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1.
Front Cell Infect Microbiol ; 12: 843463, 2022.
Article in English | MEDLINE | ID: covidwho-1779935

ABSTRACT

Background: Since the outbreak of COVID-19, a series of preventive and control measures in China have been used to effectively curb the spread of COVID-19. This study aimed to analyze the epidemiological characteristics of Mycoplasma pneumoniae (MP) and Chlamydia pneumoniae (CP) in hospitalized children with acute respiratory tract infection during the COVID-19 pandemic. Methods: MP IgM antibody and CP IgM antibody were detected in all hospitalized children due to acute respiratory tract infection in the Children's Hospital Affiliated to Zhejiang University from January 2019 to December 2020. These data were compared between 2019 and 2020 based on age and month. Results: The overall detection rate of MP and CP in 2020 was significantly lower than that in 2019 (MP: 21.5% vs 32.9%, P<0.001; CP: 0.3% vs 0.9%, P<0.001). This study found a 4-fold reduction in the number of children positive for MP and a 7.5-fold reduction in the number of children positive for CP from 2019 to 2020. The positive cases were concentrated in children aged >1 year old. In 2019, the positive rate of MP was detected more commonly in children 3 years of age or older than in younger children. In 2020, the higher positive rate of MP reached a peak in the 3- to 6-year age group (35.3%). CP was detected predominantly in children aged 6 years older in 2019 and 2020, with positive rates of 4.8% and 2.6%, respectively. Meanwhile, the positive rates of MP in 2019 were detected more commonly in July, August and September, with 47.2%, 46.7% and 46.3%, respectively. Nevertheless, the positive rates of MP from February to December 2020 apparently decreased compared to those in 2019. The positive rates of CP were evenly distributed throughout the year, with 0.5%-1.6% in 2019 and 0.0%-2.1% in 2020. Conclusions: A series of preventive and control measures for SARS-CoV-2 during the COVID-19 pandemic can not only contain the spread of SARS-CoV-2 but also sharply improve the infection of other atypical pathogens, including MP and CP.


Subject(s)
COVID-19 , Chlamydophila Infections , Chlamydophila pneumoniae , Pneumonia, Mycoplasma , Respiratory Tract Infections , Aged , COVID-19/epidemiology , Child , Child, Hospitalized , Chlamydophila Infections/epidemiology , Epidemiologic Studies , Humans , Immunoglobulin M , Infant , Mycoplasma pneumoniae , Pandemics , Pneumonia, Mycoplasma/diagnosis , Pneumonia, Mycoplasma/epidemiology , Respiratory Tract Infections/epidemiology , SARS-CoV-2
3.
Indian J Ophthalmol ; 70(4): 1371-1375, 2022 04.
Article in English | MEDLINE | ID: covidwho-1760981

ABSTRACT

Purpose: Rhino-orbital-cerebral mucormycosis (ROCM) is a rare opportunistic fungal infection with a fulminant course and an often fatal outcome. It can occur in immune-compromised patients such as those having uncontrolled diabetes, on long-term corticosteroid or immunosuppressive therapy, with COVID-19 infection, renal failure, AIDS, malignancy, or organ transplant. The aim of our study was to study the epidemiology of mucormycosis in COVID-19 patients and identify its risk factors. Methods: Ours was an epidemiological study wherein we gathered the demographic, clinical, histopathological, and radiological data of 458 patients of mucormycosis who presented to us between August 2020 and May 2021. Mucormycosis was defined through clinical and radiological findings or positive culture reports. Results: Out of all, 20.74% of patients did not have any past or concurrent history of COVID-19. The most common symptom of mucormycosis was orbital/facial pain (38.64%) and the most common sign was periocular/facial edema (50.74%). Mucormycosis involving the nose and sinuses (94.54%) was most common followed by rhino-orbital (45.41%) and brain involvement (10.04%). The most common risk factor for mucormycosis was diabetes [81.92%], followed by corticosteroid use [79.69%] and supplemental oxygen [48.90%]. Most of the patients received similar treatment with IV amphotericin B [88.64%] and local debridement [80.74%]. Conclusion: With the third wave of COVID-19 still lurking, a fatal fungal infection should be kept in mind in COVID-19 active as well as recovered patients, especially those who have co-morbid medical conditions such as uncontrolled diabetes and who are treated with large doses of corticosteroids.


