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1.
BMJ Open ; 12(4): e049383, 2022 Apr 08.
Article in English | MEDLINE | ID: covidwho-1784811

ABSTRACT

OBJECTIVES: Air temperature has been considered a modifiable and contributable variable in COVID-19 transmission. Implementation of non-pharmaceutical interventions (NPIs) has also made an impact on COVID-19 transmission, changing the transmission pattern to intrahousehold transmission under stringent containment measures. Therefore, it is necessary to re-estimate the influence of air temperature on COVID-19 transmission while excluding the influence of NPIs. DESIGN, SETTING AND PARTICIPANTS: This study is a data-based comprehensive modelling analysis. A stochastic epidemiological model, the ScEIQR model (contactable susceptible-exposed-infected-quarantined-removed), was established to evaluate the influence of air temperature and containment measures on the intrahousehold spread of COVID-19. Epidemic data on COVID-19, including daily confirmed cases, number of close contacts, etc, were collected from the National Health Commission of China. OUTCOME MEASURES: The model was fitted using the Metropolis-Hastings algorithm with a cost function based on the least squares method. The LOESS (locally weighted scatterplot smoothing) regression function was used to assess the relationship between air temperature and rate of COVID-19 transmission within the ScEIQR model. RESULTS: The ScEIQR model indicated that the optimal temperature for spread of COVID-19 peaked at 10℃ (50℉), ranging from 5℃ to 14℃ (41℉-57.2℉). In the fitted model, the fitted intrahousehold transmission rate (ß') of COVID-19 was 10.22 (IQR 8.47-12.35) across mainland China. The association between air temperature and ß' of COVID-19 suggests that COVID-19 might be seasonal. Our model also validated the effectiveness of NPIs, demonstrating that diminishing contactable susceptibility (Sc) and avoiding delay in diagnosis and hospitalisation (η) were more effective than contact tracing (κ and ρ). CONCLUSIONS: We constructed a novel epidemic model to estimate the effect of air temperature on COVID-19 transmission beyond implementation of NPIs, which can inform public health strategy and predict the transmission of COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/prevention & control , Contact Tracing/methods , Humans , Quarantine , Temperature
4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324965

ABSTRACT

The world-wide lockdown in response to the COVID-19 pandemic in year 2020 led to economic slowdown and large reduction of fossil fuel CO2 emissions, but it is unclear how much it would reduce atmospheric CO2 concentration, and whether it can be observed. We estimated that a 7.9% reduction in emissions for 4 months would result in a 0.25 ppm decrease in the Northern Hemisphere CO2, an increment that is within the capability of current CO2 analyzers, but is a few times smaller than natural CO2 variabilities caused by weather and the biosphere such as El Nino. We used a state-of-the-art atmospheric transport model to simulate CO2, driven by a new daily fossil fuel emissions dataset and hourly biospheric fluxes from a carbon cycle model forced with observed climate variability. Our results show a 0.13 ppm decrease in atmospheric column CO2 anomaly averaged over 50S-50N for the period February-April 2020 relative to a 10-year climatology. A similar decrease was observed by the carbon satellite GOSAT3. Using model sensitivity experiments, we further found that COVID, the biosphere and weather contributed 54%, 23%, and 23% respectively. This seemingly small change stands out as the largest sub-annual anomaly in the last 10 years. Measurements from global ground stations were analyzed. At city scale, on-road CO2 enhancement measured in Beijing shows reduction of 20-30 ppm, consistent with drastically reduced traffic during the lockdown. The ability of our current carbon monitoring systems in detecting the small and short-lasting COVID signal on the background of fossil fuel CO2 accumulated over the last two centuries is encouraging. The COVID-19 pandemic is an unintended experiment whose impact suggests that to keep atmospheric CO2 at a climate-safe level will require sustained effort of similar magnitude and improved accuracy and expanded spatiotemporal coverage of our monitoring systems.

5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-324133

ABSTRACT

Prolonged school closure has been adopted worldwide to control COVID-19. Such preemptive implementation was predicated on the premise that school children are a core group for COVID-19 transmission. Using surveillance data from the Chinese cities of Shenzhen and Anqing, we inferred that children aged 18 or below are only around half as susceptible to COVID-19 infection as adults. Using transmission models parameterized with synthetic contact matrices for 152 jurisdictions around the world, we showed that the lower susceptibility of school children substantially limited the effectiveness of school closure in reducing COVID-19 transmissibility. Our results, together with recent findings that clinical severity of COVID-19 in children is lower, suggest that school closure may not be ideal as a sustained, primary intervention for controlling COVID-19.

