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1.
Math Biosci ; 346: 108664, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1959838

ABSTRACT

The COVID-19 pandemic has challenged authorities at different levels of government administration around the globe. When faced with diseases of this severity, it is useful for the authorities to have prediction tools to estimate in advance the impact on the health system as well as the human, material, and economic resources that will be necessary. In this paper, we construct an extended Susceptible-Exposed-Infected-Recovered model that incorporates the social structure of Mar del Plata, the 4°most inhabited city in Argentina and head of the Municipality of General Pueyrredón. Moreover, we consider detailed partitions of infected individuals according to the illness severity, as well as data of local health resources, to bring predictions closer to the local reality. Tuning the corresponding epidemic parameters for COVID-19, we study an alternating quarantine strategy: a part of the population can circulate without restrictions at any time, while the rest is equally divided into two groups and goes on successive periods of normal activity and lockdown, each one with a duration of τ days. We also implement a random testing strategy with a threshold over the population. We found that τ=7 is a good choice for the quarantine strategy since it reduces the infected population and, conveniently, it suits a weekly schedule. Focusing on the health system, projecting from the situation as of September 30, we foresee a difficulty to avoid saturation of the available ICU, given the extremely low levels of mobility that would be required. In the worst case, our model estimates that four thousand deaths would occur, of which 30% could be avoided with proper medical attention. Nonetheless, we found that aggressive testing would allow an increase in the percentage of people that can circulate without restrictions, and the medical facilities to deal with the additional critical patients would be relatively low.


Subject(s)
COVID-19 , Argentina/epidemiology , COVID-19/prevention & control , Communicable Disease Control , Humans , Pandemics/prevention & control , Quarantine , SARS-CoV-2
3.
World Neurosurg ; 2022 Jun 18.
Article in English | MEDLINE | ID: covidwho-1960086

ABSTRACT

OBJECTIVE: Changes to neurosurgical practices during the coronavirus disease 2019 (COVID-19) pandemic have not been thoroughly analyzed. We report the effects of operative restrictions imposed under variable local COVID-19 infection rates and health care policies using a retrospective multicenter cohort study and highlight shifts in operative volumes and subspecialty practice. METHODS: Seven academic neurosurgery departments' neurosurgical case logs were collected; procedures in April 2020 (COVID-19 surge) and April 2019 (historical control) were analyzed overall and by 6 subspecialties. Patient acuity, surgical scheduling policies, and local surge levels were assessed. RESULTS: Operative volume during the COVID-19 surge decreased 58.5% from the previous year (602 vs. 1449, P = 0.001). COVID-19 infection rates within departments' counties correlated with decreased operative volume (r = 0.695, P = 0.04) and increased patient categorical acuity (P = 0.001). Spine procedure volume decreased by 63.9% (220 vs. 609, P = 0.002), for a significantly smaller proportion of overall practice during the COVID-19 surge (36.5%) versus the control period (42.0%) (P = 0.02). Vascular volume decreased by 39.5% (72 vs. 119, P = 0.01) but increased as a percentage of caseload (8.2% in 2019 vs. 12.0% in 2020, P = 0.04). Neuro-oncology procedure volume decreased by 45.5% (174 vs. 318, P = 0.04) but maintained a consistent proportion of all neurosurgeries (28.9% in 2020 vs. 21.9% in 2019, P = 0.09). Functional neurosurgery volume, which declined by 81.4% (41 vs. 220, P = 0.008), represented only 6.8% of cases during the pandemic versus 15.2% in 2019 (P = 0.02). CONCLUSIONS: Operative restrictions during the COVID-19 surge led to distinct shifts in neurosurgical practice, and local infective burden played a significant role in operative volume and patient acuity.