Subject(s)
COVID-19 , Mucormycosis , COVID-19/epidemiology , Epidemiologic Studies , Humans , India/epidemiology , Mucormycosis/diagnosis , Mucormycosis/epidemiology , Mucormycosis/microbiology , Tertiary Healthcare
4.
Am J Epidemiol ; 190(11): 2275-2279, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1722196

ABSTRACT

Epidemiologists sometimes use external sources of variation to explore highly confounded exposure-outcome relationships or exposures that cannot be randomized. These exogenous sources of variation, or natural experiments, are sometimes proposed as instrumental variables to examine the effects of given exposures on given outcomes. Previous epidemiologic studies have applied this technique using famines, earthquakes, weather events, and previous pandemics as exogenous sources of variation for other exposures; interest in applying this technique using the current severe acute respiratory system coronavirus 2 (SARS-CoV-2) pandemic is already documented. Yet large-scale events like these likely have broad and complicated impacts on human health, which almost certainly violates the exclusion restriction assumption of instrumental variable analyses. We review the assumptions of instrumental variable analyses, highlight previous applications of this method with respect to natural experiments with broad impacts or "shocks," and discuss how these relate to our current observations of the SARS-CoV-2 pandemic. While we encourage thorough investigation of the broad impacts of the SARS-CoV-2 pandemic on human health, we caution against its widespread use as an instrumental variable to study other exposures of interest.


Subject(s)
COVID-19 , Pandemics , Bias , Epidemiologic Studies , Humans , Pandemics/prevention & control , SARS-CoV-2
5.
Int J Environ Res Public Health ; 19(5)2022 Mar 01.
Article in English | MEDLINE | ID: covidwho-1715371

ABSTRACT

The large availability of both air pollution and COVID-19 data, and the simplicity to make geographical correlations between them, led to a proliferation of ecological studies relating the levels of pollution in administrative areas to COVID-19 incidence, mortality or lethality rates. However, the major drawback of these studies is the ecological fallacy that can lead to spurious associations. In this frame, an increasing concern has been addressed to clarify the possible role of contextual variables such as municipalities' characteristics (including urban, rural, semi-rural settings), those of the resident communities, the network of social relations, the mobility of people, and the responsiveness of the National Health Service (NHS), to better clarify the dynamics of the phenomenon. The objective of this paper is to identify and collect the municipalities' and community contextual factors and to synthesize their information content to produce suitable indicators in national environmental epidemiological studies, with specific emphasis on assessing the possible role of air pollution on the incidence and severity of the COVID-19 disease. A first step was to synthesize the content of spatial information, available at the municipal level, in a smaller set of "summary indexes" that can be more easily viewed and analyzed. For the 7903 Italian municipalities (1 January 2020-ISTAT), 44 variables were identified, collected, and grouped into five information dimensions a priori defined: (i) geographic characteristics of the municipality, (ii) demographic and anthropogenic characteristics, (iii) mobility, (iv) socio-economic-health area, and (v) healthcare offer (source: ISTAT, EUROSTAT or Ministry of Health, and further ad hoc elaborations (e.g., OpenStreetMaps)). Principal component analysis (PCA) was carried out for the five identified dimensions, with the aim of reducing the large number of initial variables into a smaller number of components, limiting as much as possible the loss of information content (variability). We also included in the analysis PM2.5, PM10 and NO2 population weighted exposure (PWE) values obtained using a four-stage approach based on the machine learning method, "random forest", which uses space-time predictors, satellite data, and air quality monitoring data estimated at the national level. Overall, the PCA made it possible to extract twelve components: three for the territorial characteristics dimension of the municipality (variance explained 72%), two for the demographic and anthropogenic characteristics dimension (variance explained 62%), three for the mobility dimension (variance explained 83%), two for the socio-economic-health sector (variance explained 58%) and two for the health offer dimension (variance explained 72%). All the components of the different dimensions are only marginally correlated with each other, demonstrating their potential ability to grasp different aspects of the spatial distribution of the COVID-19 pathology. This work provides a national repository of contextual variables at the municipality level collapsed into twelve informative factors suitable to be used in studies on the association between chronic exposure to air pollution and COVID-19 pathology, as well as for investigations on the role of air pollution on the health of the Italian population.