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323932

ABSTRACT

Background: Patients with severe Coronavirus Disease 2019 (COVID-19) will progress rapidly to acute respiratory failure or death. We aimed to develop a quantitative tool for early predicting mortality risk of patients with COVID-19. Methods: : 301 patients with confirmed COVID-19 admitted to Main District and Tumor Center of the Union Hospital of Huazhong University of Science and Technology (Wuhan, China) between January 1, 2020 to February 15, 2020 were enrolled in this retrospective two-centers study. Data on patient demographic characteristics, laboratory findings and clinical outcomes was analyzed. A nomogram was constructed to predict the death probability of COVID-19 patients. Results: : Age, neutrophil-to-lymphocyte ratio, D-dimer and C-reactive protein obtained on admission were identified by LASSO regression as predictors of mortality for COVID-19 patients. The nomogram demonstrated good calibration and discrimination with the area under the curve (AUC) of 0.921 and 0.975 for the derivation and validation cohort, respectively. An integrated score (named ANDC) with its corresponding death probability was derived. Using ANDC cut-off values of 59 and 101, COVID-19 patients were classified into three subgroups. The death probability of low risk group (ANDC < 59) was less than 5%, moderate risk group (59 ≤ ANDC ≤ 101) was 5% to 50%, and high risk group (ANDC > 101) was more than 50%, respectively. Conclusion: The prognostic nomogram exhibited good discrimination power in early identification of COVID-19 patients with high mortality risk, and ANDC score may help physicians to optimize patient stratification management.

7.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315578

ABSTRACT

Background: Until 24:00 of April 26th 2020, 2,918,268 laboratory-confirmed cases of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection have been reported worldwide, including 203,528 deaths. Bacterial infection is the main cause of sepsis, however, sepsis caused by virus is often ignored. Increased awareness, early recognition of viral sepsis, rapid administration of appropriate antiviral drugs, and urgent treatment can significantly reduce deaths of viral sepsis. Objectives: Given the rapid global spread of novel Corona Virus Disease (COVID-19), coupled with the high rate of missed diagnosis of viral sepsis caused by SARS-CoV-2 infection, it is urgent to evaluate the multiple organ failure score and viral sepsis in COVID-19 patients, so as to determine the clinical characteristics of viral sepsis more accurately and reveal the risk factors related to mortality. Methods: Here we provide a full description of three cases of viral sepsis and subsequent multiple organ dysfunction (MODS) caused by SARS-CoV-2 infection imported to Guiyang from Wuhan. Results: Complete laboratory examination, imaging data and treatment methods for the patients are analyzed. Sepsis-related Organ Failure Assessment score (SOFA score) and Multiple organ dysfunction scores (MOD score) were daily assessed, aim to elucidate the clinical feature of viral sepsis and MODS and to attract enough attention by clinicians. Conclusions: Therefore, we strongly suggest to daily evaluate SOFA score and MOD score in severe and critically-ill COVID-19 patients, so as to early diagnose and prevention of sepsis and MODS.

8.
Viruses ; 14(1)2022 01 04.
Article in English | MEDLINE | ID: covidwho-1614003

ABSTRACT

The coronavirus disease 2019 (COVID-19) has spread globally and variants continue to emerge, with children are accounting for a growing share of COVID-19 cases. However, the establishment of immune memory and the long-term health consequences in asymptomatic or mildly symptomatic children after severe acute respiratory syndrome coronavirus 2 infection are not fully understood. We collected clinical data and whole blood samples from discharged children for 6-8 months after symptom onset among 0-to-14-year-old children. Representative inflammation signs returned to normal in all age ranges. The infants and young children (0-4 years old) had lung lesions that persisted for 6-8 months and were less responsive for antigen-specific IgG secretion. In the 5-to-14-year-old group, lung imaging abnormalities gradually recovered, and the IgG-specific antibody response was strongest. In addition, we found a robust IgM+ memory B cell response in all age. Memory T cells specific for the spike or nucleocapsid protein were generated, with no significant difference in IFN-γ response among all ages. Our study highlights that although lung lesions caused by COVID-19 can last for at least 6-8 months in infants and young children, most children have detectable residual neutralizing antibodies and specific cellular immune responses at this stage.