4.
IJID Reg ; 4: 120-122, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1959614

ABSTRACT

Objectives: For Tanzania, including Zanzibar, the development of the COVID-19 pandemic has remained unclear since the reporting of cases was suspended during 2020/21. Our study was the first to analyze data on COVID-19 seroprevalence in the Zanzibari population before the Omicron variant wave began in late 2021. Design: During August through October 2021, representative cross-sectional data were collected from randomly selected households in 120 wards of the two main islands, Unguja and Pemba. Participants voluntarily provided blood samples to test their sera for antibodies against SARS-CoV-2 using a semiquantitative enzyme-linked immunosorbent assay (ELISA). Results: 58.9% of the 2051 sera analysed were positive, without significant differences between Unguja and Pemba or between rural and urban areas. The results were in agreement with observations from other sub-Saharan African countries. Conclusions: The antibody levels observed were most likely due to previous infections with SARS-CoV-2, since vaccination was generally not available before the survey. Therefore, this study offers the first insights into how many Zanzibari had COVID-19 before the Omicron variant emerged. Furthermore, it provides an appropriate basis for a follow-up survey addressing how this seroprevalence has influenced susceptibility to the Omicron variants, given the use of harmonized methodologies.

5.
An Pediatr (Barc) ; 97(2): 129.e1-129.e8, 2022 Aug.
Article in Spanish | MEDLINE | ID: covidwho-1959296

ABSTRACT

We present a summary of the main modifications to the «COVID-19 in Paediatrics¼ clinical practice guideline made from its initial version, published in 2021, and the version published in 2022. The document was developed following the structured steps of evidence-based medicine and applying the GRADE system to synthesize the evidence, assess its quality and, when appropriate, issue graded recommendations (based on the quality of the evidence, values and preferences, the balance between benefits, risks and costs, equity and feasibility). This update also includes the modifications proposed by external reviewers.We summarised the main modifications in the following sections: epidemiology, clinical features, diagnosis, prevention, treatment and vaccines. In relation to the body of knowledge achieved in the first year of the pandemic, the literature published in the second year contributed additional data, but without substantial modifications in many of the areas. The main changes took place in the field of vaccine research. This update was completed in December 2021, coinciding with the emergence of infections by the omicron variant, so the document will need to be updated in the future.

6.
BMJ Paediatrics Open ; 6(1), 2022.
Article in English | ProQuest Central | ID: covidwho-1962324

ABSTRACT

BackgroundAccidental poisoning is a leading cause of unintentional injuries among children in low-income and middle-income countries (LMICs). The overall aspect of this unintentional poisoning is poorly understood in Bangladesh. The objectives of this study were (1) to explore the socio-demographic factors and circumstantial context of accidental poisoning and (2) the prevalence of the type of substances causing it.MethodsA descriptive case series study was conducted from April 2019 to February 2020 at a tertiary level hospital of the capital city Dhaka in Bangladesh. Children under 10 years of age admitted to the hospital with accidental poisoning were enrolled in this study. Parents of hospitalised children were interviewed face-to-face using a structured questionnaire. Descriptive statistics were used for data analysis.ResultsA total of 223 children were recruited in this study. Children between 2 and 5 years (60%), men (61%) and children with agility (65.5%) were among the prevalent victims. The majority of cases occurred (65%) in a nuclear family setting. Most mothers (85%) of these children were non-working and most incidents took place in parents’ homes (~82%). Nearly 70% of the poisoning incidents took place in the presence of parents and over half of these occurred in the bedroom. Kerosene was the prevalent cause (33%) of accidental poisoning while insecticide/pesticide ranked second (26.5%) followed by medicines (17%) and household chemicals (12). In one-third (31.4%) of the cases, poisoning chemicals were stored in soft drink bottles while two-thirds (67.3%) of the cases were kept in containers other than original ones. Although over 80 parents somewhat knew that chemicals could be harmful to the children if ingested, most of them did not take the safety measures.ConclusionIn this present study we found that preschool-aged children were more victims of accidental poisoning mostly by ingesting kerosene and a majority of the incidents took place in the bedroom while parents were present at home. Our study findings would serve as a baseline for designing future intervention studies and policies.

