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1.
PLoS One ; 17(3): e0265579, 2022.
Article in English | MEDLINE | ID: covidwho-1765536

ABSTRACT

The second wave of SARS-CoV-2 has hit India hard and though the vaccination drive has started, moderate number of COVID affected patients is still present in the country, thereby leading to the analysis of the evolving virus strains. In this regard, multiple sequence alignment of 17271 Indian SARS-CoV-2 sequences is performed using MAFFT followed by their phylogenetic analysis using Nextstrain. Subsequently, mutation points as SNPs are identified by Nextstrain. Thereafter, from the aligned sequences temporal and spatial analysis are carried out to identify top 10 hotspot mutations in the coding regions based on entropy. Finally, to judge the functional characteristics of all the non-synonymous hotspot mutations, their changes in proteins are evaluated as biological functions considering the sequences by using PolyPhen-2 while I-Mutant 2.0 evaluates their structural stability. For both temporal and spatial analysis, there are 21 non-synonymous hotspot mutations which are unstable and damaging.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Genome, Viral/genetics , Mutation/genetics , SARS-CoV-2/genetics , COVID-19/virology , Humans , India/epidemiology , Phylogeny , Spatio-Temporal Analysis
2.
Sci Rep ; 12(1): 2373, 2022 02 11.
Article in English | MEDLINE | ID: covidwho-1684110

ABSTRACT

Prior work has shown the utility of using Internet searches to track the incidence of different respiratory illnesses. Similarly, people who suffer from COVID-19 may query for their symptoms prior to accessing the medical system (or in lieu of it). To assist in the UK government's response to the COVID-19 pandemic we analyzed searches for relevant symptoms on the Bing web search engine from users in England to identify areas of the country where unexpected rises in relevant symptom searches occurred. These were reported weekly to the UK Health Security Agency to assist in their monitoring of the pandemic. Our analysis shows that searches for "fever" and "cough" were the most correlated with future case counts during the initial stages of the pandemic, with searches preceding case counts by up to 21 days. Unexpected rises in search patterns were predictive of anomalous rises in future case counts within a week, reaching an Area Under Curve of 0.82 during the initial phase of the pandemic, and later reducing due to changes in symptom presentation. Thus, analysis of regional searches for symptoms can provide an early indicator (of more than one week) of increases in COVID-19 case counts.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Search Engine/statistics & numerical data , Cough/epidemiology , England/epidemiology , Fever/epidemiology , Humans
3.
Sci Rep ; 12(1): 1964, 2022 02 04.
Article in English | MEDLINE | ID: covidwho-1671629

ABSTRACT

With evidence-based measures, COVID-19 can be effectively controlled by advanced data analysis and prediction. However, while valuable insights are available, there is a shortage of robust and rigorous research on what factors shape COVID-19 transmissions at the city cluster level. Therefore, to bridge the research gap, we adopted a data-driven hierarchical modeling approach to identify the most influential factors in shaping COVID-19 transmissions across different Chinese cities and clusters. The data used in this study are from Chinese officials, and hierarchical modeling conclusions drawn from the analysis are systematic, multifaceted, and comprehensive. To further improve research rigor, the study utilizes SPSS, Python and RStudio to conduct multiple linear regression and polynomial best subset regression (PBSR) analysis for the hierarchical modeling. The regression model utilizes the magnitude of various relative factors in nine Chinese city clusters, including 45 cities at a different level of clusters, to examine these aspects from the city cluster scale, exploring the correlation between various factors of the cities. These initial 12 factors are comprised of 'Urban population ratio', 'Retail sales of consumer goods', 'Number of tourists', 'Tourism Income', 'Ratio of the elderly population (> 60 year old) in this city', 'population density', 'Mobility scale (move in/inbound) during the spring festival', 'Ratio of Population and Health facilities', 'Jobless rate (%)', 'The straight-line distance from original epicenter Wuhan to this city', 'urban per capita GDP', and 'the prevalence of the COVID-19'. The study's results provide rigorously-tested and evidence-based insights on most instrumental factors that shape COVID-19 transmissions across cities and regions in China. Overall, the study findings found that per capita GDP and population mobility rates were the most affected factors in the prevalence of COVID-19 in a city, which could inform health experts and government officials to design and develop evidence-based and effective public health policies that could curb the spread of the COVID-19 pandemic.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Urban Population/statistics & numerical data , China , Cities/epidemiology , Humans , Prevalence , Regression Analysis
4.
Nat Commun ; 13(1): 554, 2022 01 27.
Article in English | MEDLINE | ID: covidwho-1655581

