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1.
Front Immunol ; 12: 789735, 2021.
Article in English | MEDLINE | ID: covidwho-1581322

ABSTRACT

Background: The host immune response has a prominent role in the progression and outcome of SARS-CoV-2 infection. Lymphopenia has been described as an important feature of SARS-CoV-2 infection and has been associated with severe disease manifestation. Lymphocyte dysregulation and hyper-inflammation have been shown to be associated with a more severe clinical course; however, a T cell subpopulation whose dysfunction correlate with disease progression has yet to be identify. Methods: We performed an immuno-phenotypic analysis of T cell sub-populations in peripheral blood from patients affected by different severity of COVID-19 (n=60) and undergoing a different clinical evolution. Clinical severity was established based on a modified WHO score considering both ventilation support and respiratory capacity (PaO2/FiO2 ratio). The ability of circulating cells at baseline to predict the probability of clinical aggravation was explored through multivariate regression analyses. Results: The immuno-phenotypic analysis performed by multi-colour flow cytometry confirmed that patients suffering from severe COVID-19 harboured significantly reduced circulating T cell subsets, especially for CD4+ T, Th1, and regulatory T cells. Peripheral T cells also correlated with parameters associated with disease severity, i.e., PaO2/FiO2 ratio and inflammation markers. CD4+ T cell subsets showed an important significant association with clinical evolution, with patients presenting markedly decreased regulatory T cells at baseline having a significantly higher risk of aggravation. Importantly, the combination of gender and regulatory T cells allowed distinguishing between improved and worsened patients with an area under the ROC curve (AUC) of 82%. Conclusions: The present study demonstrates the association between CD4+ T cell dysregulation and COVID-19 severity and progression. Our results support the importance of analysing baseline regulatory T cell levels, since they were revealed able to predict the clinical worsening during hospitalization. Regulatory T cells assessment soon after hospital admission could thus allow a better clinical stratification and patient management.


Subject(s)
COVID-19/epidemiology , COVID-19/immunology , Hospitalization , Lymphocyte Count , SARS-CoV-2/immunology , T-Lymphocytes, Regulatory/immunology , Biomarkers , COVID-19/diagnosis , COVID-19/virology , COVID-19 Serological Testing , Cytokines/blood , Cytokines/metabolism , Disease Progression , Humans , Immunophenotyping , Inflammation Mediators/blood , Inflammation Mediators/metabolism , Prognosis , Public Health Surveillance , ROC Curve , Severity of Illness Index , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , T-Lymphocytes, Regulatory/metabolism
2.
Front Immunol ; 12: 794642, 2021.
Article in English | MEDLINE | ID: covidwho-1581317

ABSTRACT

Background: The relationships of the coronavirus disease 2019 (COVID-19) vaccination with reactogenicity and the humoral immune response are important to study. The current study aimed to assess the reactogenicity and immunogenicity of the Pfizer and AstraZeneca COVID-19 vaccines among adults in Madinah, Saudi Arabia. Methods: A cross-sectional study, including 365 randomly selected adult Pfizer or AstraZeneca vaccine recipients who received a homologous prime-boost vaccination between February 1st and June 30th, 2021. Data of height and weight were collected to assess the weight status of percipients. An evaluation of seropositivity for anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies was assessed using enzyme-linked immunosorbent assay (ELISA). Results: Among the participants, 69% (n = 250) reported at least one vaccine-related symptom. Pain at the injection site was the most frequently reported vaccine-related symptom. The mean total score for vaccine-related symptoms was significantly higher among participants who received the AstraZeneca vaccine, women, and participants with no previous COVID-19 infection (p < 0.05). Spike-specific IgG antibodies were detected in 98.9% of participants after the receipt of two vaccine doses, including 99.5% of Pfizer vaccine recipients and 98.3% of AstraZeneca vaccine recipients. Significantly, higher proportions of participants in the <35-year age group developed a humoral immune response after the first vaccine dose compared with the participants in other age groups. Conclusion: Participants who received the Pfizer COVID-19 vaccine reported fewer vaccine-related complications compared with those who received the AstraZeneca COVID-19 vaccine, but no serious side effects were reported in response to either vaccine. Health status and age were factors that may influence COVID-19 vaccine effectiveness for the generation of antibodies against the SARS-CoV-2 spike protein.