7.
5th International Conference on Traffic Engineering and Transportation System, ICTETS 2021 ; 12058, 2021.
Article in English | Scopus | ID: covidwho-1962042

ABSTRACT

The COVID-19 epidemic is spreading globally, and the efficient operation of emergency logistics can effectively reduce the harm caused by the epidemic. Considering the characteristics of COVID-19 and the speed of response required by emergency logistics, this paper takes the COVID-19 epidemic as the background and the circulation of medical supplies as the research object, constructs the operation framework of emergency logistics, designs the operation process of emergency logistics under the COVID-19 epidemic, and makes a detailed analysis of each link. It is expected to provide a reference for improving the emergency management system in China. © 2021 SPIE

8.
5th International Conference on Traffic Engineering and Transportation System, ICTETS 2021 ; 12058, 2021.
Article in English | Scopus | ID: covidwho-1962039

ABSTRACT

The spread of the COVID-19 epidemic in 2020 has extremely serious negative impacts on the global freight supply chain with regional port groups as its core. In order to reconstruct the global freight supply chain as soon as possible, alleviate the vicious competition of regional port groups and promote the development of regional integration, the advantages of port integration are increasingly prominent. To this end, based on Gounod's game theory, a three-stage game model of port integration is constructed with the overall objective of obtaining the maximum economic benefits for the regional port group, based on the current characteristics of the global freight supply chain impacted by the COVID-19 epidemic, and empirical analysis is conducted using the data of the Liaoning port group, and the reverse induction method is used to quantitatively analyze the specific impact of regional port integration on the economic benefits of the port and determine the performance of the regional port group under the background of the epidemic The theoretical basis is laid for the rational decision of port managers. The calculation results show that there is a threshold effect in the integration process of the Liaoning regional port group, and the gradual deepening of the integration of the Liaoning regional port group can effectively mitigate the negative impact of the COVID-19 epidemic on the regional port group. © 2021 SPIE

9.
Journal of the Operational Research Society ; 2022.
Article in English | Scopus | ID: covidwho-1960658

ABSTRACT

This study addresses two key issues, ie, the “cold-start problem” in transmission prediction of new or rare epidemics and the collaborative allocation of emergency medical resources considering multiple objectives. These two issues have not yet been well addressed in data-driven emergency medical resource allocation systems. A decision support prediction-then-optimization framework combing deep learning and optimization is developed to address these two issues. Two transfer learning based convolutional neural network models are built for epidemic transmission predictions in the initial and the subsequent outbreak regions using transfer learning to deal with the “cold-start problem”. A prediction-driven collaborative emergency medical resource allocation model is built to address the issue of collaborative decisions by simultaneously considering the inter- and intra-echelon resource flows in a multi-echelon system and considering the efficiency and fairness as the objective functions. A case study of the COVID-19 pandemic shows that combining transfer learning and convolutional neural networks can improve the performances of epidemic transmission predictions, and good predictions can improve both the efficiency and fairness of emergency medical resource allocation decisions. Moreover, the computational results show that the prediction errors are asymmetrically amplified in the optimization stage, and the shortage of the resource reserve quantity mediates the asymmetrical amplification effect. © Operational Research Society 2022.

10.
Inj Prev ; 28(4): 374-378, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1962341

ABSTRACT

IntroductionFirearm injuries are a public health crisis in the US. The National Death Index (NDI) is a well-established, comprehensive database managed by the National Center for Health Statistics at the CDC. In this methodology paper we describe our experience accessing and linking data from the NDI to our regional, hospital-based violent injury database to identify out-of-hospital deaths from firearms. METHODS: We outline the key steps of our submission to the NDI. Data were collected from research team meeting notes, team member emails with NDI staff, and information provided from the NDI website and supplementary guides. Few of our collaborators or university partner investigators had accessed or used data from the NDI. We discuss the online NDI Processing Portal data request, data preparation and receipt from the NDI, troubleshooting tips, and a timeline of events. RESULTS: Our query to the NDI returned 12 034 records of 12 219 firearm-injured patient records from 2010 and 2019. The record match rate was 98.5%. DISCUSSION: Linking hospital-based data sets with NDI data can provide valuable information on out-of-hospital deaths. This has the potential to improve the quality of longitudinal morbidity and mortality calculations in hospital-based patient cohorts. We encountered logistic and administrative challenges in completing the online NDI Processing Portal and in preparing and receiving data from the NDI. It is our hope that the lessons learnt presented herein will help facilitate easy and streamlined acquisition of valuable NDI data for other clinical researchers. WHAT THIS STUDY ADDS: - A step-by-step guide for clinical researchers of how to apply to access data from the National Death Index (NDI).- Advice and lessons learned on how to efficiently and effectively access data from the NDI.- A well-described methodology to improve the quality of longitudinal morbdity and mortality calculations in hospital-based cohorts of firearm injured patients.What is already known on this subject:- There is a need for robust, longitudinal data sources that reliably track morbidity and mortality among firearm injured patients in the United States.- The NDI is a well-established, comprehensive database that holds death records for all 50 states, which provides valuable mortality data to the public health and medical research community.