ABSTRACT

We aim to identify those measures that effectively control the spread of SARS-CoV-2 in Austrian schools. Using cluster tracing data we calibrate an agent-based epidemiological model and consider situations where the B1.617.2 (delta) virus strain is dominant and parts of the population are vaccinated to quantify the impact of non-pharmaceutical interventions (NPIs) such as room ventilation, reduction of class size, wearing of masks during lessons, vaccinations, and school entry testing by SARS-CoV2-antigen tests. In the data we find that 40% of all clusters involved no more than two cases, and 3% of the clusters only had more than 20 cases. The model shows that combinations of NPIs together with vaccinations are necessary to allow for a controlled opening of schools under sustained community transmission of the SARS-CoV-2 delta variant. For plausible vaccination rates, primary (secondary) schools require a combination of at least two (three) of the above NPIs.


Subject(s)
COVID-19/prevention & control , COVID-19/transmission , Primary Prevention/methods , Vaccination/statistics & numerical data , Adolescent , Austria/epidemiology , COVID-19/epidemiology , COVID-19 Vaccines/immunology , Child , Contact Tracing , Disease Hotspot , Humans , Masks , Quarantine , SARS-CoV-2 , Schools/statistics & numerical data , Ventilation
5.
Medicine (Baltimore) ; 100(42): e27512, 2021 Oct 22.
Article in English | MEDLINE | ID: covidwho-1480011

ABSTRACT

ABSTRACT: To analyze the epidemiological characteristics of coronavirus disease 2019 (COVID-19) clusters in Hainan, and to provide a basis for the prevention and control of disease clusters.Descriptive epidemiology was used to retrospectively analyze the characteristics of disease clusters in 168 cases of COVID-19.Of the 168 COVID-19 cases, 99 (58.93%) comprised 29 clusters, 22 (75.86%) of which were imported and included 63 cases (63.64%), while 7 clusters (24.14%) were local and included 36 cases (36.36%). Of the cluster cases, 49 were men (49.49%) and 50 were women (50.50%), the median age was 52 years, and the maximum number of cases from 41 to 60 was at 37 years (37.37%). There were 67 first generation cases (67.68%), 28 (28.28%) second generation, and 4 (4.04%) third generation. Of the clusters, 68.97% occurred from January 31 to February 7, with the highest peak on February 6. The local disease clusters occurred with a time lag. The 2 cities with the most reported incidents were Sanya (10 cases, 34.48%) and Haikou (5 cases, 17.24%). Family clusters were most frequent, with 18 clusters (62.07%) involving 62 cases (62.63%), followed by social clusters, with 3 clusters (10.34%). The most complex clusters involved 3 cluster types (family, travel, and community). There was a statistically significant difference in the infectivity of the imported clusters versus the local clusters, with imported clusters being lower (Z = -2.851, P = .004). The infectivity of all cases or family members was highest in Haikou and lowest in Sanya. The infectivity of all cases with an incubation period of ≤7 days was 1.53 ±â€Š1.01, in which the infectivity of family members was 1.29 ±â€Š1.10. The infectivity of all cases with an incubation period of ≤14 days was 1.89 ±â€Š1.23, in which the infectivity of family members was 1.43 ±â€Š1.37.COVID-19 clusters in Hainan mainly occurred in families, and local clusters had high infectivity. Therefore, key populations and regions should be monitored, and targeted preventive measures should be carried out to provide a reference for the prevention and control of disease clusters.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Adolescent , Adult , Aged , Child , Child, Preschool , China/epidemiology , Female , Humans , Male , Middle Aged , Retrospective Studies , SARS-CoV-2 , Young Adult
6.
Viruses ; 13(10)2021 10 18.
Article in English | MEDLINE | ID: covidwho-1471002