Subject(s)
COVID-19 Vaccines/immunology , COVID-19 Vaccines/standards , COVID-19/prevention & control , Immunogenicity, Vaccine , SARS-CoV-2/immunology , Adult , Aged , Antibody Formation/immunology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/virology , Cross-Sectional Studies , Factor Analysis, Statistical , Female , Host-Pathogen Interactions/immunology , Humans , Immunization, Secondary , Immunoglobulin G , Male , Middle Aged , Online Systems , Public Health Surveillance , Surveys and Questionnaires
3.
J Med Internet Res ; 23(2): e26081, 2021 02 09.
Article in English | MEDLINE | ID: covidwho-1575190

ABSTRACT

BACKGROUND: The COVID-19 pandemic has had profound and differential impacts on metropolitan areas across the United States and around the world. Within the United States, metropolitan areas that were hit earliest with the pandemic and reacted with scientifically based health policy were able to contain the virus by late spring. For other areas that kept businesses open, the first wave in the United States hit in mid-summer. As the weather turns colder, universities resume classes, and people tire of lockdowns, a second wave is ascending in both metropolitan and rural areas. It becomes more obvious that additional SARS-CoV-2 surveillance is needed at the local level to track recent shifts in the pandemic, rates of increase, and persistence. OBJECTIVE: The goal of this study is to provide advanced surveillance metrics for COVID-19 transmission that account for speed, acceleration, jerk and persistence, and weekly shifts, to better understand and manage risk in metropolitan areas. Existing surveillance measures coupled with our dynamic metrics of transmission will inform health policy to control the COVID-19 pandemic until, and after, an effective vaccine is developed. Here, we provide values for novel indicators to measure COVID-19 transmission at the metropolitan area level. METHODS: Using a longitudinal trend analysis study design, we extracted 260 days of COVID-19 data from public health registries. We used an empirical difference equation to measure the daily number of cases in the 25 largest US metropolitan areas as a function of the prior number of cases and weekly shift variables based on a dynamic panel data model that was estimated using the generalized method of moments approach by implementing the Arellano-Bond estimator in R. RESULTS: Minneapolis and Chicago have the greatest average number of daily new positive results per standardized 100,000 population (which we refer to as speed). Extreme behavior in Minneapolis showed an increase in speed from 17 to 30 (67%) in 1 week. The jerk and acceleration calculated for these areas also showed extreme behavior. The dynamic panel data model shows that Minneapolis, Chicago, and Detroit have the largest persistence effects, meaning that new cases pertaining to a specific week are statistically attributable to new cases from the prior week. CONCLUSIONS: Three of the metropolitan areas with historically early and harsh winters have the highest persistence effects out of the top 25 most populous metropolitan areas in the United States at the beginning of their cold weather season. With these persistence effects, and with indoor activities becoming more popular as the weather gets colder, stringent COVID-19 regulations will be more important than ever to flatten the second wave of the pandemic. As colder weather grips more of the nation, southern metropolitan areas may also see large spikes in the number of cases.


Subject(s)
COVID-19/epidemiology , Communicable Disease Control , COVID-19/prevention & control , COVID-19/transmission , Health Policy , Humans , Longitudinal Studies , Models, Statistical , Pandemics , Public Health , Public Health Surveillance , Registries , SARS-CoV-2 , United States/epidemiology
4.
CMAJ Open ; 9(4): E1175-E1180, 2021.
Article in English | MEDLINE | ID: covidwho-1575909

ABSTRACT

BACKGROUND: Reliable reports on hand hygiene performance throughout the COVID-19 pandemic are lacking as most hospitals continue to rely on direct observation to measure this quality indicator. Using group electronic hand hygiene monitoring, we sought to assess the impact of COVID-19 on adherence to hand hygiene. METHODS: Across 12 Ontario hospitals (5 university and 7 community teaching hospitals), a group electronic hand hygiene monitoring system was installed before the pandemic to provide continuous measurement of hand hygiene adherence across 978 ward and 367 critical care beds. We performed an interrupted time-series study of institutional hand hygiene adherence in association with a COVID-19 inpatient census and the Ontario daily count of COVID-19 cases during a baseline period (Nov. 1, 2019, to Feb. 29, 2020), the pre-peak period of the first wave of the pandemic (Mar. 1 to Apr. 24, 2020), and the post-peak period of the first wave (Apr. 25 to July 5, 2020). We used a Poisson regression model to assess the association between the hospital COVID-19 census and institutional hand hygiene adherence while adjusting for the correlation within inpatient units. RESULTS: At baseline, the rate of hand hygiene adherence was 46.0% (6 325 401 of 13 750 968 opportunities) and this improved beginning in March 2020 to a daily peak of 79.3% (66 640 of 84 026 opportunities) on Mar. 30, 2020. Each patient admitted with COVID-19 was associated with improved hand hygiene adherence (incidence rate ratio [IRR] 1.0621, 95% confidence interval [CI] 1.0619-1.0623). Increasing Ontario daily case count was similarly associated with improved hand hygiene (IRR 1.0026, 95% CI 1.0021-1.0032). After peak COVID-19 community and inpatient numbers, hand hygiene adherence declined and returned to baseline. INTERPRETATION: The first wave of the COVID-19 pandemic was associated with significant improvement in hand hygiene adherence, measured using a group electronic monitoring system. Future research should seek to determine whether strategies that focus on health care worker perception of personal risk can achieve sustainable improvements in hand hygiene performance.


