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1.
Psychol Health Med ; : 1-6, 2021 May 11.
Article in English | MEDLINE | ID: covidwho-1223229

ABSTRACT

This study aimed to explore which age group out of the patients in quarantine wards with novel coronavirus pneumonia is the most susceptible to anxiety. The data of 32 Covid-19 patients isolated in the quarantine wards of the second Infectious Diseases Department of Baoding Hospital and 71 Covid-19 patients in Tangshan City Infectious Disease Hospital from January 24th to March 5th, 2020, a total of 103 patients, were analyzed. Among these patients, 97 isolated patients were scored with a self-rating anxiety scale (SAS) score seven days after quarantine, and the correlation between age and score was analyzed. These 97 isolated patients were then divided into three groups according to age: group A (up to 35 years old), group B (36-60 years), and group C (over 60 years). One-way analysis of variance was used to compare the scores among groups. The Q-test was used for pairwise comparison.P < 0.05 was considered statistically significant.There was a negative correlation between age and SAS score in isolated Covid-19 patients, and the differences in the score among groups were statistically significant. Patients under 35 years old were more prone to anxiety when they were isolated for seven days. Isolated patients aged up to 35 years old need more attention from quarantine medical staff, communication should be strengthened, and psychological intervention from psychotherapists should be given if necessary.

2.
China CDC Weekly ; : 1-3, 2021.
Article | WHO COVID | ID: covidwho-1220220

ABSTRACT

On April 15, 2021, a 62-year-old male (Patient A, XG4122) and a 58-year-old female (Patient B, XG4123) traveled from Canada via airplane and were transferred to a central isolation hotel after being tested by the laboratory of Guangzhou Customs using nose swab tests for coronavirus disease 2019 (COVID-19) The results for both patients returned COVID-19 positive and the couple were transported to the Guangzhou Eighth People’s Hospital for isolated treatment by ambulance on April 16, 2021 Patient A had inflamed lungs while Patient B had mild inflammation in her lungs according to the chest computed tomography (CT) examination Both of their 28 close contacts underwent centralized isolation and medical observation On April 21, 2021, Guangdong Provincial CDC received the samples and began virus isolation and gene sequencing analysis On April 27, 2021, the 2 samples were sequenced using Nanopore GridION On April 30, 2021, the sequencing analysis concluded that the 2 virus genomes belonged to lineage P 1, 20J/501Y V3, which was first found in four Brazilians after a routine check at Japan’s Haneda airport in late December 2020 The variant was then widely spread to Manaus in the northern State of Amazona in Brazil The Brazil variant has been reported in 40 different countries as of April 30, 2021(1) Compared with the Wuhan reference sequence (EPI_ISL_ 402119) (2-3), the strain from Patient A (XG4122) displayed 33 nucleotide variation sites (C241T, T733C, C2749T, C3037T, C3828T, A5648C, A6319G, A6613G, G9105A, C12778T, C14408T, G17259T, C21614T, C21621A, C21638T, G21974T, G22132T, A22812C, G23012A, A23063T, C23380T, A23403G, C23525T, C24642T, G25088T, T26149C, G28167A, C28512G, A28877T, G28878C, G28881A, G28882A, and G28883C) belonged to the Pangolin lineage P 1 (Figure 1) Patient B (XG4123) strain displayed 34 nucleotide variation sites (C241T, T733C, C2749T, C3037T, C3828T, A5648C, A6319G, A6613G, G9105A, C12778T, C13860T, C14408T, G17259T, C21614T, C21621A, C21638T, G21974T, G22132T, A22812C, G23012A, A23063T, C23380T, A23403G, C23525T, C24642T, G25088T, T26149C, G28167A, C28512G, A28877T, G28878C, G28881A, G28882A, and G28883C) Furthermore, 23 amino acid mutation sites (N:P80R, N:R203K, N:G204R, ORF1a:S1188L, ORF1a:K1795Q, ORF1a:S2947N, ORF1b:P314L, ORF1b:E1264D, ORF3a:S253P, ORF8:E92K, ORF9b:Q77E, S:L18F, S:T20N, S:P26S, S:D138Y, S:R190S, S:K417T, S:E484K, S:N501Y, S:D614G, S:H655Y, S:T1027I, and S:V1176F) and 3 amino acid deletions (ORF1a:S3675-, ORF1a:G3676-, and ORF1a:F3677-) were detected in the protein that corresponded to the features of the Brazil variant (P 1) (4) Both variants have 12 mutations to the spike protein, including 3 mutations of concern in common with 20H/501Y V2 (K417N/T, E484K, and N501Y) which may affect transmissibility and host immune response (4-5) The P 1 lineage and the B 1 1 7 first described in the United Kingdom share the spike N501Y mutation and a deletion in ORF1b (del 3675-3677 SGF) The P 1 lineage and the B 1 351 (also known as 501Y V2) lineage described in South Africa share 3 mutation positions in common in the spike protein (K417N/T, E484K, and N501Y) Both the P 1 and the B 1 351 lineage also have the ORF1b deletion (del 3675-3677 SGF) (6) This is the fourth recent detection of a major international variant following the detection of the United Kingdom 501Y V1 variant, the South African 501Y V2 variant, and the Nigerian B 1 525 variant in Guangdong (7-9) The transmissibility and pathogenicity of these mutant variants urgently needs further study