ABSTRACT

West Java Health Laboratory (WJHL) is one of the many institutions in Indonesia that have sequenced SARS-CoV-2 genome. Although having submitted a large number of sequences since September 2020, however, these submitted data lack advanced analyses. Therefore, in this study, we analyze the variant distribution, hotspot mutation, and its impact on protein structure and function of SARS-CoV-2 from the collected samples from WJHL. As many as one hundred sixty-three SARS-CoV-2 genome sequences submitted by West Java Health Laboratory (WJHL), with collection dates between September 2020 and June 2021, were retrieved from GISAID. Subsequently, the frequency and distribution of non-synonymous mutations across different cities and regencies from these samples were analyzed. The effect of the most prevalent mutations from dominant variants on the stability of their corresponding proteins was examined. The samples mostly consisted of people of working-age, and were distributed between female and male equally. All of the sample sequences showed varying levels of diversity, especially samples from West Bandung which carried the highest diversity. Dominant variants are the VOC B.1.617.2 (Delta) variant, B.1.466.2 variant, and B.1.470 variant. The genomic regions with the highest number of mutations are the spike, NSP3, nucleocapsid, NSP12, and ORF3a protein. Mutation analysis showed that mutations in structural protein might increase the stability of the protein. Oppositely, mutations in non-structural protein might lead to a decrease in protein stability. However, further research to study the impact of mutations on the function of SARS-CoV-2 proteins are required.


Subject(s)
Genome, Viral/genetics , SARS-CoV-2/genetics , Viral Proteins/genetics , Viral Proteins/metabolism , COVID-19/pathology , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus Papain-Like Proteases/genetics , Coronavirus RNA-Dependent RNA Polymerase/genetics , Disease Hotspot , Female , Humans , Indonesia , Male , Molecular Docking Simulation , Mutation/genetics , Phosphoproteins/genetics , Protein Stability , Spike Glycoprotein, Coronavirus/genetics , Viroporin Proteins/genetics , Whole Genome Sequencing
7.
Viruses ; 13(10)2021 10 07.
Article in English | MEDLINE | ID: covidwho-1463837

ABSTRACT

In summer 2020, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was detected on mink farms in Utah. An interagency One Health response was initiated to assess the extent of the outbreak and included sampling animals from on or near affected mink farms and testing them for SARS-CoV-2 and non-SARS coronaviruses. Among the 365 animals sampled, including domestic cats, mink, rodents, raccoons, and skunks, 261 (72%) of the animals harbored at least one coronavirus. Among the samples that could be further characterized, 127 alphacoronaviruses and 88 betacoronaviruses (including 74 detections of SARS-CoV-2 in mink) were identified. Moreover, at least 10% (n = 27) of the coronavirus-positive animals were found to be co-infected with more than one coronavirus. Our findings indicate an unexpectedly high prevalence of coronavirus among the domestic and wild free-roaming animals tested on mink farms. These results raise the possibility that mink farms could be potential hot spots for future trans-species viral spillover and the emergence of new pandemic coronaviruses.


Subject(s)
Alphacoronavirus/isolation & purification , COVID-19/epidemiology , COVID-19/veterinary , SARS-CoV-2/isolation & purification , Alphacoronavirus/classification , Alphacoronavirus/genetics , Animals , Animals, Domestic/virology , Animals, Wild/virology , Cats , Disease Hotspot , Female , Male , Mephitidae/virology , Mice , Mink/virology , Raccoons/virology , SARS-CoV-2/classification , SARS-CoV-2/genetics , Utah/epidemiology
8.
Viruses ; 13(10)2021 10 07.
Article in English | MEDLINE | ID: covidwho-1463835

ABSTRACT

In the present study, we provide a retrospective genomic epidemiology analysis of the SARS-CoV-2 pandemic in the state of Rio de Janeiro, Brazil. We gathered publicly available data from GISAID and sequenced 1927 new genomes sampled periodically from March 2021 to June 2021 from 91 out of the 92 cities of the state. Our results showed that the pandemic was characterized by three different phases driven by a successive replacement of lineages. Interestingly, we noticed that viral supercarriers accounted for the overwhelming majority of the circulating virus (>90%) among symptomatic individuals in the state. Moreover, SARS-CoV-2 genomic surveillance also revealed the emergence and spread of two new variants (P.5 and P.1.2), firstly reported in this study. Our findings provided important lessons learned from the different epidemiological aspects of the SARS-CoV-2 dynamic in Rio de Janeiro. Altogether, this might have a strong potential to shape future decisions aiming to improve public health management and understanding mechanisms underlying virus dispersion.