Subject(s)
Firearms , Wounds, Gunshot , Cause of Death , Hospitals , Humans , Population Surveillance , United States/epidemiology , Violence
11.
BMJ Open ; 12(7): e061013, 2022 07 26.
Article in English | MEDLINE | ID: covidwho-1962307

ABSTRACT

OBJECTIVES: To analyse associations between living in social housing and smoking in England and to evaluate progress towards reducing disparities in smoking prevalence among residents of social housing compared with other housing types. DESIGN: Cross-sectional analysis of nationally representative data collected between January 2015 and February 2020. SETTING: England. PARTICIPANTS: 105 562 adults (≥16 years). PRIMARY AND SECONDARY OUTCOME MEASURES: Linear and logistic regression were used to analyse associations between living in social housing (vs other housing types) and smoking status, cigarettes per day, time to first cigarette, exposure to others' smoking, motivation to stop smoking, quit attempts and use of cessation support. Analyses were adjusted for sex, age, social grade, region and year. RESULTS: Adults living in social housing had two times the odds of being a smoker (ORadj=2.17, 95% CI 2.08 to 2.27), and the decline in smoking prevalence between 2015 and 2020 was less pronounced in this high-risk group (-7%; ORadj=0.98, 95% CI 0.96 to 1.01) than among adults living in other housing types (-24%; ORadj=0.95, 95% CI 0.94 to 0.96; housing tenure-survey year interaction p=0.020). Smokers living in social housing were more addicted than those in other housing types (smoking within 30 min of waking: ORadj=1.50, 95% CI 1.39 to 1.61), but were no less motivated to stop smoking (ORadj=1.06, 95% CI 0.96 to 1.17) and had higher odds of having made a serious attempt to quit in the past year (ORadj=1.16, 95% CI 1.07 to 1.25). Among smokers who had tried to quit, those living in social housing had higher odds of using evidence-based cessation support (ORadj=1.22, 95% CI 1.07 to 1.39) but lower odds of remaining abstinent (ORadj=0.63, 95% CI 0.52 to 0.76). CONCLUSIONS: There remain stark inequalities in smoking and quitting behaviour by housing tenure in England, with declines in prevalence stalling between 2015 and 2020 despite progress in the rest of the population. In the absence of targeted interventions to boost quitting among social housing residents, inequalities in health are likely to worsen.


Subject(s)
Smoking Cessation , Adult , Cross-Sectional Studies , England/epidemiology , Housing , Humans , Smoking/epidemiology
12.
BMJ Open ; 12(7): e060739, 2022 07 27.
Article in English | MEDLINE | ID: covidwho-1962302

ABSTRACT

OBJECTIVE: The primary objectives were to determine the magnitude of COVID-19 infections in the general population and age-specific cumulative incidence, as determined by seropositivity and clinical symptoms of COVID-19, and to determine the magnitude of asymptomatic or subclinical infections. DESIGN, SETTING AND PARTICIPANTS: We describe a population-based, cross-sectional, age-stratified seroepidemiological study conducted throughout Afghanistan during June/July 2020. Participants were interviewed to complete a questionnaire, and rapid diagnostic tests were used to test for SARS-CoV-2 antibodies. This national study was conducted in eight regions of Afghanistan plus Kabul province, considered a separate region. The total sample size was 9514, and the number of participants required in each region was estimated proportionally to the population size of each region. For each region, 31-44 enumeration areas (EAs) were randomly selected, and a total of 360 clusters and 16 households per EA were selected using random sampling. To adjust the seroprevalence for test sensitivity and specificity, and seroreversion, Bernoulli's model methodology was used to infer the population exposure in Afghanistan. OUTCOME MEASURES: The main outcome was to determine the prevalence of current or past COVID-19 infection. RESULTS: The survey revealed that, to July 2020, around 10 million people in Afghanistan (31.5% of the population) had either current or previous COVID-19 infection. By age group, COVID-19 seroprevalence was reported to be 35.1% and 25.3% among participants aged ≥18 and 5-17 years, respectively. This implies that most of the population remained at risk of infection. However, a large proportion of the population had been infected in some localities, for example, Kabul province, where more than half of the population had been infected with COVID-19. CONCLUSION: As most of the population remained at risk of infection at the time of the study, any lifting of public health and social measures needed to be considered gradually.