3.
Archives of Medical Science ; 17(3):829-837, 2021.
Article | WHO COVID | ID: covidwho-1217138

ABSTRACT

Introduction: Information has the power to protect against unexpected events and control any crisis such as the COVID-19 pandemic Since COVID-19 has already rapidly spread all over the world, only technology-driven data management can provide accurate information to manage the crisis This study aims to explore the potential of big data technologies for controlling COVID-19 transmission and managing it effectively Methods: A systematic review guided by PRISMA guidelines has been performed to obtain the key elements Results: This study identified the thirty-two most relevant documents for qualitative analysis This study also reveals 10 possible sources and 8 key applications of big data for analyzing the virus infection trend, transmission pattern, virus association, and differences of genetic modifications It also explores several limitations of big data usage including unethical use, privacy, and exploitative use of data Conclusions: The findings of the study will provide new insight and help policymakers and administrators to develop data-driven initiatives to tackle and manage the COVID-19 crisis [ABSTRACT FROM AUTHOR] Copyright of Archives of Medical Science is the property of Termedia Publishing House and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission However, users may print, download, or email articles for individual use This abstract may be abridged No warranty is given about the accuracy of the copy Users should refer to the original published version of the material for the full abstract (Copyright applies to all Abstracts )

4.
Stress and Health: Journal of the International Society for the Investigation of Stress ; : No Pagination Specified, 2021.
Article | WHO COVID | ID: covidwho-1210228

ABSTRACT

This study aimed to explore influencing factors for the psychological impact of coronavirus disease 2019 (COVID-19) on Wuhan college teachers, posttraumatic stress symptoms in particular, so as to inform evidence-based strategy development to ameliorate such adverse impacts An online survey was conducted from 26 to 29 April 2020, and 1650 teachers (47 54% male;M = 40 28 years, SD = 8 3 years) enrolled in Wuhan universities and colleges participated The results showed that the overall incidence of posttraumatic stress disorder (PTSD) among college teachers was as high as 24 55%, but the average level of PTSD score was low (M = 1 06, SD = 0 72) Logistic regression analysis showed that for those with confirmed COVID-19, the ratio was much higher, up to 2 814 (95% confidence interval [CI]: [1 542, 5 136], p < 0 001);that is, compared with those without symptoms, the ratio of PTSD increased by 181% For those who had family members or relatives who died of COVID-19, the ratio was 5 592 (95% CI: [2 271, 13 766], p < 0 001), 459% higher than those who had no one who died But the living places during the pandemic had no significant effect on PTSD The findings suggest that mental health services reducing PTSD should be provided Teachers who confirmed COVID-19 or lost loved ones to COVID-19 should be given particular care (PsycInfo Database Record (c) 2021 APA, all rights reserved)

5.
eNeurologicalSci ; : 100336, 2021 Mar 20.
Article in English | MEDLINE | ID: covidwho-1188538

ABSTRACT

[This corrects the article DOI: 10.1016/j.ensci.2020.100275.].