Subject(s)
COVID-19/epidemiology , Genome, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/mortality , Child , Child, Preschool , Disease Hotspot , Epidemiological Monitoring , Female , Gene Library , Humans , Infant , Infant, Newborn , Male , Middle Aged , Phylogeny , Retrospective Studies , Young Adult
9.
Sci Rep ; 11(1): 17905, 2021 09 09.
Article in English | MEDLINE | ID: covidwho-1402120

ABSTRACT

COVID-19 epidemics have varied dramatically in nature across the United States, where some counties have clear peaks in infections, and others have had a multitude of unpredictable and non-distinct peaks. Our lack of understanding of how the pandemic has evolved leads to increasing errors in our ability to predict the spread of the disease. This work seeks to explain this diversity in epidemic progressions by considering an extension to the compartmental SEIRD model. The model we propose uses a neural network to predict the infection rate as a function of both time and the disease's prevalence. We provide a methodology for fitting this model to available county-level data describing aggregate cases and deaths. Our method uses Expectation-Maximization to overcome the challenge of partial observability, due to the fact that the system's state is only partially reflected in available data. We fit a single model to data from multiple counties in the United States exhibiting different behavior. By simulating the model, we show that it can exhibit both single peak and multi-peak behavior, reproducing behavior observed in counties both in and out of the training set. We then compare the error of simulations from our model with a standard SEIRD model, and show that ours substantially reduces errors. We also use simulated data to compare our methodology for handling partial observability with a standard approach, showing that ours is significantly better at estimating the values of unobserved quantities.


Subject(s)
COVID-19/epidemiology , Computer Simulation , Disease Hotspot , Models, Statistical , Computational Biology , Disease Outbreaks/statistics & numerical data , Humans , Neural Networks, Computer , Prevalence , SARS-CoV-2 , United States/epidemiology
11.
Respir Res ; 22(1): 168, 2021 Jun 04.
Article in English | MEDLINE | ID: covidwho-1259197

ABSTRACT

BACKGROUND: In hospitalized patients with SARS-CoV-2 infection, outcomes markedly differ between locations, regions and countries. One possible cause for these variations in outcomes could be differences in patient treatment limitations (PTL) in different locations. We thus studied their role as predictor for mortality in a population of hospitalized patients with COVID-19. METHODS: In a region with high incidence of SARS-CoV-2 infection, adult hospitalized patients with PCR-confirmed SARS-CoV-2 infection were prospectively registered and characterized regarding sex, age, vital signs, symptoms, comorbidities (including Charlson comorbidity index (CCI)), transcutaneous pulse oximetry (SpO2) and laboratory values upon admission, as well as ICU-stay including respiratory support, discharge, transfer to another hospital and death. PTL assessed by routine clinical procedures comprised the acceptance of ICU-therapy, orotracheal intubation and/or cardiopulmonary resuscitation. RESULTS: Among 526 patients included (median [quartiles] age 73 [57; 82] years, 47% female), 226 (43%) had at least one treatment limitation. Each limitation was associated with age, dementia and eGFR (p < 0.05 each), that regarding resuscitation additionally with Charlson comorbidity index (CCI) and cardiac disease. Overall mortality was 27% and lower (p < 0.001) in patients without treatment limitation (12%) compared to those with any limitation (47%). In univariate analyses, age and comorbidities (diabetes, cardiac, cerebrovascular, renal, hepatic, malignant disease, dementia), SpO2, hemoglobin, leucocyte numbers, estimated glomerular filtration rate (eGFR), C-reactive protein (CRP), Interleukin-6 and LDH were predictive for death (p < 0.05 each). In multivariate analyses, the presence of any treatment limitation was an independent predictor of death (OR 4.34, 95%-CI 2.10-12.30; p = 0.001), in addition to CCI, eGFR < 55 ml/min, neutrophil number > 5 G/l, CRP > 7 mg/l and SpO2 < 93% (p < 0.05 each). CONCLUSION: In hospitalized patients with SARS-CoV-2, the percentage of patients with treatment limitations was high. PTL were linked to age, comorbidities and eGFR assessed upon admission and strong, independent risk factors for mortality. These findings might be useful for further understanding of COVID-19 mortality and its regional variations. Clinical trial registration ClinicalTrials.gov Identifier: NCT04344171.