Subject(s)
COVID-19/epidemiology , Hand Hygiene , Health Personnel , Hospitals , Infection Control/statistics & numerical data , COVID-19/virology , Hand Hygiene/methods , Health Impact Assessment , Humans , Infection Control/methods , Public Health Surveillance
5.
MMWR Morb Mortal Wkly Rep ; 70(50): 1731-1734, 2021 Dec 17.
Article in English | MEDLINE | ID: covidwho-1575734

ABSTRACT

A new variant of SARS-CoV-2 (the virus that causes COVID-19), B.1.1.529 (Omicron) (1), was first reported to the World Health Organization (WHO) by South Africa on November 24, 2021. Omicron has numerous mutations with potential to increase transmissibility, confer resistance to therapeutics, or partially escape infection- or vaccine-induced immunity (2). On November 26, WHO designated B.1.1.529 as a variant of concern (3), as did the U.S. SARS-CoV-2 Interagency Group (SIG)* on November 30. On December 1, the first case of COVID-19 attributed to the Omicron variant was reported in the United States. As of December 8, a total of 22 states had identified at least one Omicron variant case, including some that indicate community transmission. Among 43 cases with initial follow-up, one hospitalization and no deaths were reported. This report summarizes U.S. surveillance for SARS-CoV-2 variants, characteristics of the initial persons investigated with COVID-19 attributed to the Omicron variant and public health measures implemented to slow the spread of Omicron in the United States. Implementation of concurrent prevention strategies, including vaccination, masking, increasing ventilation, testing, quarantine, and isolation, are recommended to slow transmission of SARS-CoV-2, including variants such as Omicron, and to protect against severe illness and death from COVID-19.


Subject(s)
COVID-19/virology , Public Health Surveillance , SARS-CoV-2/genetics , Adolescent , Adult , Aged , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , Centers for Disease Control and Prevention, U.S. , Communicable Disease Control/methods , Female , Humans , Male , Middle Aged , Mutation , SARS-CoV-2/isolation & purification , Travel-Related Illness , United States/epidemiology , Young Adult
6.
Proc Natl Acad Sci U S A ; 118(51)2021 12 21.
Article in English | MEDLINE | ID: covidwho-1569348

ABSTRACT

Simultaneously tracking the global impact of COVID-19 is challenging because of regional variation in resources and reporting. Leveraging self-reported survey outcomes via an existing international social media network has the potential to provide standardized data streams to support monitoring and decision-making worldwide, in real time, and with limited local resources. The University of Maryland Global COVID-19 Trends and Impact Survey (UMD-CTIS), in partnership with Facebook, has invited daily cross-sectional samples from the social media platform's active users to participate in the survey since its launch on April 23, 2020. We analyzed UMD-CTIS survey data through December 20, 2020, from 31,142,582 responses representing 114 countries/territories weighted for nonresponse and adjusted to basic demographics. We show consistent respondent demographics over time for many countries/territories. Machine Learning models trained on national and pooled global data verified known symptom indicators. COVID-like illness (CLI) signals were correlated with government benchmark data. Importantly, the best benchmarked UMD-CTIS signal uses a single survey item whereby respondents report on CLI in their local community. In regions with strained health infrastructure but active social media users, we show it is possible to define COVID-19 impact trajectories using a remote platform independent of local government resources. This syndromic surveillance public health tool is the largest global health survey to date and, with brief participant engagement, can provide meaningful, timely insights into the global COVID-19 pandemic at a local scale.


Subject(s)
COVID-19/epidemiology , Public Health Surveillance/methods , Social Media , COVID-19/diagnosis , COVID-19 Testing , Cross-Sectional Studies , Epidemiologic Methods , Humans , Internationality , Machine Learning , Pandemics/statistics & numerical data
7.
Arch Dis Child ; 106(11): 1050-1055, 2021 11.
Article in English | MEDLINE | ID: covidwho-1501685

ABSTRACT

BACKGROUND: Globally, injuries cause >5 million deaths annually and children and young people are particularly vulnerable. Injuries are the leading cause of death in people aged 5-24 years and a leading cause of disability. In most low-income and middle-income countries where the majority of global child injury burden occurs, systems for routinely collecting injury data are limited. METHODS: A new model of injury surveillance for use in emergency departments in Nepal was designed and piloted. Data from patients presenting with injuries were collected prospectively over 12 months and used to describe the epidemiology of paediatric injury presentations. RESULTS: The total number of children <18 years of age presenting with injury was 2696, representing 27% of all patients presenting with injuries enrolled. Most injuries in children presenting to the emergency departments in this study were unintentional and over half of children were <10 years of age. Falls, animal bites/stings and road traffic injuries accounted for nearly 75% of all injuries with poisonings, burns and drownings presenting proportionately less often. Over half of injuries were cuts, bites and open wounds. In-hospital child mortality from injury was 1%. CONCLUSION: Injuries affecting children in Nepal represent a significant burden. The data on injuries observed from falls, road traffic injuries and injuries related to animals suggest potential areas for injury prevention. This is the biggest prospective injury surveillance study in Nepal in recent years and supports the case for using injury surveillance to monitor child morbidity and mortality through improved data.