Subject(s)
COVID-19/immunology , Convalescence , Adolescent , Antibodies, Neutralizing/blood , Antibodies, Neutralizing/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/pathology , Child , Child, Preschool , Coronavirus Nucleocapsid Proteins/immunology , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Infant , Infant, Newborn , Lung/pathology , Male , /immunology , Phosphoproteins/immunology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/immunology
9.
Front Microbiol ; 12: 768740, 2021.
Article in English | MEDLINE | ID: covidwho-1572296

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most important emerging pathogen worldwide, but its early transcriptional dynamics and host immune response remain unclear. Herein, the expression profiles of viral interactions with different types of hosts were comprehensively dissected to shed light on the early infection strategy of SARS-CoV-2 and the host immune response against infection. SARS-CoV-2 was found to exhibit a two-stage transcriptional strategy within the first 24 h of infection, comprising a lag phase that ends with the virus being paused and a log phase that starts when the viral load increases rapidly. Interestingly, the host innate immune response was found not to be activated (latent period) until the virus entered the log stage. Noteworthy, when intracellular immunity is suppressed, SARS-CoV-2 shows a correlation with dysregulation of metal ion homeostasis. Herein, the inhibitory activity of copper ions against SARS-CoV-2 was further validated in in vitro experiments. Coronavirus disease 2019-related genes (including CD38, PTX3, and TCN1) were also identified, which may serve as candidate host-restricted factors for interventional therapy. Collectively, these results confirm that the two-stage strategy of SARS-CoV-2 effectively aids its survival in early infection by regulating the host intracellular immunity, highlighting the key role of interferon in viral infection and potential therapeutic candidates for further investigations on antiviral strategies.

11.
Philos Trans A Math Phys Eng Sci ; 380(2214): 20210124, 2022 Jan 10.
Article in English | MEDLINE | ID: covidwho-1528261

ABSTRACT

Prolonged school closure has been adopted worldwide to control COVID-19. Indeed, UN Educational, Scientific and Cultural Organization figures show that two-thirds of an academic year was lost on average worldwide due to COVID-19 school closures. Such pre-emptive implementation was predicated on the premise that school children are a core group for COVID-19 transmission. Using surveillance data from the Chinese cities of Shenzhen and Anqing together, we inferred that compared with the elderly aged 60 and over, children aged 18 and under and adults aged 19-59 were 75% and 32% less susceptible to infection, respectively. Using transmission models parametrized with synthetic contact matrices for 177 jurisdictions around the world, we showed that the lower susceptibility of school children substantially limited the effectiveness of school closure in reducing COVID-19 transmissibility. Our results, together with recent findings that clinical severity of COVID-19 in children is lower, suggest that school closure may not be ideal as a sustained, primary intervention for controlling COVID-19. This article is part of the theme issue 'Data science approach to infectious disease surveillance'.


Subject(s)
COVID-19 , Aged , Child , Humans , Middle Aged , SARS-CoV-2 , Schools
12.
Nutr Metab Cardiovasc Dis ; 32(4): 1001-1009, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1521443

ABSTRACT

BACKGROUND AND AIMS: Observational studies showed that coronavirus disease (2019) (COVID-19) attacks universally and its most menacing progression uniquely endangers the elderly with cardiovascular disease (CVD). The causal association between COVID-19 infection or its severity and susceptibility of atrial fibrillation (AF) remains unknown. METHODS AND RESULTS: The bidirectional causal relationship between COVID-19 (including COVID-19, hospitalized COVID-19 compared with not hospitalized COVID-19, hospitalized COVID-19 compared with the general population, and severe COVID-19) and AF are determined by using two-sample Mendelian randomization (MR) analysis. Genetically predicted severe COVID-19 was not significantly associated with the risk of AF [odds ratio (OR), 1.037; 95% confidence interval (CI), 1.005-1.071; P = 0.023, q = 0.115]. In addition, genetically predicted AF was also not causally associated with severe COVID-19 (OR, 0.993; 95% CI, 0.888-1.111; P = 0.905, q = 0.905). There was no evidence to support the association between genetically determined COVID-19 and the risk of AF (OR, 1.111; 95% CI, 0.971-1.272; P = 0.127, q = 0.318), and vice versa (OR, 1.016; 95% CI, 0.976-1.058; P = 0.430, q = 0.851). Besides, no significant association was observed for hospitalized COVID-19 with AF. MR-Egger analysis indicated no evidence of directional pleiotropy. CONCLUSION: Overall, this MR study provides no clear evidence that COVID-19 is causally associated with the risk of AF.