Subject(s)
COVID-19/mortality , COVID-19/therapy , Disease Hotspot , Health Services Accessibility , Healthcare Disparities , Hospitalization , Age Factors , Aged , COVID-19/diagnosis , Comorbidity , Female , Germany/epidemiology , Glomerular Filtration Rate , Health Status , Hospital Mortality , Humans , Incidence , Kidney/physiopathology , Male , Middle Aged , Prospective Studies , Risk Assessment , Risk Factors , Time Factors , Treatment Outcome
12.
Int J Hyg Environ Health ; 235: 113771, 2021 06.
Article in English | MEDLINE | ID: covidwho-1240386

ABSTRACT

PURPOSE: The objective of the ongoing study was to investigate how SARS-CoV-2 infection spread within two hospitals in North Rhine-Westphalia, Germany by testing the employees working in high-risk, intermediate-risk and low-risk-areas for the presence of SARS-CoV-2 IgG antibodies. Presented intermediate results evaluate the first infection period until the end of September 2020. METHODS: The study "COVID-19: Hotspot hospital?- Seroprevalence of SARS-CoV-2 antibodies in hospital employees in a secondary care hospital network in Germany " is a prospective, single centre observational cohort study conducted at the St. Vincenz Hospital Datteln with 316 beds. The presented data include one other hospital: St. Laurentius Stift Waltrop, Germany with 172 beds. RESULTS: Between June 2020 and September 2020 we analyzed serum samples of 907 employees which represents 62.1% of all employees. Thirteen employees (1.4%), respectively 13/696 healthcare workers (HCWs) (1.9%) had detectable SARS-CoV-2 IgG antibodies. Among them, 4 (30.8%) were aware of COVID-19 exposure, and 5 (38.5%) reported clinical symptoms. HCWs working in high-risk areas had a seroprevalence rate of 1.6% (1/64), HCWs working in intermediate-risk area 1.7% (11/632) and 0.5% employees (1/211) in low-risk areas with no contact to patients were seropositive. CONCLUSION: Even if we treated COVID-19 positive patients, we found no clear evidence that infection was transmitted to HCWs in contact to these patients. As knowledge about SARS-CoV-2 transmission evolves, the concept of infection prevention must be continuously reviewed and adapted as needed to keep hospitals a safe place.


Subject(s)
COVID-19/epidemiology , Health Personnel/statistics & numerical data , SARS-CoV-2/immunology , Secondary Care Centers/statistics & numerical data , Adolescent , Adult , Antibodies, Viral/blood , COVID-19/diagnosis , COVID-19/prevention & control , Disease Hotspot , Female , Germany/epidemiology , Humans , Immunoglobulin G/blood , Longitudinal Studies , Male , Prospective Studies , Risk Factors , SARS-CoV-2/isolation & purification , Seroepidemiologic Studies , Young Adult
13.
Emerg Microbes Infect ; 10(1): 1148-1155, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1238129

ABSTRACT

Several lineages of SARS-CoV-2 are currently circulating worldwide. During SARS-CoV-2 diagnostic activities performed in Abruzzo region (central Italy) several strains belonging to the B.1.177.75 lineage tested negative for the N gene but positive for the ORF1ab and S genes (+/+/- pattern) by the TaqPath COVID-19 CE-IVD RT-PCR Kit manufactured by Thermofisher. By sequencing, a unique mutation, synonymous 28948C > T, was found in the N-negative B.1.177.75 strains. Although we do not have any knowledge upon the nucleotide sequences of the primers and probe adopted by this kit, it is likely that N gene dropout only occurs when 28948C > T is coupled with 28932C > T, this latter present, in turn, in all B.1.177.75 sequences available on public databases. Furthermore, epidemiological analysis was also performed. The majority of the N-negative B.1.177.75 cases belonged to two clusters apparently unrelated to each other and both clusters involved young people. However, the phylogeny for sequences containing the +/+/- pattern strongly supports a genetic connection and one common source for both clusters. Though, genetic comparison suggests a connection rather than indicating the independent emergence of the same mutation in two apparently unrelated clusters. This study highlights once more the importance of sharing genomic data to link apparently unrelated epidemiological clusters and to, remarkably, update molecular tests.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Coronavirus Nucleocapsid Proteins/genetics , SARS-CoV-2/genetics , COVID-19/diagnosis , Disease Hotspot , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Humans , Italy/epidemiology , Nucleocapsid/genetics , Phosphoproteins/genetics , Polymorphism, Single Nucleotide/genetics , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification
15.
J Med Virol ; 93(3): 1748-1751, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196460