Subject(s)
Emergency Service, Hospital/statistics & numerical data , Global Burden of Disease/economics , Public Health Surveillance/methods , Wounds and Injuries/epidemiology , Accidental Falls/statistics & numerical data , Accidents, Traffic/statistics & numerical data , Adolescent , Animals , Bites and Stings/epidemiology , Burns/epidemiology , Child , Child, Preschool , Drowning/epidemiology , Emergency Service, Hospital/trends , Female , Humans , Male , Nepal/epidemiology , Poisoning/epidemiology , Prospective Studies , Trauma Severity Indices , Wounds and Injuries/mortality , Wounds and Injuries/prevention & control
8.
JMIR Public Health Surveill ; 7(11): e32639, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1496857

ABSTRACT

BACKGROUND: The Eastern Mediterranean Region (EMR) hosts some of the world's worst humanitarian and health crises. The implementation of health surveillance in this region has faced multiple constraints. New and novel approaches in surveillance are in a constant state of high and immediate demand. Identifying the existing literature on surveillance helps foster an understanding of scientific development and thus potentially supports future development directions. OBJECTIVE: This study aims to illustrate the scientific production, quantify the scholarly impact, and highlight the characteristics of publications on public health surveillance in the EMR over the past decade. METHODS: We performed a Scopus search using keywords related to public health surveillance or its disciplines, cross-referenced with EMR countries, from 2011 to July 2021. Data were exported and analyzed using Microsoft Excel and Visualization of Similarities Viewer. Quality of journals was determined using SCImago Journal Rank and CiteScore. RESULTS: We retrieved 1987 documents, of which 1927 (96.98%) were articles or reviews. There has been an incremental increase in the number of publications (exponential growth, R2=0.80) over the past decade. Publications were mostly affiliated with Iran (501/1987, 25.21%), the United States (468/1987, 23.55%), Pakistan (243/1987, 12.23%), Egypt (224/1987, 11.27%), and Saudi Arabia (209/1987, 10.52%). However, Iran only had links with 40 other countries (total link strength 164), and the biggest collaborator from the EMR was Egypt, with 67 links (total link strength 402). Within the other EMR countries, only Morocco, Lebanon, and Jordan produced ≥79 publications in the 10-year period. Most publications (1551/1987, 78.06%) were affiliated with EMR universities. Most journals were categorized as medical journals, and the highest number of articles were published in the Eastern Mediterranean Health Journal (SCImago Journal Rank 0.442; CiteScore 1.5). Retrieved documents had an average of 18.4 (SD 125.5) citations per document and an h-index of 66. The top-3 most cited documents were from the Global Burden of Diseases study. We found 70 high-frequency terms, occurring ≥10 times in author keywords, connected in 3 clusters. COVID-19, SARS-CoV-2, and pandemic represented the most recent 2020 cluster. CONCLUSIONS: This is the first research study to quantify the published literature on public health surveillance and its disciplines in the EMR. Research productivity has steadily increased over the past decade, and Iran has been the leading country publishing relevant research. Recurrent recent surveillance themes included COVID-19 and SARS-CoV-2. This study also sheds light on the gaps in surveillance research in the EMR, including inadequate publications on noncommunicable diseases and injury-related surveillance.


Subject(s)
COVID-19 , Public Health Surveillance , Bibliometrics , Humans , Mediterranean Region , SARS-CoV-2 , United States
9.
Public Health Rep ; 136(1_suppl): 72S-79S, 2021.
Article in English | MEDLINE | ID: covidwho-1495836

ABSTRACT

OBJECTIVE: Traditional public health surveillance of nonfatal opioid overdose relies on emergency department (ED) billing data, which can be delayed substantially. We compared the timeliness of 2 new data sources for rapid drug overdose surveillance-emergency medical services (EMS) and syndromic surveillance-with ED billing data. METHODS: We used data on nonfatal opioid overdoses in Kentucky captured in EMS, syndromic surveillance, and ED billing systems during 2018-2019. We evaluated the time-series relationships between EMS and ED billing data and syndromic surveillance and ED billing data by calculating cross-correlation functions, controlling for influences of autocorrelations. A case example demonstrates the usefulness of EMS and syndromic surveillance data to monitor rapid changes in opioid overdose encounters in Kentucky during the COVID-19 epidemic. RESULTS: EMS and syndromic surveillance data showed moderate-to-strong correlation with ED billing data on a lag of 0 (r = 0.694; 95% CI, 0.579-0.782; t = 9.73; df = 101; P < .001; and r = 0.656; 95% CI, 0.530-0.754; t = 8.73; df = 101; P < .001; respectively) at the week-aggregated level. After the COVID-19 emergency declaration, EMS and syndromic surveillance time series had steep increases in April and May 2020, followed by declines from June through September 2020. The ED billing data were available for analysis 3 months after the end of a calendar quarter but closely followed the trends identified by the EMS and syndromic surveillance data. CONCLUSION: Data from EMS and syndromic surveillance systems can be reliably used to monitor nonfatal opioid overdose trends in Kentucky in near-real time to inform timely public health response.