Subject(s)
COVID-19 , Adult , Afghanistan/epidemiology , Antibodies, Viral , COVID-19/epidemiology , Cross-Sectional Studies , Humans , Prevalence , SARS-CoV-2 , Seroepidemiologic Studies , Young Adult
13.
BMJ Open ; 12(4): e057846, 2022 04 05.
Article in English | MEDLINE | ID: covidwho-1962255

ABSTRACT

OBJECTIVES: Few studies reported COVID-19 cases in schools during the 2020/21 academic year in a setting of uninterrupted in-person schooling. The main objective was to determine the SARS-CoV-2 seroprevalence among school staff in Vancouver public schools. DESIGN: Cumulative incident COVID-19 cases among all students and school staff based on public health data, with an embedded cross-sectional serosurvey among a school staff sample that was compared to period, age, sex and geographical location-weighted data from blood donors. SETTING: Vancouver School District (British Columbia, Canada) from kindergarten to grade 12. PARTICIPANTS: Active school staff enrolled from 3 February to 23 April 2021 with serology testing from 10 February to 15 May 2021. MAIN OUTCOME MEASURES: SARS-CoV-2 seroprevalence among school staff, based on spike (S)-based (unvaccinated staff) or N-based serology testing (vaccinated staff). RESULTS: Public health data showed the cumulative incidence of COVID-19 among students attending in-person was 9.8 per 1000 students (n=47 280), and 13 per 1000 among school staff (n=7071). In a representative sample of 1689 school staff, 78.2% had classroom responsibilities, and spent a median of 17.6 hours in class per week (IQR: 5.0-25 hours). Although 21.5% (363/1686) of surveyed staff self-reported close contact with a COVID-19 case outside of their household (16.5% contacts were school-based), 5 cases likely acquired the infection at school based on viral testing. Sensitivity/Specificity-adjusted seroprevalence in 1556/1689 staff (92.1%) was 2.3% (95% CI: 1.6% to 3.2%), comparable to a sex, age, date and residency area-weighted seroprevalence of 2.6% (95% CI: 2.2% to 3.1%) among 5417 blood donors. CONCLUSION: Seroprevalence among staff was comparable to a reference group of blood donors from the same community. These data show that in-person schooling could be safely maintained during the 2020/21 school year with mitigation measures, in a large school district in Vancouver, Canada.


Subject(s)
COVID-19 , SARS-CoV-2 , British Columbia/epidemiology , COVID-19/epidemiology , Cross-Sectional Studies , Humans , Seroepidemiologic Studies
14.
BMJ Open ; 12(7): e057197, 2022 07 28.
Article in English | MEDLINE | ID: covidwho-1962241

ABSTRACT

OBJECTIVES: The objective of the study was to assess psychological distress (depression, anxiety and stress) and associated factors among healthcare professionals working at the University of Gondar Comprehensive Specialized Hospital, Ethiopia. DESIGN: Institution-based cross-sectional study. SETTING: This study was conducted at the University of Gondar Comprehensive Specialized Hospital. PARTICIPANTS: Study participants were healthcare professionals from University of Gondar Comprehensive Specialized Hospital. They were selected for the study using a stratified sampling technique. MEASUREMENT: Data were collected using a self-administered questionnaire. The 21-item Depression, Anxiety and Stress Scale was used to assess the depression, anxiety and stress levels. Descriptive and analytical statistics were used to present the findings. To determine the predictor variables for depression, anxiety and stress, a binary logistic regression model was fitted. Finally, variables with p value <0.05 in the final model were declared as significantly associated with psychological distress. RESULT: Almost half (49.5) of the participants have psychological distress. The prevalence of depression, anxiety and stress during the COVID-19 pandemic among healthcare workers was 167 (42.7%), 201 (51.4%) and 242 (61.9%), respectively. In multivariable analysis, respondents found in the ages between 35 and 44; unmarried marital status; educational status with specialty, subspecialty and PhD holders; anaesthesia professionals; and healthcare professionals with known medical illness were significantly associated with depression. Unmarried marital status, anaesthesia professional, laboratory technologist and living with family were significantly associated with anxiety. Unmarried marital status; educational status with specialty, subspecialty and PhD holders; and anaesthesia professional were also statistically significant with stress. CONCLUSION AND RECOMMENDATION: The prevalence of depression, anxiety and stress during the COVID-19 pandemic among the Gondar University healthcare professionals was high. This could contribute to implementation of mitigation measures in a standardised and sustainable manner and emphasis should be given to this aspect of health even for future similar and unanticipated events.