Subject(s)
Air Pollution , COVID-19 , Air Pollution/adverse effects , Air Pollution/analysis , COVID-19/epidemiology , Environmental Exposure/analysis , Epidemiologic Studies , Humans , SARS-CoV-2 , State Medicine
6.
PLoS One ; 17(2): e0263981, 2022.
Article in English | MEDLINE | ID: covidwho-1690696

ABSTRACT

INTRODUCTION: The Coronavirus Disease 2019 (COVID19) pandemic has struck Latin America and the Caribbean (LAC) particularly hard. One of the crucial areas in the international community's response relates to accelerating research and knowledge sharing. The aim of this article is to map and characterise the existing empirical research related to COVID-19 in LAC countries and contribute to identify opportunities for strengthening future research. METHODS: In this scoping review, articles published between December 2019 and 11 November 2020 were selected if they included an empirical component (explicit scientific methods to collect and analyse primary data), LAC population was researched, and the research was about the COVID-19 pandemic, regardless of publication status or language. MEDLINE, EMBASE, LILACS, Scielo, CENTRAL and Epistemonikos were searched. All titles and abstracts, and full texts were screened by two independent reviewers. Data from included studies was extracted by one reviewer and checked by a second independent reviewer. RESULTS: 14,406 records were found. After removing duplicates, 5,458 titles and abstracts were screened, of which 2,323 full texts were revised to finally include 1,626 empirical studies. The largest portion of research came from people/population of Brazil (54.6%), Mexico (19.1%), Colombia (11.2%), Argentina (10.4%), Peru (10.3%) and Chile (10%), while Caribbean countries concentrated 15.3%. The methodologies most used were cross-sectional studies (34.7%), simulation models (17.5%) and randomized controlled trials (RCTs) (13.6%). Using a modified version of WHO's COVID-19 Coordinated Global Research Roadmap classification, 54.2% were epidemiological studies, followed by clinical management (22.3%) and candidate therapeutics (12.2%). Government and public funds support were reported in 19.2% of studies, followed by universities or research centres (9%), but 47.5% did not include any funding statement. CONCLUSION: During the first part of the COVID-19 pandemic, LAC countries have contributed to the global research effort primarily with epidemiological studies, with little participation on vaccines research, meaning that this type of knowledge would be imported from elsewhere. Research agendas could be further coordinated aiming to enhance shared self-sufficiency regarding knowledge needs in the region.


Subject(s)
COVID-19 , Empirical Research , Caribbean Region/epidemiology , Epidemiologic Studies , Humans , Latin America/epidemiology , Pandemics , SARS-CoV-2
7.
Int J Environ Res Public Health ; 19(3)2022 01 26.
Article in English | MEDLINE | ID: covidwho-1686732

ABSTRACT

Humans are exposed to a diverse mixture of chemical and non-chemical exposures across their lifetimes. Well-designed epidemiology studies as well as sophisticated exposure science and related technologies enable the investigation of the health impacts of mixtures. While existing statistical methods can address the most basic questions related to the association between environmental mixtures and health endpoints, there were gaps in our ability to learn from mixtures data in several common epidemiologic scenarios, including high correlation among health and exposure measures in space and/or time, the presence of missing observations, the violation of important modeling assumptions, and the presence of computational challenges incurred by current implementations. To address these and other challenges, NIEHS initiated the Powering Research through Innovative methods for Mixtures in Epidemiology (PRIME) program, to support work on the development and expansion of statistical methods for mixtures. Six independent projects supported by PRIME have been highly productive but their methods have not yet been described collectively in a way that would inform application. We review 37 new methods from PRIME projects and summarize the work across previously published research questions, to inform methods selection and increase awareness of these new methods. We highlight important statistical advancements considering data science strategies, exposure-response estimation, timing of exposures, epidemiological methods, the incorporation of toxicity/chemical information, spatiotemporal data, risk assessment, and model performance, efficiency, and interpretation. Importantly, we link to software to encourage application and testing on other datasets. This review can enable more informed analyses of environmental mixtures. We stress training for early career scientists as well as innovation in statistical methodology as an ongoing need. Ultimately, we direct efforts to the common goal of reducing harmful exposures to improve public health.