Subject(s)
Analgesics, Opioid/poisoning , Drug Overdose/epidemiology , Emergency Medical Services/statistics & numerical data , Opioid-Related Disorders/epidemiology , Population Surveillance/methods , Public Health Surveillance/methods , Sentinel Surveillance , Analgesics, Opioid/administration & dosage , COVID-19/epidemiology , Drug Overdose/prevention & control , Emergencies/epidemiology , Emergency Medical Services/trends , Humans , Kentucky/epidemiology , Pandemics , Public Health , SARS-CoV-2
10.
Pediatr Infect Dis J ; 40(11): e418-e423, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1494050

ABSTRACT

BACKGROUND: School closures are a subject of debate during the present coronavirus disease 2019 (COVID-19) pandemic. Because children are not the main driver of COVID-19 transmission in the community, school education must be prioritized in conjunction with appropriate infection prevention and control measures, as determined by local COVID-19 incidence. METHODS: We investigated the causes and transmission routes of a primary school cluster of COVID-19 that occurred during November and December 2020 in Niigata, Japan. RESULTS: In the cluster, the virus spread among teachers, then from teachers to students, and then to their family members. This primary school cluster comprised 26 infected patients and included teachers (13/33, 39%), students (9/211, 4%), and family members (4/65, 6%). The secondary attack rate from the 3 index teachers to the remaining 30 teachers was 33%; however, the rate to students was only 4%. Factors contributing to cluster formation include the fact that 2 of the index teachers continued working while symptomatic and that the environment and infection prevention measures in the teachers' room were inadequate. CONCLUSIONS: To open schools safely and without interruption, adequate measures to prevent COVID-19 infection in schools should be emphasized not only for children but also for teachers and their environment.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Disease Outbreaks , SARS-CoV-2 , School Teachers , Schools , Adolescent , Adult , Aged , COVID-19/diagnosis , COVID-19/transmission , Child , Female , Humans , Incidence , Japan/epidemiology , Male , Middle Aged , Public Health Surveillance , Young Adult
11.
JAMA ; 326(14): 1390-1399, 2021 10 12.
Article in English | MEDLINE | ID: covidwho-1490611

ABSTRACT

Importance: Safety surveillance of vaccines against COVID-19 is critical to ensure safety, maintain trust, and inform policy. Objectives: To monitor 23 serious outcomes weekly, using comprehensive health records on a diverse population. Design, Setting, and Participants: This study represents an interim analysis of safety surveillance data from Vaccine Safety Datalink. The 10 162 227 vaccine-eligible members of 8 participating US health plans were monitored with administrative data updated weekly and supplemented with medical record review for selected outcomes from December 14, 2020, through June 26, 2021. Exposures: Receipt of BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna) COVID-19 vaccination, with a risk interval of 21 days for individuals after vaccine dose 1 or 2 compared with an interval of 22 to 42 days for similar individuals after vaccine dose 1 or 2. Main Outcomes and Measures: Incidence of serious outcomes, including acute myocardial infarction, Bell palsy, cerebral venous sinus thrombosis, Guillain-Barré syndrome, myocarditis/pericarditis, pulmonary embolism, stroke, and thrombosis with thrombocytopenia syndrome. Incidence of events that occurred among vaccine recipients 1 to 21 days after either dose 1 or 2 of a messenger RNA (mRNA) vaccine was compared with that of vaccinated concurrent comparators who, on the same calendar day, had received their most recent dose 22 to 42 days earlier. Rate ratios (RRs) were estimated by Poisson regression, adjusted for age, sex, race and ethnicity, health plan, and calendar day. For a signal, a 1-sided P < .0048 was required to keep type I error below .05 during 2 years of weekly analyses. For 4 additional outcomes, including anaphylaxis, only descriptive analyses were conducted. Results: A total of 11 845 128 doses of mRNA vaccines (57% BNT162b2; 6 175 813 first doses and 5 669 315 second doses) were administered to 6.2 million individuals (mean age, 49 years; 54% female individuals). The incidence of events per 1 000 000 person-years during the risk vs comparison intervals for ischemic stroke was 1612 vs 1781 (RR, 0.97; 95% CI, 0.87-1.08); for appendicitis, 1179 vs 1345 (RR, 0.82; 95% CI, 0.73-0.93); and for acute myocardial infarction, 935 vs 1030 (RR, 1.02; 95% CI, 0.89-1.18). No vaccine-outcome association met the prespecified requirement for a signal. Incidence of confirmed anaphylaxis was 4.8 (95% CI, 3.2-6.9) per million doses of BNT162b2 and 5.1 (95% CI, 3.3-7.6) per million doses of mRNA-1273. Conclusions and Relevance: In interim analyses of surveillance of mRNA COVID-19 vaccines, incidence of selected serious outcomes was not significantly higher 1 to 21 days postvaccination compared with 22 to 42 days postvaccination. While CIs were wide for many outcomes, surveillance is ongoing.