Subject(s)
COVID-19 , Psychological Distress , Adult , Anxiety/epidemiology , COVID-19/epidemiology , Cross-Sectional Studies , Delivery of Health Care , Depression/epidemiology , Ethiopia/epidemiology , Health Personnel/psychology , Humans , Pandemics , Stress, Psychological/epidemiology
15.
BMJ Open ; 12(4): e052514, 2022 04 19.
Article in English | MEDLINE | ID: covidwho-1962188

ABSTRACT

OBJECTIVES: Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabilistic reporting methodology, can inform infection prevention and control (IPC) practice within NHS hospital settings. DESIGN: Multicentre, prospective, interventional, superiority study. SETTING: 14 participating NHS hospitals over winter-spring 2020/2021 in the UK. PARTICIPANTS: Eligible patients must be admitted to hospital with first-confirmed SARS-CoV-2 PCR-positive test result >48 hour from time of admission, where COVID-19 diagnosis not suspected on admission. The projected sample size is 2380 patients. INTERVENTION: The intervention is the return of a sequence report, within 48 hours in one phase (rapid local lab processing) and within 5-10 days in a second phase (mimicking central lab), comparing the viral genome from an eligible study participant with others within and outside the hospital site. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcomes are incidence of Public Health England (PHE)/IPC-defined SARS-CoV-2 hospital-acquired infection during the baseline and two interventional phases, and proportion of hospital-onset cases with genomic evidence of transmission linkage following implementation of the intervention where such linkage was not suspected by initial IPC investigation. Secondary outcomes include incidence of hospital outbreaks, with and without sequencing data; actual and desirable changes to IPC actions; periods of healthcare worker (HCW) absence. Health economic analysis will be conducted to determine cost benefit of the intervention. A process evaluation using qualitative interviews with HCWs will be conducted alongside the study. TRIAL REGISTRATION NUMBER: ISRCTN50212645. Pre-results stage. This manuscript is based on protocol V.6.0. 2 September 2021.


Subject(s)
COVID-19 , Cross Infection , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Testing , Cross Infection/epidemiology , Cross Infection/prevention & control , Hospitals , Humans , Multicenter Studies as Topic , Pandemics/prevention & control , Prospective Studies , SARS-CoV-2/genetics , State Medicine , Treatment Outcome , United Kingdom/epidemiology
16.
Ann Rheum Dis ; 2022 Jul 22.
Article in English | MEDLINE | ID: covidwho-1962122

ABSTRACT

OBJECTIVES: To evaluate long-term kinetics of the BNT162b2 mRNA vaccine-induced immune response in adult patients with autoimmune inflammatory rheumatic diseases (AIIRD) and immunocompetent controls. METHODS: A prospective multicentre study investigated serum anti-SARS-CoV-2 S1/S2 IgG titre at 2-6 weeks (AIIRD n=720, controls n=122) and 6 months (AIIRD n=628, controls n=116) after the second vaccine, and 2-6 weeks after the third vaccine dose (AIIRD n=169, controls n=45). T-cell immune response to the third vaccine was evaluated in a small sample. RESULTS: The two-dose vaccine regimen induced a higher humoral response in controls compared with patients, postvaccination seropositivity rates of 100% versus 84.72%, p<0.0001, and 96.55% versus 74.26%, p<0.0001 at 2-6 weeks and at 6 months, respectively. The third vaccine dose restored the seropositive response in all controls and 80.47% of patients with AIIRD, p=0.0028. All patients treated with methotrexate monotherapy, anticytokine biologics, abatacept and janus kinase (JAK) inhibitors regained the humoral response after the third vaccine, compared with only a third of patients treated with rituximab, entailing a 16.1-fold risk for a negative humoral response, p≤0.0001. Cellular immune response in rituximab-treated patients was preserved before and after the third vaccine and was similar to controls. Breakthrough COVID-19 rate during the Delta surge was similar in patients and controls, 1.83% versus 1.43%, p=1. CONCLUSIONS: The two-dose BNTb262 regimen was associated with similar clinical efficacy and similar waning of the humoral response over 6 months among patients with AIIRD and controls. The third vaccine dose restored the humoral response in all of the controls and the majority of patients.