Subject(s)
National Institute of Environmental Health Sciences (U.S.) , Research Design , Environmental Exposure/analysis , Epidemiologic Methods , Epidemiologic Studies , Humans , Risk Assessment , United States
8.
JMIR Public Health Surveill ; 8(2): e32638, 2022 02 10.
Article in English | MEDLINE | ID: covidwho-1686321

ABSTRACT

BACKGROUND: COVID-19, which emerged in December 2019, has spread rapidly around the world and has become a serious public health event endangering human life. With regard to COVID-19, there are still many unknowns, such as the exact case fatality rate (CFR). OBJECTIVE: The main objective of this study was to explore the value of the discharged CFR (DCFR) to make more accurate forecasts of epidemic trends of COVID-19 in Italy. METHODS: We retrieved the epidemiological data of COVID-19 in Italy published by the John Hopkins Coronavirus Resource Center. We then used the proportion of deaths to discharged cases(including deaths and recovered cases) to calculate the total DCFR (tDCFR), monthly DCFR (mDCFR), and stage DCFR (sDCFR). Furthermore, we analyzed the trend in the mDCFR between January and December 2020 using joinpoint regression analysis, used ArcGIS version 10.7 to visualize the spatial distribution of the epidemic CFR, and assigned different colors to each province based on the CFR or tDCFR. RESULTS: We calculated the numbers and obtained the new indices of the tDCFR and mDCFR for calculating the fatality rate. The results showed that the tDCFR and mDCFR fluctuated greatly from January to May. They first showed a rapid increase followed by a rapid decline after reaching the peak. The map showed that the provinces with a high tDCFR were Emilia-Romagna, Puglia, and Lombardia. The change trend of the mDCFR over time was divided into the following 2 stages: the first stage (from January to May) and the second stage (from June to December). With regard to worldwide COVID-19 statistics, among 6 selected countries, the United States had the highest tDCFR (4.26%), while the tDCFR of the remaining countries was between 0.98% and 2.72%. CONCLUSIONS: We provide a new perspective for assessing the fatality of COVID-19 in Italy, which can use ever-changing data to calculate a more accurate CFR and scientifically predict the development trend of the epidemic.


Subject(s)
COVID-19 , Epidemiologic Studies , Humans , Italy/epidemiology , SARS-CoV-2 , United States
9.
Am J Epidemiol ; 191(1): 234-236, 2022 01 01.
Article in English | MEDLINE | ID: covidwho-1662102
10.
Am J Epidemiol ; 191(1): 234-236, 2022 01 01.
Article in English | MEDLINE | ID: covidwho-1631735
11.
Microbes Infect ; 24(1): 104911, 2022 02.
Article in English | MEDLINE | ID: covidwho-1625930

ABSTRACT

Considering common childhood respiratory viruses and SARS-CoV-2 share similar transmission routes, non-pharmaceutical interventions (NPIs) to prevent SARS-CoV-2 may affect the epidemiology of respiratory viruses. Therefore, our study aimed to observe the epidemiologic characteristics of common childhood respiratory viruses in 2020 (after the pandemic) compared with 2019 (before the pandemic) in Hangzhou, China. The data were compared between 2019 and 2020 based on age and month, respectively. One or more viruses were detected in 3135/21452 (14.61%) specimens in 2019, which was significantly lower in 1110/8202 (13.53%) specimens in 2020. Respiratory syncytial virus (RSV) was the most commonly detected virus in 2019 and 2020. The positive rate of adenovirus (ADV), parainfluenza virus (PIV)1, PIV2, and PIV3 in 2020 was significantly decreased in 2019. In 2020, RSV replaced ADV as the most predominant virus in children aged 1-6 years, and the positive rate of influenza virus A (FluA), influenza virus B (FluB), PIV1, and PIV2 was not correlated to age. FluA, FluB, and PIV2 were not almost detected from February 2020. The positive rates of ADV and PIV1 were uncorrelated to the month in 2020. By strict NPIs, besides controlling the COVID-19 pandemic, incredible progress has been made to reduce the prevalence of common childhood respiratory viruses.