Subject(s)
Atrial Fibrillation , COVID-19 , Aged , Atrial Fibrillation/diagnosis , Atrial Fibrillation/epidemiology , Atrial Fibrillation/genetics , COVID-19/epidemiology , COVID-19/genetics , Genome-Wide Association Study , Humans , Mendelian Randomization Analysis , Polymorphism, Single Nucleotide
14.
Free Radic Biol Med ; 175: 216-225, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1377715

ABSTRACT

Nitric oxide (NO) plays an important role in cardiovascular and immune systems. Quantification of blood nitrite and nitrate, two relatively stable metabolites of NO (generally as NOx), has been acknowledged, in part, representing NO bioactivity. Dysregulation of NOx had been reported in SARS-CoV-2 infected populations, but whether patients recovered from COVID-19 disease present with restored NOx is unknown. In this study, serum NO2- and NO3- were quantified and analyzed among 109 recovered adults in comparison to a control group of 166 uninfected adults. Nitrite or nitrate levels were not significantly different among mild-, common-, severe- and critical-type patients. However, these recovered patients had dramatically lower NO2- and NO2-/NO3- than the uninfected group (p < 0.0001), with significantly higher NO3- levels (p = 0.0023) than the uninfected group. Nitrate and nitrite/nitrate were positively and negatively correlated with patient age, respectively, with age 65 being a turning point among recovered patients. These results indicate that low NO2-, low NO2-/NO3- and high NO3- may be potential biomarkers of long-term poor or irreversible outcomes after SARS-CoV-2 infection. It suggests that NO metabolites might serve as a predictor to track the health status of recovered COVID-19 patients, highlighting the need to elucidate the role of NO after SARS-CoV-2 infection.


Subject(s)
COVID-19 , Nitrites , Adult , Aged , Biomarkers , Humans , Nitrates , Nitric Oxide , SARS-CoV-2
15.
mBio ; 12(4): e0106721, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1297962

ABSTRACT

The coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an ongoing global public crisis. Although viral RNA modification has been reported based on the transcriptome architecture, the types and functions of RNA modification are still unknown. In this study, we evaluated the roles of RNA N6-methyladenosine (m6A) modification in SARS-CoV-2. Our methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and Nanopore direct RNA sequencing (DRS) analysis showed that SARS-CoV-2 RNA contained m6A modification. Moreover, SARS-CoV-2 infection not only increased the expression of methyltransferase-like 3 (METTL3) but also altered its distribution. Modification of METTL3 expression by short hairpin RNA or plasmid transfection for knockdown or overexpression, respectively, affected viral replication. Furthermore, the viral key protein RdRp interacted with METTL3, and METTL3 was distributed in both the nucleus and cytoplasm in the presence of RdRp. RdRp appeared to modulate the sumoylation and ubiquitination of METTL3 via an unknown mechanism. Taken together, our findings demonstrated that the host m6A modification complex interacted with viral proteins to modulate SARS-CoV-2 replication. IMPORTANCE Internal chemical modifications of viral RNA play key roles in the regulation of viral replication and gene expression. Although potential internal modifications have been reported in SARS-CoV-2 RNA, the function of the SARS-CoV-2 N6-methyladenosine (m6A) modification in the viral life cycle is unclear. In the current study, we demonstrated that SARS-CoV-2 RNA underwent m6A modification by host m6A machinery. SARS-CoV-2 infection altered the expression pattern of methyltransferases and demethylases, while the expression level of methyltransferase-like 3 (METTL3) and fat mass and obesity-associated protein (FTO) was linked to the viral replication. Further study showed that METTL3 interacted with viral RNA polymerase RNA-dependent RNA polymerase (RdRp), which influenced not only the distribution but also the posttranslational modification of METTL3. Our study provided evidence that host m6A components interacted with viral proteins to modulate viral replication.