17.
Microb Genom ; 8(7)2022 07.
Article in English | MEDLINE | ID: covidwho-1961306

ABSTRACT

The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Genome, Viral/genetics , Humans , Lebanon/epidemiology , Pandemics , Phylogeny , Prospective Studies , Retrospective Studies , SARS-CoV-2/genetics
18.
J Travel Med ; 2022 Jul 24.
Article in English | MEDLINE | ID: covidwho-1961105

ABSTRACT

BACKGROUND: Italy was the first country after China to be severely affected by the COVID-19 pandemic, in early 2020. The country responded swiftly to the outbreak with a nationwide two-step lockdown, the first one light, and the second one tight. By analysing 2020 national mobile phone movements, we assessed how lockdown compliance influenced its efficacy. METHODS: We measured individual mobility during the first epidemic wave with mobile phone movements tracked through carrier networks, and related this mobility to daily new SARS-CoV-2 infections, hospital admissions, intensive care admissions and deaths attributed to COVID-19, taking into account reason for travel (work-related or not) and the means of transport. RESULTS: The tight lockdown resulted in an 82% reduction in mobility for the entire country and was effective in swiftly curbing the outbreak as indicated by a shorter time-to-peak of all health outcomes, particularly for provinces with the highest mobility reductions and the most intense COVID-19 spread. Reduction of work-related mobility was accompanied by a nearly linear benefit in outbreak containment; work-unrelated movements had a similar effect only for restrictions exceeding 50%. Reduction in mobility by car and by airplane was nearly linearly associated with a decrease in most COVID-19 health outcomes, while for train travel reductions exceeding 55% had no additional beneficial effects. The absence of viral variants and vaccine availability during the study period eliminated confounding from these two sources. CONCLUSIONS: Adherence to the COVID-19 tight lockdown during the first wave in Italy was high and effective in curtailing the outbreak. Any work-related mobility reduction was effective, but only high reductions in work-unrelated mobility restrictions were effective. For train travel, there was a threshold above which no further benefit occurred. These findings could be particular to the spread of SARS-CoV-2, but might also apply to other communicable infections with comparable transmission dynamics.

19.
Commun Med (Lond) ; 2: 93, 2022.
Article in English | MEDLINE | ID: covidwho-1960516

ABSTRACT

Background: SARS-CoV-2 variants of concern, such as Omicron (B.1.1.529), continue to emerge. Assessing the impact of their potential viral properties on the probability of future transmission dominance and public health burden is fundamental in guiding ongoing COVID-19 control strategies. Methods: With an individual-based transmission model, OpenCOVID, we simulated three viral properties; infectivity, severity, and immune-evading ability, all relative to the Delta variant, to identify thresholds for Omicron's or any emerging VOC's potential future dominance, impact on public health, and risk to health systems. We further identify for which combinations of viral properties current interventions would be sufficient to control transmission. Results: We show that, with first-generation SARS-CoV-2 vaccines and limited physical distancing in place, a VOC's potential future dominance is primarily driven by its infectivity, which does not always lead to an increased public health burden. However, we also show that highly immune-evading variants that become dominant, even in the case of reduced variant severity, would likely require alternative measures to avoid strain on health systems, such as strengthened physical distancing measures, novel treatments, and second-generation vaccines. Expanded vaccination, that includes a booster dose for adults and child vaccination strategies, is projected to have the biggest public health benefit for a highly infective, highly severe VOC with low immune-evading capacity. Conclusions: These findings provide quantitative guidance to decision-makers at a critical time while Omicron's properties are being assessed and preparedness for emerging VOCs is eminent. We emphasise the importance of both genomic and population epidemiological surveillance.

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