Subject(s)
COVID-19 , Respiratory Tract Infections , Child , Epidemiologic Studies , Hospitals , Humans , Infant , Influenza B virus , Pandemics/prevention & control , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/prevention & control , SARS-CoV-2
12.
Am J Epidemiol ; 191(1): 234-236, 2022 01 01.
Article in English | MEDLINE | ID: covidwho-1621544
13.
Med Pr ; 72(6): 711-720, 2021 Dec 22.
Article in Polish | MEDLINE | ID: covidwho-1609128

ABSTRACT

"Long-COVID" is described as long-term effects of SARS­ CoV­2 infection that last >4 weeks after the acutephase of infection. The aim of this narrative reviews to evaluate the frequency of occurrence of 3 symptoms often observed in Long-COVID, i.e., chronic fatigue, shortness of breath and cough, and whether comorbidities such as diabetes and arterial hypertension increase the risk of complications after a history of SARS­ CoV­2 infection. The method of narrative review was used in this paper. PubMed (May 31, 2021) search was performed to retrieve articles concerning the occurrence of long COVID-19 chronic fatigue, dyspnoea and chronic cough. Studies in which the observation period was <30 days and the average age of subjects exceeded 60 years, as well as studies with no information on the methodology used, in particular without the method of recruiting people for the study, were excluded. Populations with a high frequency of diabetes were defined as the prevalence >10%, and in the case of arterial hypertension >40%. The average frequency of diabetes <10%, hypertension 40%. It can be concluded that in the period of >30 days after discharge from the hospital, in populations with a high incidence of diabetes and hypertension, the incidence of chronic fatigue and cough was higher than in the other analyzed groups. Symptoms of dyspnea were most frequently reported in populations with high rates of diabetes, but at the same time in the average percentage of people with arterial hypertension. Persistent symptoms specific to "Long-COVID" can significantly reduce the ability to perform work. In this situation, check-ups performed before returning to work after long-term leave tape on a new dimension. Med Pr. 2021;72(6):711-20.


Subject(s)
COVID-19 , COVID-19/complications , Cough/epidemiology , Cough/etiology , Dyspnea/epidemiology , Epidemiologic Studies , Humans , Middle Aged , SARS-CoV-2
15.
J Perinat Med ; 50(2): 132-138, 2022 Feb 23.
Article in English | MEDLINE | ID: covidwho-1559337

ABSTRACT

OBJECTIVES: The SARS-CoV-2 virus continues wreaking worldwide havoc on health and between March and August 2020, the first outbreak of COVID-19 hit Chile. The pregnant population is especially vulnerable to infection. Studies have been published that associate socioeconomic status, overcrowding, and poverty with a higher prevalence of SARS-CoV-2 infection. There are few studies about the development of this pandemic in Latin American countries so far. This study seeks to show the prevalence and sociodemographic and perinatal characteristics in pregnant women at the time of delivery, comparing both groups with positive and negative COVID-19 PCR results. METHODS: A prospective, cross-sectional study of pregnant women who delivered at the San Juan de Dios Hospital in Santiago between April 15, 2020 and June 15, 2020. Analysis of epidemiological, sociodemographic, obstetric, perinatal and sociodemographic data of patients with positive and negative COVID-19 PCR results. RESULTS: There were 701 patients included in the study. The prevalence of those with a positive COVID-19 PCR was 9.7% and 67.7% being asymptomatic. Pre-term delivery was significantly higher in the group of positive patients (23.5%) vs. negative patients (8.7%), which was not the same rate as with cesarean sections (C-sections). A 13.2% of patients required management of the pathology in the Critical Care Unit (CCU) and there were no cases of maternal or fetal deaths. We found no significant difference between both groups when analyzing socioeconomic variables, though we noted a trend of greater overcrowding among the group of patients with infection. CONCLUSIONS: The majority of pregnant patients with SARS-CoV-2 infection are asymptomatic. COVID-19 increases the rate of premature births, but this rate is not same with C-sections. Sociodemographic conditions and overcrowding do not show a higher infection rate in a homogeneous population in relation to the economic, social and demographic level.