Subject(s)
COVID-19 Vaccines/adverse effects , Adolescent , Adult , Aged , Anaphylaxis/epidemiology , Anaphylaxis/etiology , Child , Female , Follow-Up Studies , Humans , Male , Middle Aged , Myocarditis/epidemiology , Myocarditis/etiology , Public Health Surveillance , Time Factors , Vaccines, Synthetic/adverse effects , Young Adult
12.
Lancet Glob Health ; 9(12): e1658-e1666, 2021 12.
Article in English | MEDLINE | ID: covidwho-1475185

ABSTRACT

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.


Subject(s)
COVID-19/epidemiology , Epidemics , Genome, Viral , Public Health Surveillance , SARS-CoV-2/genetics , Travel-Related Illness , Adolescent , Adult , COVID-19/transmission , COVID-19/virology , Child , Child, Preschool , Female , Humans , Infant , Male , Middle Aged , Molecular Epidemiology , Retrospective Studies , Whole Genome Sequencing , Young Adult , Zimbabwe/epidemiology
13.
JMIR Public Health Surveill ; 7(9): e29413, 2021 09 28.
Article in English | MEDLINE | ID: covidwho-1470726

ABSTRACT

BACKGROUND: Harnessing health-related data posted on social media in real time can offer insights into how the pandemic impacts the mental health and general well-being of individuals and populations over time. OBJECTIVE: This study aimed to obtain information on symptoms and medical conditions self-reported by non-Twitter social media users during the COVID-19 pandemic, to determine how discussion of these symptoms and medical conditions changed over time, and to identify correlations between frequency of the top 5 commonly mentioned symptoms post and daily COVID-19 statistics (new cases, new deaths, new active cases, and new recovered cases) in the United States. METHODS: We used natural language processing (NLP) algorithms to identify symptom- and medical condition-related topics being discussed on social media between June 14 and December 13, 2020. The sample posts were geotagged by NetBase, a third-party data provider. We calculated the positive predictive value and sensitivity to validate the classification of posts. We also assessed the frequency of health-related discussions on social media over time during the study period, and used Pearson correlation coefficients to identify statistically significant correlations between the frequency of the 5 most commonly mentioned symptoms and fluctuation of daily US COVID-19 statistics. RESULTS: Within a total of 9,807,813 posts (nearly 70% were sourced from the United States), we identified a discussion of 120 symptom-related topics and 1542 medical condition-related topics. Our classification of the health-related posts had a positive predictive value of over 80% and an average classification rate of 92% sensitivity. The 5 most commonly mentioned symptoms on social media during the study period were anxiety (in 201,303 posts or 12.2% of the total posts mentioning symptoms), generalized pain (189,673, 11.5%), weight loss (95,793, 5.8%), fatigue (91,252, 5.5%), and coughing (86,235, 5.2%). The 5 most discussed medical conditions were COVID-19 (in 5,420,276 posts or 66.4% of the total posts mentioning medical conditions), unspecified infectious disease (469,356, 5.8%), influenza (270,166, 3.3%), unspecified disorders of the central nervous system (253,407, 3.1%), and depression (151,752, 1.9%). Changes in posts in the frequency of anxiety, generalized pain, and weight loss were significant but negatively correlated with daily new COVID-19 cases in the United States (r=-0.49, r=-0.46, and r=-0.39, respectively; P<.05). Posts on the frequency of anxiety, generalized pain, weight loss, fatigue, and the changes in fatigue positively and significantly correlated with daily changes in both new deaths and new active cases in the United States (r ranged=0.39-0.48; P<.05). CONCLUSIONS: COVID-19 and symptoms of anxiety were the 2 most commonly discussed health-related topics on social media from June 14 to December 13, 2020. Real-time monitoring of social media posts on symptoms and medical conditions may help assess the population's mental health status and enhance public health surveillance for infectious disease.


Subject(s)
COVID-19/epidemiology , Pandemics , Public Health Surveillance/methods , Self Report , Social Media/statistics & numerical data , Adult , Female , Humans , Male , United States/epidemiology
14.
Sci Rep ; 11(1): 20271, 2021 10 12.
Article in English | MEDLINE | ID: covidwho-1467133

ABSTRACT

To support public health policymakers in Connecticut, we developed a flexible county-structured compartmental SEIR-type model of SARS-CoV-2 transmission and COVID-19 disease progression. Our goals were to provide projections of infections, hospitalizations, and deaths, and estimates of important features of disease transmission and clinical progression. In this paper, we outline the model design, implementation and calibration, and describe how projections and estimates were used to meet the changing requirements of policymakers and officials in Connecticut from March 2020 to February 2021. The approach takes advantage of our unique access to Connecticut public health surveillance and hospital data and our direct connection to state officials and policymakers. We calibrated this model to data on deaths and hospitalizations and developed a novel measure of close interpersonal contact frequency to capture changes in transmission risk over time and used multiple local data sources to infer dynamics of time-varying model inputs. Estimated epidemiologic features of the COVID-19 epidemic in Connecticut include the effective reproduction number, cumulative incidence of infection, infection hospitalization and fatality ratios, and the case detection ratio. We conclude with a discussion of the limitations inherent in predicting uncertain epidemic trajectories and lessons learned from one year of providing COVID-19 projections in Connecticut.


