusions
Associations may be related to parental health literacy and monitoring behaviours. Physically active behaviours may include coparticipation with others and exposure to SARS-CoV-2. A risk-versus-benefit approach must be considered in relation to promoting these health behaviours, given the importance of health-related behaviours such as childhood physical activity for development.

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Settembre 2022

Primary biliary cholangitis and SARS-CoV-2 infection: incidence, susceptibility and outcomes

We read with interest the work by Mansoor et al1 regarding the outcomes of COVID-19 in coeliac disease. The impact of pre-existing chronic liver diseases on COVID-19 outcomes has been largely evaluated,2–4 and consequently specific recommendations have been made in these patients.5 However, the relationship between primary biliary cholangitis (PBC) and SARS-CoV-2 remains unknown.6 We aimed to determine (1) the cumulative incidence of SARS-CoV-2 infection in a population of patients with PBC, comparing with the general Spanish cumulative incidence by the end of April 2021; (2) the baseline factors associated with a higher susceptibility to SARS-CoV-2 infection; and (3) the baseline factors associated with COVID-19-related hospitalisation. We performed a multicentre retrospective study enrolling 1151 patients from 13 Spanish referral hospitals. We collected information about SARS-CoV-2 infection from medical records of all patients with PBC from January 2020…

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Settembre 2022

How has the emergence of the Omicron SARS-CoV-2 variant of concern influenced worry, perceived risk and behaviour in the UK? A series of cross-sectional surveys

Objectives
To investigate changes in beliefs and behaviours following news of the Omicron variant and changes to guidance understanding of Omicron-related guidance, and factors associated with engaging with protective behaviours.

Design
Series of cross-sectional surveys (1 November to 16 December 2021, five waves of data collection).

Setting
Online.

Participants
People living in England, aged 16 years or over (n=1622–1902 per wave).

Primary and secondary outcome measures
Levels of worry and perceived risk, and engagement with key behaviours (out-of-home activities, risky social mixing, wearing a face covering and testing uptake).

Results
Degree of worry and perceived risk of COVID-19 (to oneself and people in the UK) fluctuated over time, increasing slightly around the time of the announcement about Omicron (p

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Agosto 2022

Seropositivity of SARS-CoV-2 in an unvaccinated cohort in British Columbia, Canada: a cross-sectional survey with dried blood spot samples

Objectives
Gathering population-based data on prevalence of SARS-CoV-2 infection is vital to the public health response and planning. Current seroprevalence data in BC are limited with respect to considerations of how socioeconomic and demographic factors, such as age, sex, gender, income, identifying as a visibility minority and occupation, are related to SARS-CoV-2 antibody detection due to infection-acquired immunity. We aimed to estimate the SARS-CoV-2 seropositivity in a cohort of British Columbians, using at-home self-collected dried blood spot (DBS) samples.

Design
This cross-sectional study included online surveys that collected sociodemographic and COVID-19 vaccine receipt information, and an at-home DBS collection kit.

Setting
British Columbia (BC), Canada.

Participants
Eligible participants were aged 25–69 years and residents of BC.

Primary outcome measure
SARS-CoV-2 anti-spike IgG antibody detection in unvaccinated individuals. Adjusted incidence rate ratios (aIRR) explored factors associated with seropositivity.

Results
SARS-CoV-2 serology was performed on a total of 4048 unvaccinated participants 25–69 years of age who submitted DBS samples taken from November 2020 to June 2021. A total of 118 seropositive cases were identified, for an estimated overall seropositivity of 2.92% (95% CI 2.42% to 3.48%). Participants identifying as a visible minority had a higher seropositivity, 5.1% vs 2.6% (p=0.003), compared with non-visible minority participants. After adjustment by age and sex, identifying as a visible minority (aIRR=1.85, 95% CI 1.20 to 2.84) remained the only significant factor associated with SARS-CoV-2 antibody detection in this cohort of unvaccinated individuals.

Conclusions
SARS-CoV-2 seropositivity in the BC population due to infection-acquired immunity was low. Seropositivity indicated that among those unvaccinated, visible minority communities have been most impacted. Continued monitoring of SARS-CoV-2 serology due to both infection-acquired and vaccine-acquired immunity will be vital in public health planning and pandemic response.

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Agosto 2022

Why do people consent to receiving SARS-CoV-2 vaccinations? A representative survey in Germany

Objective
To answer the question: Why do people consent to being vaccinated with novel vaccines against SARS-CoV-2?

Design
Representative survey.

Setting
Online panel.

Participants
1032 respondents of the general German population.

Method
A representative survey among German citizens in November/December 2021 that resulted in 1032 complete responses on vaccination status, sociodemographic parameters and opinions about the COVID-19 situation.