Subject(s)
COVID-19/epidemiology , Hospitals, Public/statistics & numerical data , Pregnancy Complications, Infectious/epidemiology , Adolescent , Adult , Chile/epidemiology , Epidemiologic Studies , Female , Humans , Middle Aged , Pregnancy , Prevalence , Young Adult
16.
Med Pr ; 72(6): 711-720, 2021 Dec 22.
Article in Polish | MEDLINE | ID: covidwho-1547810

ABSTRACT

"Long-COVID" is described as long-term effects of SARS­ CoV­2 infection that last >4 weeks after the acutephase of infection. The aim of this narrative reviews to evaluate the frequency of occurrence of 3 symptoms often observed in Long-COVID, i.e., chronic fatigue, shortness of breath and cough, and whether comorbidities such as diabetes and arterial hypertension increase the risk of complications after a history of SARS­ CoV­2 infection. The method of narrative review was used in this paper. PubMed (May 31, 2021) search was performed to retrieve articles concerning the occurrence of long COVID-19 chronic fatigue, dyspnoea and chronic cough. Studies in which the observation period was <30 days and the average age of subjects exceeded 60 years, as well as studies with no information on the methodology used, in particular without the method of recruiting people for the study, were excluded. Populations with a high frequency of diabetes were defined as the prevalence >10%, and in the case of arterial hypertension >40%. The average frequency of diabetes <10%, hypertension 40%. It can be concluded that in the period of >30 days after discharge from the hospital, in populations with a high incidence of diabetes and hypertension, the incidence of chronic fatigue and cough was higher than in the other analyzed groups. Symptoms of dyspnea were most frequently reported in populations with high rates of diabetes, but at the same time in the average percentage of people with arterial hypertension. Persistent symptoms specific to "Long-COVID" can significantly reduce the ability to perform work. In this situation, check-ups performed before returning to work after long-term leave tape on a new dimension. Med Pr. 2021;72(6):711-20.


Subject(s)
COVID-19 , COVID-19/complications , Cough/epidemiology , Cough/etiology , Dyspnea/epidemiology , Epidemiologic Studies , Humans , Middle Aged , SARS-CoV-2
17.
BMJ Open ; 11(11): e053595, 2021 11 26.
Article in English | MEDLINE | ID: covidwho-1537955

ABSTRACT

BACKGROUND: The first case of SARS-CoV-2 was reported in Argentina on 3 March 2020. Measures to limit the spread of the virus were implemented, including complete lockdown (26 March). Nonetheless, the virus spread throughout the country, with a first peak of almost a million cases in October. On 30 November, the government's recommendation switched from social, preventive and compulsory isolation, to social, preventive and compulsory distancing. OBJECTIVES: To describe a tailored public health strategy to mitigate the spread of SARS-CoV-2 and determine its behaviour in San Antonio de Areco district from Buenos Aires province (Argentina) through a private-public association. DESIGN, SETTING AND PARTICIPANTS: Surveillance of the virus was performed with the local healthcare system, through early identification of cases and the systematic study of each infected individual and contact, regardless of symptomatology, using telemedicine and a COVID-19-specific outpatient clinic. Real-time PCR was used for detection using both individual and pooled samples, with a 12-hour turnaround time. RESULTS: Up to 30 November, a total of 2426 suspected cases were analysed and 578 were confirmed. Surveillance of health personnel and at-risk populations proved effective, mitigating viral spread. Pooling samples allowed reduction of operator time, helped reduce costs, and allowed detection of both symptomatic and asymptomatic cases. CONCLUSION: After 8 months of protocol implementation, the strategy to intensively survey groups at higher epidemiological risk and the systematic search for asymptomatic cases with the incorporation of pooled PCR for diagnosis, in combination with individual testing, is an efficient and viable option in populations with similar characteristics, in the frame of social isolation.


Subject(s)
COVID-19 , SARS-CoV-2 , Argentina/epidemiology , Communicable Disease Control , Delivery of Health Care , Epidemiologic Studies , Humans , Public Health , Watchful Waiting
18.
Microbiol Spectr ; 9(3): e0188221, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1522930

ABSTRACT

Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called variants of concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated health care professionals (HCP). Our postvaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network identified all vaccinated HCPs who tested positive for COVID-19 after routine screening or after self-reporting. From 1 January 2021 to 30 April 2021, 23,687 HCPs received either mRNA-1273 or BNT162b2 mRNA vaccine. All available postvaccination SARS-CoV-2 samples and a random collection from nonvaccinated patients during the similar time frame were subjected to VOC screening and whole-genome sequencing (WGS). Sixty-two percent (23,697/37,500) of HCPs received at least one vaccine dose, with 60% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; percentage of concurrent nonvaccinated samples was 37% (523/1,404) and 20% (284/1,394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and nonvaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any receptor-binding domain (RBD)/N-terminal domain (NTD) polymorphism between groups (P > 0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent VOCs among nonvaccinated populations. IMPORTANCE A number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants with high transmission potential and immune evasion properties, the so-called variants of concern (VOC), continue to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from partial/fully vaccinated health care professionals and probe specifically for VOC enrichment. Our findings support the high level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the nonvaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered postvaccination appears to proportionally represent the observed viral diversity within the community.