6.
Sci Rep ; 11(1): 7477, 2021 04 05.
Article in English | MEDLINE | ID: covidwho-1169408

ABSTRACT

We aim to describe a case series of critically and non-critically ill COVID-19 patients in Singapore. This was a multicentered prospective study with clinical and laboratory details. Details for fifty uncomplicated COVID-19 patients and ten who required mechanical ventilation were collected. We compared clinical features between the groups, assessed predictors of intubation, and described ventilatory management in ICU patients. Ventilated patients were significantly older, reported more dyspnea, had elevated C-reactive protein and lactate dehydrogenase. A multivariable logistic regression model identified respiratory rate (aOR 2.83, 95% CI 1.24-6.47) and neutrophil count (aOR 2.39, 95% CI 1.34-4.26) on admission as independent predictors of intubation with area under receiver operating characteristic curve of 0.928 (95% CI 0.828-0.979). Median APACHE II score was 19 (IQR 17-22) and PaO2/FiO2 ratio before intubation was 104 (IQR 89-129). Median peak FiO2 was 0.75 (IQR 0.6-1.0), positive end-expiratory pressure 12 (IQR 10-14) and plateau pressure 22 (IQR 18-26) in the first 24 h of ventilation. Median duration of ventilation was 6.5 days (IQR 5.5-13). There were no fatalities. Most COVID-19 patients in Singapore who required mechanical ventilation because of ARDS were extubated with no mortality.


Subject(s)
/pathology , Adult , Area Under Curve , C-Reactive Protein/metabolism , Dyspnea/etiology , Female , Humans , Intensive Care Units , L-Lactate Dehydrogenase/metabolism , Logistic Models , Male , Middle Aged , Neutrophils/cytology , Prospective Studies , ROC Curve , Respiration, Artificial , Respiratory Rate , Severity of Illness Index , Singapore
7.
Lancet Infect Dis ; 2020 Nov 02.
Article in English | MEDLINE | ID: covidwho-1164676

ABSTRACT

BACKGROUND: The proportion of asymptomatic carriers and transmission risk factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among household and non-household contacts remains unclear. In Singapore, extensive contact tracing by the Ministry of Health for every diagnosed COVID-19 case, and legally enforced quarantine and intensive health surveillance of close contacts provided a rare opportunity to determine asymptomatic attack rates and SARS-CoV-2 transmission risk factors among community close contacts of patients with COVID-19. METHODS: This retrospective cohort study involved all close contacts of confirmed COVID-19 cases in Singapore, identified between Jan 23 and April 3, 2020. Household contacts were defined as individuals who shared a residence with the index COVID-19 case. Non-household close contacts were defined as those who had contact for at least 30 min within 2 m of the index case. All patients with COVID-19 in Singapore received inpatient treatment, with access restricted to health-care staff. All close contacts were quarantined for 14 days with thrice-daily symptom monitoring via telephone. Symptomatic contacts underwent PCR testing for SARS-CoV-2. Secondary clinical attack rates were derived from the prevalence of PCR-confirmed SARS-CoV-2 among close contacts. Consenting contacts underwent serology testing and detailed exposure risk assessment. Bayesian modelling was used to estimate the prevalence of missed diagnoses and asymptomatic SARS-CoV-2-positive cases. Univariable and multivariable logistic regression models were used to determine SARS-CoV-2 transmission risk factors. FINDINGS: Between Jan 23 and April 3, 2020, 7770 close contacts (1863 household contacts, 2319 work contacts, and 3588 social contacts) linked to 1114 PCR-confirmed index cases were identified. Symptom-based PCR testing detected 188 COVID-19 cases, and 7582 close contacts completed quarantine without a positive SARS-CoV-2 PCR test. Among 7518 (96·8%) of the 7770 close contacts with complete data, the secondary clinical attack rate was 5·9% (95% CI 4·9-7·1) for 1779 household contacts, 1·3% (0·9-1·9) for 2231 work contacts, and 1·3% (1·0-1·7) for 3508 social contacts. Bayesian analysis of serology and symptom data obtained from 1150 close contacts (524 household contacts, 207 work contacts, and 419 social contacts) estimated that a symptom-based PCR-testing strategy missed 62% (95% credible interval 55-69) of COVID-19 diagnoses, and 36% (27-45) of individuals with SARS-CoV-2 infection were asymptomatic. Sharing a bedroom (multivariable odds ratio [OR] 5·38 [95% CI 1·82-15·84]; p=0·0023) and being spoken to by an index case for 30 min or longer (7·86 [3·86-16·02]; p<0·0001) were associated with SARS-CoV-2 transmission among household contacts. Among non-household contacts, exposure to more than one case (multivariable OR 3·92 [95% CI 2·07-7·40], p<0·0001), being spoken to by an index case for 30 min or longer (2·67 [1·21-5·88]; p=0·015), and sharing a vehicle with an index case (3·07 [1·55-6·08]; p=0·0013) were associated with SARS-CoV-2 transmission. Among both household and non-household contacts, indirect contact, meal sharing, and lavatory co-usage were not independently associated with SARS-CoV-2 transmission. INTERPRETATION: Targeted community measures should include physical distancing and minimising verbal interactions. Testing of all household contacts, including asymptomatic individuals, is warranted. FUNDING: Ministry of Health of Singapore, National Research Foundation of Singapore, and National Natural Science Foundation of China.