Subject(s)
COVID-19 , Models, Statistical , Pandemics , Public Health Surveillance/methods , COVID-19/epidemiology , COVID-19/transmission , Connecticut/epidemiology , Forecasting , Humans , Pandemics/prevention & control , Pandemics/statistics & numerical data
15.
JAMA Netw Open ; 4(10): e2128615, 2021 10 01.
Article in English | MEDLINE | ID: covidwho-1453504

ABSTRACT

Importance: The number of clinics marketing stem cell products for joint diseases, chronic pain, and most recently, COVID-19, has increased despite warnings from the US Food and Drug Administration that stem cell products for these and other indications have not been proven safe or effective. Objective: To examine bacterial infections in 20 patients who received umbilical cord blood-derived products marketed as stem cell treatment. Design, Setting, and Participants: This case series is a national public health investigation including case-finding, medical record review and abstraction, and laboratory investigation, including sterility testing of products and whole-genome sequencing of patient and product isolates. Participants included patients who developed bacterial infections following administration of umbilical cord blood-derived products marketed as stem cell treatment during August 2017 to September 2018. Data analysis was performed from March 2019 to September 2021. Exposures: Umbilical cord blood-derived products marketed as stem cell treatment. Main Outcomes and Measures: Data were collected on patient infections and exposures. The Centers for Disease Control and Prevention performed sterility testing on undistributed and distributed vials of product marketed as stem cell treatment and performed whole-genome sequencing to compare patient and product bacterial isolates. Results: Culture-confirmed bacterial infections were identified in 20 patients (median [range] age, 63 [2-89] years; 13 male patients [65%]) from 8 US states who sought stem cell treatment for conditions including pain, osteoarthritis, rheumatoid arthritis, and injury; all but 1 required hospitalization. The most frequently isolated bacteria from patients with infections were common enteric species, including Escherichia coli (14 patients) and Enterobacter cloacae (7 patients). Of unopened, undistributed products sampled for testing, 65% (22 of 34 vials) were contaminated with at least 1 of 16 bacterial species, mostly enteric. A patient isolate from Arizona matched isolates obtained from products administered to patients in Florida, and patient isolates from Texas matched undistributed product sent from the company in California. Conclusions and Relevance: Unapproved stem cell products can expose patients to serious risks without proven benefit. Sequencing results suggest a common source of extensive contamination, likely occurring during the processing of cord blood into product. Patients and health care practitioners who are considering the use of unapproved products marketed as stem cell treatment should be aware of their unproven benefits and potential risks, including serious infections.


Subject(s)
Bacterial Infections/etiology , Blood Safety/statistics & numerical data , Cord Blood Stem Cell Transplantation/adverse effects , Disease Outbreaks , Adolescent , Adult , Aged , Aged, 80 and over , Bacterial Infections/epidemiology , Bacterial Infections/prevention & control , Blood Safety/standards , Centers for Disease Control and Prevention, U.S. , Child , Child, Preschool , Cord Blood Stem Cell Transplantation/standards , Female , Humans , Male , Marketing , Middle Aged , Outcome Assessment, Health Care , Public Health Surveillance , United States/epidemiology , United States Food and Drug Administration , Young Adult
16.
CMAJ ; 193(38): E1483-E1493, 2021 09 27.
Article in English | MEDLINE | ID: covidwho-1448587

ABSTRACT

BACKGROUND: Risk factors for severe outcomes of SARS-CoV-2 infection are not well established in children. We sought to describe pediatric hospital admissions associated with SARS-CoV-2 infection in Canada and identify risk factors for more severe disease. METHODS: We conducted a national prospective study using the infrastructure of the Canadian Paediatric Surveillance Program (CPSP). Cases involving children who were admitted to hospital with microbiologically confirmed SARS-CoV-2 infection were reported from Apr. 8 to Dec. 31 2020, through weekly online questionnaires distributed to the CPSP network of more than 2800 pediatricians. We categorized hospital admissions as related to COVID-19, incidental, or for social or infection control reasons and determined risk factors for disease severity in hospital. RESULTS: Among 264 hospital admissions involving children with SARS-CoV-2 infection during the 9-month study period, 150 (56.8%) admissions were related to COVID-19 and 100 (37.9%) were incidental infections (admissions for other reasons and found to be positive for SARS-CoV-2 on screening). Infants (37.3%) and adolescents (29.6%) represented most cases. Among hospital admissions related to COVID-19, 52 (34.7%) had critical disease, 42 (28.0%) of whom required any form of respiratory or hemodynamic support, and 59 (39.3%) had at least 1 underlying comorbidity. Children with obesity, chronic neurologic conditions or chronic lung disease other than asthma were more likely to have severe or critical COVID-19. INTERPRETATION: Among children who were admitted to hospital with SARS-CoV-2 infection in Canada during the early COVID-19 pandemic period, incidental SARS-CoV-2 infection was common. In children admitted with acute COVID-19, obesity and neurologic and respiratory comorbidities were associated with more severe disease.