Subject(s)
COVID-19 Vaccines , COVID-19/epidemiology , Epidemiologic Studies , Genomics , Health Personnel , Molecular Epidemiology , SARS-CoV-2/genetics , Vaccination , Adult , Aged , COVID-19/virology , Female , Genotype , Humans , Male , Middle Aged , Mutation , New Jersey , Pandemics , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus , Whole Genome Sequencing , Young Adult
19.
J Infect ; 84(1): 56-63, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1510025

ABSTRACT

BACKGROUND: Real-time surveillance of search behavior on the internet has achieved accessibility in measuring disease activity. In this study, we systematically assessed the associations between internet search trends of gastrointestinal (GI) symptom terms and daily newly confirmed COVID-19 cases at both global and regional levels. METHODS: Relative search volumes (RSVs) of GI symptom terms were derived from internet search engines. Time-series analyses with autoregressive integrated moving average models were conducted to fit and forecast the RSV trends of each GI symptom term before and after the COVID-19 outbreak. Generalized additive models were used to quantify the effects of RSVs of GI symptom terms on the incidence of COVID-19. In addition, dose-response analyses were applied to estimate the shape of the associations. RESULTS: The RSVs of GI symptom terms could be characterized by seasonal variation and a high correlation with symptoms of "fever" and "cough" at both global and regional levels; in particular, "diarrhea" and "loss of taste" were abnormally increased during the outbreak period of COVID-19, with elevated point changes of 1.31 and 8 times, respectively. In addition, these symptom terms could effectively predict a COVID-19 outbreak in advance, underlying the lag correlation at 12 and 5 days, respectively, and with mutual independence. The dose-response curves showed a consistent increase in daily COVID-19 risk with increasing search volumes of "diarrhea" and "loss of taste". CONCLUSION: This is the first and largest epidemiologic study that comprehensively revealed the advanced prediction of COVID-19 outbreaks at both global and regional levels via GI symptom indicators.


Subject(s)
COVID-19 , Disease Outbreaks , Epidemiologic Studies , Humans , Internet , SARS-CoV-2
20.
Syst Rev ; 10(1): 289, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1496222

ABSTRACT

BACKGROUND: The coronavirus disease 19 (covid-19) pandemic has underscored the need to expedite clinical research, which may lead investigators to shift away from measuring patient-important outcomes (PIO), limiting research applicability. We aim to investigate if randomized controlled trials (RCTs) of covid-19 pharmacological therapies include PIOs. METHODS: We will perform a meta-epidemiological study of RCTs that included people at risk for, or with suspected, probable, or confirmed covid-19, examining any pharmacological treatment or blood product aimed at prophylaxis or treatment. We will obtain data from all RCTs identified in a living network metanalysis (NMA). The main data sources are the living WHO covid-19 database up to 1 March 2021 and six additional Chinese databases up to 20 February 2021. Two reviewers independently will review each citation, full-text article, and abstract data. To categorize the outcomes according to their importance to patients, we will adapt a previously defined hierarchy: a) mortality, b) quality of life/ functional status/symptoms, c) morbidity, and d) surrogate outcomes. Outcomes within the category a) and b) will be considered critically important to patients, and outcomes within the category c) will be regarded as important. We will use descriptive statistics to assess the proportion of studies that report each category of outcomes. We will perform univariable and multivariable analysis to explore associations between trial characteristics and the likelihood of reporting PIOs. DISCUSSION: The findings from this meta-epidemiological study will help health care professionals and researchers understand if the current covid-19 trials are effectively assessing and reporting the outcomes that are important to patients. If a deficiency in capturing PIOs is identified, this information may help inform the development of future RCTs in covid-19. SYSTEMATIC REVIEW REGISTRATIONS: Open Science Framework registration: osf.io/6xgjz .


Subject(s)
COVID-19 , Epidemiologic Studies , Humans , Patient Reported Outcome Measures , Randomized Controlled Trials as Topic , SARS-CoV-2 , Systematic Reviews as Topic
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