8.
Journal of Intensive Medicine ; 2021.
Article | WHO COVID | ID: covidwho-1157520

ABSTRACT

Background : The outbreak of coronavirus disease 2019 (COVID-19) has posed a huge threat to human health However, little is known regarding the risk factors associated with COVID-19 severity We aimed to explore early-stage disease risk factors associated with eventual disease severity Methods : This study enrolled 486 hospitalized, non-intensive care unit (ICU)-admitted adult patients with COVID-19 (age ≥ 18 years) treated at Wuhan Jinyintan Hospital, who were divided into three groups according to disease severity The demographic, clinical, and laboratory data at admission and clinical outcomes were compared among severity groups, and the risk factors for disease severity were identified by multiple regression analysis Results : Of 486 patients with COVID-19, 405 (83 33%) were discharged, 33 (6 71%) died outside of the ICU, and 48 (7 20%) were still being treated in the ICU by the time the study period ended Significant differences in age, lymphocyte counts, and the levels of procalcitonin, aspartate aminotransferase, and D-dimer (P < 0 001 for all) among the three groups Further analysis showed that older age, decreased lymphocyte counts, and increased procalcitonin, aspartate aminotransferase, and D-dimer levels were significantly associated with disease progression Conclusion : Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may impair the immune system, the blood coagulation system, and hepatic and cardiac function Some clinical characteristics and laboratory findings can help identify patients with a high risk of disease severity, which can be significant for appropriate resource allocation during the COVID-19 pandemic

9.
Clin Infect Dis ; 71(16): 2150-2157, 2020 11 19.
Article in English | MEDLINE | ID: covidwho-1153175

ABSTRACT

BACKGROUND: Thymosin alpha 1 (Tα1) had been used in the treatment of viral infections as an immune response modifier for many years. However, clinical benefits and the mechanism of Tα1 treatment for COVID-19 patients are still unclear. METHODS: We retrospectively reviewed the clinical outcomes of 76 severe COVID-19 cases admitted to 2 hospitals in Wuhan, China, from December 2019 to March 2020. The thymus output in peripheral blood mononuclear cells from COVID-19 patients was measured by T-cell receptor excision circles (TRECs). The levels of T-cell exhaustion markers programmed death-1 (PD-1) and T-cell immunoglobulin and mucin domain protein 3 (Tim-3) on CD8+ T cells were detected by flow cytometry. RESULTS: Compared with the untreated group, Tα1 treatment significantly reduced the mortality of severe COVID-19 patients (11.11% vs 30.00%, P = .044). Tα1 enhanced blood T-cell numbers in COVID-19 patients with severe lymphocytopenia. Under such conditions, Tα1 also successfully restored CD8+ and CD4+ T-cell numbers in elderly patients. Meanwhile, Tα1 reduced PD-1 and Tim-3 expression on CD8+ T cells from severe COVID-19 patients compared with untreated cases. It is of note that restoration of lymphocytopenia and acute exhaustion of T cells were roughly parallel to the rise of TRECs. CONCLUSIONS: Tα1 treatment significantly reduced mortality of severe COVID-19 patients. COVID-19 patients with counts of CD8+ T cells or CD4+ T cells in circulation less than 400/µL or 650/µL, respectively, gained more benefits from Tα1. Tα1 reversed T-cell exhaustion and recovered immune reconstitution through promoting thymus output during severe acute respiratory syndrome-coronavirus 2 infection.