Subject(s)
COVID-19/epidemiology , Hospitalization , Severity of Illness Index , Acute Disease , Adolescent , COVID-19/diagnosis , COVID-19/etiology , COVID-19/therapy , COVID-19 Testing , Canada/epidemiology , Child , Child, Preschool , Comorbidity , Female , Humans , Incidental Findings , Infant , Infant, Newborn , Male , Prospective Studies , Public Health Surveillance , Risk Factors
17.
MMWR Morb Mortal Wkly Rep ; 70(36): 1242-1244, 2021 Sep 10.
Article in English | MEDLINE | ID: covidwho-1441395

ABSTRACT

Wastewater surveillance, the measurement of pathogen levels in wastewater, is used to evaluate community-level infection trends, augment traditional surveillance that leverages clinical tests and services (e.g., case reporting), and monitor public health interventions (1). Approximately 40% of persons infected with SARS-CoV-2, the virus that causes COVID-19, shed virus RNA in their stool (2); therefore, community-level trends in SARS-CoV-2 infections, both symptomatic and asymptomatic (2) can be tracked through wastewater testing (3-6). CDC launched the National Wastewater Surveillance System (NWSS) in September 2020 to coordinate wastewater surveillance programs implemented by state, tribal, local, and territorial health departments to support the COVID-19 pandemic response. In the United States, wastewater surveillance was not previously implemented at the national level. As of August 2021, NWSS includes 37 states, four cities, and two territories. This report summarizes NWSS activities and describes innovative applications of wastewater surveillance data by two states, which have included generating alerts to local jurisdictions, allocating mobile testing resources, evaluating irregularities in traditional surveillance, refining health messaging, and forecasting clinical resource needs. NWSS complements traditional surveillance and enables health departments to intervene earlier with focused support in communities experiencing increasing concentrations of SARS-CoV-2 in wastewater. The ability to conduct wastewater surveillance is not affected by access to health care or the clinical testing capacity in the community. Robust, sustainable implementation of wastewater surveillance requires public health capacity for wastewater testing, analysis, and interpretation. Partnerships between wastewater utilities and public health departments are needed to leverage wastewater surveillance data for the COVID-19 response for rapid assessment of emerging threats and preparedness for future pandemics.


Subject(s)
COVID-19/prevention & control , Pandemics/prevention & control , Public Health Surveillance/methods , SARS-CoV-2/isolation & purification , Waste Water/virology , COVID-19/epidemiology , Centers for Disease Control and Prevention, U.S. , Humans , United States/epidemiology
19.
Viruses ; 13(9)2021 09 07.
Article in English | MEDLINE | ID: covidwho-1430972

ABSTRACT

From March to June 2021, India experienced a deadly second wave of COVID-19, with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason for these breakthroughs, we collected 677 clinical samples (throat swab/nasal swabs) of individuals from 17 states/Union Territories of the country who had received two doses (n = 592) and one dose (n = 85) of vaccines and tested positive for COVID-19. These cases were telephonically interviewed and clinical data were analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both groups. Analysis of both groups determined that 86.69% (n = 443) of them belonged to the Delta variant, along with Alpha, Kappa, Delta AY.1, and Delta AY.2. The Delta variant clustered into four distinct sub-lineages. Sub-lineage I had mutations in ORF1ab A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, and A6319V, and in N G215C; Sub-lineage II had mutations in ORF1ab P309L, A3209V, V3718A, G5063S, P5401L, and ORF7a L116F; Sub-lineage III had mutations in ORF1ab A3209V, V3718A, T3750I, G5063S, and P5401L and in spike A222V; Sub-lineage IV had mutations in ORF1ab P309L, D2980N, and F3138S and spike K77T. This study indicates that majority of the breakthrough COVID-19 clinical cases were infected with the Delta variant, and only 9.8% cases required hospitalization, while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , Genomics , SARS-CoV-2/genetics , Adult , COVID-19/diagnosis , Comorbidity , Disease Outbreaks , Female , Geography, Medical , High-Throughput Nucleotide Sequencing , Humans , India/epidemiology , Male , Middle Aged , Phylogeny , Public Health Surveillance , SARS-CoV-2/classification
20.
Viruses ; 13(9)2021 09 10.
Article in English | MEDLINE | ID: covidwho-1411077

ABSTRACT

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5' and two in 3' UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough "space" for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the "hotspots" in the generation of new variants.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , Mutation , SARS-CoV-2/genetics , Brazil/epidemiology , COVID-19/history , Evolution, Molecular , Genotype , History, 21st Century , Humans , Models, Theoretical , Mutation Rate , Phylogeny , Phylogeography , Public Health Surveillance
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