Results
Almost 83% of the respondents were vaccinated. The major motivation was fear of medical consequences of an infection and the wish to lead a normal life again. The major motivation to be not vaccinated was the fear of side effects and scepticism about long-term effectiveness and safety. Sixteen per cent of vaccinated respondents reported some serious side effect, while more than 30% reported health improvements, mostly due to the relief of psychological stress and social reintegration. We also validated a ‘Corona Orthodoxy Score—COS’ consisting of seven items reflecting opinions on COVID-19. The scale is reliable (alpha=0.76) and unidimensional. The COS was a highly significant predictor of vaccination status and readiness to be vaccinated in a multivariable logistic regression model. Those who were vaccinated were more likely to live in smaller households (OR=0.82, p=0.024), had a higher income (OR=1.27, p

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Agosto 2022

Combination therapy of infliximab and thiopurines, but not monotherapy with infliximab or vedolizumab, is associated with attenuated IgA and neutralisation responses to SARS-CoV-2 in inflammatory bowel disease

The effect of immunomodulator and biological therapy for IBD on the immune response to SARS-CoV-2 is of substantial interest to patients and clinicians worldwide. The CLARITY IBD study recently reported attenuated serological responses in patients with IBD treated with infliximab in comparison with vedolizumab,1 with the effect greatest in those on infliximab/thiopurine combination therapy. Independently, the global SECURE-IBD registry highlighted that infliximab/thiopurine combination therapy, but not infliximab or vedolizumab monotherapies, was associated with more severe clinical outcomes upon SARS-CoV-2 infection.2 3 However, these studies have not addressed treatment effects on neutralising antibody responses, which are associated with protection to SARS-CoV-2; nor have they analysed the range of serological signatures that may influence clinical outcomes.4 5 To answer these questions, we performed an extended analysis of serological responses to SARS-CoV-2 infection in patients with seropositive IBD treated with either infliximab…

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Agosto 2022

Antibody response to the BNT162b2 SARS-CoV-2 vaccine in paediatric patients with inflammatory bowel disease treated with anti-TNF therapy

We read with interest the recent findings by Kennedy et al, which concluded that infliximab (IFX) impairs antibody responses to a single dose of the mRNA-BNT162b2 SARS-CoV-2 vaccine in adult patients with IBD.1 2 Interestingly, another study showed that antibodies against SARS-CoV-2 diminish over time following infection in adult patients with IBD.3 In general, more robust antibody responses have been observed in adolescents compared with adults in the BNT162b2 vaccine trial.4 However, the true impact of immunosuppressant therapies on SARS-CoV-2 vaccine efficacy in paediatric IBD (PIBD) patients is unknown as they were excluded from the trials. Therefore, analysing vaccine responses directly in these patients is necessary to determine the best strategy.5 6 We undertook a study to evaluate immunogenicity of mRNA-based SARS-CoV-2 vaccines in PIBD patients treated with anti-TNF therapies. Given the urgent need for data, we…

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Agosto 2022

Diagnostic yield of screening for SARS-CoV-2 among patients admitted to hospital for alternate diagnoses: an observational cohort study

Objectives
To determine the diagnostic yield of screening patients for SARS-CoV-2 who were admitted with a diagnosis unrelated to COVID-19 and to identify risk factors for positive tests.

Design
Cohort from the Canadian COVID-19 Emergency Department Rapid Response Network registry.

Setting
30 acute care hospitals across Canada.

Participants
Patients hospitalised for non-COVID-19-related diagnoses who were tested for SARS-CoV-2 between 1 March and 29 December 2020.

Main outcome
Positive nucleic acid amplification test for SARS-CoV-2.

Outcome measure
Diagnostic yield.

Results
We enrolled 15 690 consecutive eligible adults who were admitted to hospital without clinically suspected COVID-19. Among these patients, 122 tested positive for COVID-19, resulting in a diagnostic yield of 0.8% (95% CI 0.64% to 0.92%). Factors associated with a positive test included presence of fever, being a healthcare worker, having a positive household contact or institutional exposure, and living in an area with higher 7-day average incident COVID-19 cases.

Conclusions
Universal screening of hospitalised patients for COVID-19 across two pandemic waves had a low diagnostic yield and should be informed by individual-level risk assessment in addition to regional COVID-19 prevalence.

Trial registration number
NCT04702945.

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Agosto 2022

Three-month follow-up of durability of response to the third dose of the SARS-CoV-2 BNT162b2 vaccine in adults aged 60 years and older: a prospective cohort study

Objective
To evaluate the durability of response 3 months after the third BNT162b2 vaccine in adults aged 60 years and older.

Design
Prospective cohort study.

Setting
Single tertiary centre.

Participants
Healthcare workers/family members aged ≥60 years old who received the third BNT162b2 dose.

Interventions
Blood samples were drawn immediately before (T0), 10–19 days (T1) and 74–103 days (T2) after the third dose.

Primary and secondary outcome measures
Anti-spike IgG titres were determined using a commercial assay and seropositivity was defined as ≥50 arbitrary units (AU)/mL. Neutralising antibody titres were determined at T2. Adverse events, COVID-19 infections and Clinical Frailty Scale (CFS) levels were documented.

Results
The analysis included 97 participants (median age, 70 years (IQR, 66–74), 58% CFS level 2). IgG titres, which increased significantly from T0 to T1 (median, 440 AU/mL (IQR, 294–923) and median, 25 429 AU/mL (IQR, 14 203–36 114), respectively; p

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Agosto 2022