ABSTRACT

Human-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) interaction can have an array of various outcomes-it could be mortal, morbid or merely carrying minor health consequences. The very rapid global spread has raised the issue whether there are further multi-dimensional consequences of SARS-CoV-2 infection on human behavior, the key of its transmission. During the coronavirus crisis, odd, abnormal, and irresponsible behavior has been reported in coronavirus disease 2019 (COVID-19) individuals, particularly in super-spreaders, that is, persons with a high viral load, thus constituting also super-emitters. Indeed, cases of infected persons ignoring self-confinement orders, intentionally disregarding physical distancing and multiplying social interactions, or even deliberately sneezing, spitting or coughing were reported. While it is known that some other viruses, such as rabies and even influenza do change human behavior, this remains unclear for SARS-CoV-2. In this perspective, we highlight the possibility that COVID-19 is facilitated by altered human social behavior that benefits SARS-CoV-2 transmission, through showcasing similar virus-induced changed behavior by other pathogens and relating this to reports from the gray literature.


Subject(s)
COVID-19/psychology , COVID-19/transmission , Dangerous Behavior , Social Behavior , Behavior Control , Disease Hotspot , Humans , Physical Distancing , SARS-CoV-2
16.
J Med Virol ; 93(3): 1414-1420, 2021 03.
Article in English | MEDLINE | ID: covidwho-1196438

ABSTRACT

There is limited information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clustering within families with children. We aimed to study the transmission dynamics of SARS-CoV-2 within families with children in Greece. We studied 23 family clusters of coronavirus disease 2019 (COVID-19). Infection was diagnosed by reverse-transcriptase polymerase chain reaction in respiratory specimens. The level of viral load was categorized as high, moderate, or low based on the cycle threshold values. There were 109 household members (66 adults and 43 children). The median attack rate per cluster was 60% (range: 33.4%-100%). An adult member with COVID-19 was the first case in 21 (91.3%) clusters. Transmission of infection occurred from an adult to a child in 19 clusters and/or from an adult to another adult in 12 clusters. There was no evidence of child-to-adult or child-to-child transmission. In total 68 household members (62.4%) tested positive. Children were more likely to have an asymptomatic SARS-CoV-2 infection compared to adults (40% vs 10.5%; P = .021). In contrast, adults were more likely to develop a severe clinical course compared with children (8.8% vs 0%; P = .021). In addition, infected children were significantly more likely to have a low viral load while adults were more likely to have a moderate viral load (40.7% and 18.6% vs 13.8% and 51.7%, respectively; P = .016). In conclusion, while children become infected by SARS-CoV-2, they do not appear to transmit infection to others. Furthermore, children more frequently have an asymptomatic or mild course compared to adults. Further studies are needed to elucidate the role of viral load on these findings.


Subject(s)
COVID-19/transmission , Disease Hotspot , Adolescent , Adult , Aged , Aged, 80 and over , Asymptomatic Infections , COVID-19/epidemiology , COVID-19/physiopathology , COVID-19/virology , Child , Child, Preschool , Family Health , Female , Greece/epidemiology , Humans , Infant , Male , Middle Aged , SARS-CoV-2/physiology , Severity of Illness Index , Viral Load , Young Adult
17.
Infect Dis Now ; 51(4): 391-394, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1157346