Subject(s)
Adenosine/analogs & derivatives , Methyltransferases/genetics , Methyltransferases/metabolism , SARS-CoV-2/growth & development , Virus Replication/genetics , Adenosine/chemistry , Adenosine/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism , COVID-19/pathology , Gene Expression Regulation/genetics , Humans , Methylation , Protein Processing, Post-Translational/physiology , RNA, Viral/chemistry , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , SARS-CoV-2/genetics
16.
Antibiotics (Basel) ; 10(5)2021 May 06.
Article in English | MEDLINE | ID: covidwho-1241234

ABSTRACT

The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China's efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.

17.
J Clin Transl Hepatol ; 9(2): 269-273, 2021 Apr 28.
Article in English | MEDLINE | ID: covidwho-1234939

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic continues worldwide. We report here two cases of chronic hepatitis B patients with acute respiratory syndrome coronavirus 2 infection treated with tenofovir disoproxil fumarate who demonstrated a favorable outcome. This report adds some evidence that concurrent HBV infection may not worsen COVID-19 infection and tenofovir disoproxil fumarate treatment may have partial positive effect on COVID-19 rapid recovery.

18.
Front Med ; 15(4): 507-527, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1188167

ABSTRACT

The avian influenza A (H7N9) virus is a zoonotic virus that is closely associated with live poultry markets. It has caused infections in humans in China since 2013. Five waves of the H7N9 influenza epidemic occurred in China between March 2013 and September 2017. H7N9 with low-pathogenicity dominated in the first four waves, whereas highly pathogenic H7N9 influenza emerged in poultry and spread to humans during the fifth wave, causing wide concern. Specialists and officials from China and other countries responded quickly, controlled the epidemic well thus far, and characterized the virus by using new technologies and surveillance tools that were made possible by their preparedness efforts. Here, we review the characteristics of the H7N9 viruses that were identified while controlling the spread of the disease. It was summarized and discussed from the perspectives of molecular epidemiology, clinical features, virulence and pathogenesis, receptor binding, T-cell responses, monoclonal antibody development, vaccine development, and disease burden. These data provide tools for minimizing the future threat of H7N9 and other emerging and re-emerging viruses, such as SARS-CoV-2.


Subject(s)
COVID-19 , Influenza A Virus, H7N9 Subtype , Influenza in Birds , Influenza, Human , Animals , China/epidemiology , Humans , Influenza in Birds/epidemiology , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Poultry , SARS-CoV-2
19.
Virol Sin ; 36(5): 901-912, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1182321

ABSTRACT

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background. To address this issue, we modified and evaluated an approach by utilizing SARS-CoV-2-specific amplicon amplification and Oxford Nanopore PromethION platform. This workflow started with the throat swab of the COVID-19 patient, combined reverse transcript PCR, and multi-amplification in one-step to shorten the experiment time, then can quickly and steadily obtain high-quality SARS-CoV-2 genome within 24 h. A comprehensive evaluation of the method was conducted in 42 samples: the sequencing quality of the method was correlated well with the viral load of the samples; high-quality SARS-CoV-2 genome could be obtained stably in the samples with Ct value up to 39.14; data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20; variation analysis indicated that the method can detect the existing and emerging genomic mutations as well; Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing, making it as low as 0.4/10,000 bp. In summary, high-quality SARS-CoV-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARS-CoV-2.


Subject(s)
COVID-19 , Nanopore Sequencing , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Pandemics , RNA, Viral/genetics , SARS-CoV-2
20.
Cell Discov ; 7(1): 19, 2021 Mar 30.
Article in English | MEDLINE | ID: covidwho-1160081

ABSTRACT

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, poses a severe threat to humanity. Rapid and comprehensive analysis of both pathogen and host sequencing data is critical to track infection and inform therapies. In this study, we performed unbiased metatranscriptomic analysis of clinical samples from COVID-19 patients using a recently developed RNA-seq library construction method (TRACE-seq), which utilizes tagmentation activity of Tn5 on RNA/DNA hybrids. This approach avoids the laborious and time-consuming steps in traditional RNA-seq procedure, and hence is fast, sensitive, and convenient. We demonstrated that TRACE-seq allowed integrated characterization of full genome information of SARS-CoV-2, putative pathogens causing coinfection, antibiotic resistance, and host response from single throat swabs. We believe that the integrated information will deepen our understanding of pathogenesis and improve diagnostic accuracy for infectious diseases.

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