ABSTRACT

OBJECTIVE: In March 2020, we implemented screening of the contacts of a COVID-19 cluster having occurred in the Lot-et-Garonne department, the first department of the Nouvelle-Aquitaine region to be affected by the active circulation of SARS-CoV-2. We aimed to describe the impact of this screening on the local SARS-CoV-2 outbreak. METHODS: All high-risk contacts, as well as the individuals living in their households, were screened. We detailed the evolution of the number of confirmed COVID-19 cases in the Lot-et-Garonne department and the rest of the Nouvelle-Aquitaine region. RESULTS: Among the 89 screened individuals, 10 new cases were confirmed, including 4 asymptomatic persons. In Lot-et-Garonne, the number of confirmed COVID-19 cases immediately decreased after this screening and no epidemic peak occurred, contrary to what was observed in the rest of the region. CONCLUSION: The early screening of high-risk contacts of COVID-19 cases and members of their household implemented a few days before the first lockdown probably helped to prevent the spread of the virus in the department.


Subject(s)
COVID-19/diagnosis , COVID-19/epidemiology , Disease Hotspot , Disease Outbreaks , Mass Screening , France/epidemiology , Humans
18.
Epidemiol Infect ; 149: e70, 2021 02 24.
Article in English | MEDLINE | ID: covidwho-1142396

ABSTRACT

As most children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present with mild symptoms or they are asymptomatic, the optimal strategy for molecular testing it is not well defined. The aim of the study was to determine the extent and aetiology of molecular testing for SARS-CoV-2 in Greek paediatric departments during the first phase of the pandemic and identify possible differences in incidence, depending on the age group and geographical area. We conducted a nationwide study of molecular testing for SARS-CoV-2 of children in paediatric departments between March and June 2020. A total of 65 paediatric departments participated in the study, representing 4901 children who were tested for SARS-CoV-2 and 90 (1.8%) were positive. Most paediatric cases were associated with topical outbreaks. Adolescents 11-16 years had the highest positivity rate (3.6%) followed by children 6-10 years (1.9%). However, since the testing rate significantly differed between age groups, the modified incidence of SARS-CoV-2 infection per age group was highest in infants <1 year (19.25/105 population). Most children tested presented with fever (70.9%), respiratory (50.1%) or gastrointestinal symptoms (28.1%). Significant differences were detected between public and private hospitals regarding the positivity rate (2.34% vs. 0.39%, P-value <0.001). Significant variation in SARS-CoV-2 molecular testing positivity rate and incidence between age groups indicate discrepancies in risk factors among different age groups that shall be considered when ordering molecular testing.


Subject(s)
COVID-19/epidemiology , Hospital Departments , Pediatrics , Adolescent , COVID-19/diagnosis , COVID-19/physiopathology , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Disease Hotspot , Female , Greece/epidemiology , Humans , Incidence , Infant , Infant, Newborn , Male , SARS-CoV-2
19.
Crit Care Med ; 49(7): 1068-1082, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1137999

ABSTRACT

OBJECTIVES: Eleven months into the coronavirus disease 2019 pandemic, the country faces accelerating rates of infections, hospitalizations, and deaths. Little is known about the experiences of critical care physicians caring for the sickest coronavirus disease 2019 patients. Our goal is to understand how high stress levels and shortages faced by these physicians during Spring 2020 have evolved. DESIGN: We surveyed (October 23, 2020 to November 16, 2020) U.S. critical care physicians treating coronavirus disease 2019 patients who participated in a National survey earlier in the pandemic (April 23, 2020 to May 3, 2020) regarding their stress and shortages they faced. SETTING: ICU. PATIENTS: Coronavirus disease 2019 patients. INTERVENTION: Irrelevant. MEASUREMENT: Physician emotional distress/physical exhaustion: low (not at all/not much), moderate, or high (a lot/extreme). Shortage indicators: insufficient ICU-trained staff and shortages in medication, equipment, or personal protective equipment requiring protocol changes. MAIN RESULTS: Of 2,375 U.S. critical care attending physicians who responded to the initial survey, we received responses from 1,356 (57.1% response rate), 97% of whom (1,278) recently treated coronavirus disease 2019 patients. Two thirds of physicians (67.6% [864]) reported moderate or high levels of emotional distress in the Spring versus 50.7% (763) in the Fall. Reports of staffing shortages persisted with 46.5% of Fall respondents (594) reporting a staff shortage versus 48.3% (617) in the Spring. Meaningful shortages of medication and equipment reported in the Spring were largely alleviated. Although personal protective equipment shortages declined by half, they remained substantial. CONCLUSIONS: Stress, staffing, and, to a lesser degree, personal protective equipment shortages faced by U.S. critical care physicians remain high. Stress levels were higher among women. Considering the persistence of these findings, rising levels of infection nationally raise concerns about the capacity of the U.S. critical care system to meet ongoing and future demands.


Subject(s)
COVID-19/psychology , Critical Care/psychology , Occupational Stress , Physicians/psychology , Psychological Distress , Adult , Disease Hotspot , Equipment and Supplies, Hospital/supply & distribution , Female , Humans , Male , Middle Aged , Personal Protective Equipment/supply & distribution , SARS-CoV-2 , Surveys and Questionnaires , United States/epidemiology , Workforce , Workplace
20.
JAMA Netw Open ; 4(3): e211283, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-1125121

ABSTRACT

Importance: Risks for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among health care personnel (HCP) are unclear. Objective: To evaluate the risk factors associated with SARS-CoV-2 seropositivity among HCP with the a priori hypothesis that community exposure but not health care exposure was associated with seropositivity. Design, Setting, and Participants: This cross-sectional study was conducted among volunteer HCP at 4 large health care systems in 3 US states. Sites shared deidentified data sets, including previously collected serology results, questionnaire results on community and workplace exposures at the time of serology, and 3-digit residential zip code prefix of HCP. Site-specific responses were mapped to a common metadata set. Residential weekly coronavirus disease 2019 (COVID-19) cumulative incidence was calculated from state-based COVID-19 case and census data. Exposures: Model variables included demographic (age, race, sex, ethnicity), community (known COVID-19 contact, COVID-19 cumulative incidence by 3-digit zip code prefix), and health care (workplace, job role, COVID-19 patient contact) factors. Main Outcome and Measures: The main outcome was SARS-CoV-2 seropositivity. Risk factors for seropositivity were estimated using a mixed-effects logistic regression model with a random intercept to account for clustering by site. Results: Among 24 749 HCP, most were younger than 50 years (17 233 [69.6%]), were women (19 361 [78.2%]), were White individuals (15 157 [61.2%]), and reported workplace contact with patients with COVID-19 (12 413 [50.2%]). Many HCP worked in the inpatient setting (8893 [35.9%]) and were nurses (7830 [31.6%]). Cumulative incidence of COVID-19 per 10 000 in the community up to 1 week prior to serology testing ranged from 8.2 to 275.6; 20 072 HCP (81.1%) reported no COVID-19 contact in the community. Seropositivity was 4.4% (95% CI, 4.1%-4.6%; 1080 HCP) overall. In multivariable analysis, community COVID-19 contact and community COVID-19 cumulative incidence were associated with seropositivity (community contact: adjusted odds ratio [aOR], 3.5; 95% CI, 2.9-4.1; community cumulative incidence: aOR, 1.8; 95% CI, 1.3-2.6). No assessed workplace factors were associated with seropositivity, including nurse job role (aOR, 1.1; 95% CI, 0.9-1.3), working in the emergency department (aOR, 1.0; 95% CI, 0.8-1.3), or workplace contact with patients with COVID-19 (aOR, 1.1; 95% CI, 0.9-1.3). Conclusions and Relevance: In this cross-sectional study of US HCP in 3 states, community exposures were associated with seropositivity to SARS-CoV-2, but workplace factors, including workplace role, environment, or contact with patients with known COVID-19, were not. These findings provide reassurance that current infection prevention practices in diverse health care settings are effective in preventing transmission of SARS-CoV-2 from patients to HCP.


Subject(s)
COVID-19/epidemiology , Disease Hotspot , Disease Transmission, Infectious/statistics & numerical data , Health Personnel/statistics & numerical data , Occupational Exposure/statistics & numerical data , Adult , COVID-19/transmission , COVID-19 Serological Testing , Cross-Sectional Studies , Female , Georgia/epidemiology , Humans , Illinois/epidemiology , Male , Maryland/epidemiology , Middle Aged , Residence Characteristics , Risk Factors , SARS-CoV-2 , Seroepidemiologic Studies , United States/epidemiology
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