10.
China CDC Weekly ; : 1-3, 2021.
Article | WHO COVID | ID: covidwho-1139040

ABSTRACT

On February 19, 2021, a 48-year-old male (Case A, XG2275) returning from Nigeria and a 38-year-old female (Case B, XG2276) returning from Ukraine via airplane were tested by the laboratory of Guangzhou Customs using nose swabs to test for coronavirus disease 2019 (COVID-19) Both of them tested positive and were transported by ambulance from the isolation point to Guangzhou Eighth People’s Hospital They are still undergoing centralized medical observation in the hospital after recovery On March 5, Guangdong CDC received the samples and began virus isolation and genome sequencing analysis On March 10, the 2 samples were sequenced using Nanopore GridION On March 12, the sequencing analysis concluded that the 2 virus genomes belonged to lineage B 1 525, a new COVID-19 variant first emerging in Nigeria, which was first detected by genome sequencing in mid-December in Nigeria but was also quickly found in cases in the United Kingdom, France, and elsewhere As of March 8, 2021, a total of 577 counted sequences in 30 countries were found in the world (1) Compared with the Wuhan reference sequence (EPI_ISL_402119) (2–3), the strain from Case A (XG2275) displayed 24 nucleotide variation sites (C241T, C1498T, A1807G, G2659A, C3037T, C6285T, T8593C, C9565T, C14407T, C14408T, C18171T, A20724G, A21717G, C21762T, G23012A, A23403G, G23593C, T24224C, C24748T, T26767C, C28308G, A28699G, C28887T, and G29543T) including the single nucleotide polymorphisms (SNPs) that defined the L-lineage European branch and belonged to the Pangolin lineage B 1 525 (Figure 1) Furthermore, 10 amino acid mutation sites (E:L21X, M:I82T, N:A12G, N:T205I, S:Q52R, S:A67V, S:E484K, S:D614G, S:Q677H, and S:F888L) and 3 amino acid deletions (H69del, V70del, and Y144del) were detected in the protein that corresponded to the features of the Nigerian variant (B 1 525) (4) Compared with the Wuhan reference sequence (EPI_ISL_402119) (2–3), the Case B (XG2276) strain displayed 22 nucleotide variation sites (C241T, C1498T, A1807G, C3037T, C6285T, T8593C, C9565T, C14407T, C14408T, C18171T, A20724G, C21762T, G23012A, A23403G, G23593C, T24224C, C24748T, T26767C, C28308G, A28699G, C28887T, and G29543T) including the SNPs that defined the L-lineage European branch and belonged to the Pangolin lineage B 1 525 (Figure 1) Furthermore, 9 amino acid mutation sites (E:L21X, M:I82T, N:A12G, N:T205I, S:A67V, S:E484K, S:D614G, S:Q677H, and S:F888L) and 3 amino acid deletions (H69del, V70del, and Y144del) were detected in the protein that corresponded to the features of the Nigerian variant (B 1 525) The variant first emerging in Nigeria (B 1 525) shares the same 3 amino acid deletions (H69del, V70del, and Y144del) with the 501Y V1 variant (also known as the B 1 1 7) The mutation E484K is also present in the 501Y V2 variant first emerging in South Africa (also known as the B 1 351) and Brazilian strains (501Y V3) The amino acid substitution at position 677 (Q677H) is identical to that found in variants recently described in the United States The amino acid substitutions Q52R and A67V are unique to the B 1 525 (4) This is the third recent detection of a major international variant following the detection of the United Kingdom 501Y V1 variant and the South African 501Y V2 variant The transmissibility and pathogenicity of these mutant variants urgently needs further study (5–6)

11.
Singapore Med J ; 2021 Mar 12.
Article in English | MEDLINE | ID: covidwho-1136645
12.
Int J Environ Res Public Health ; 18(5)2021 03 02.
Article in English | MEDLINE | ID: covidwho-1124943

ABSTRACT

College students represent a large group of people who frequently travel across regions, which increased their risk of infection and exacerbated the risk of COVID-19 spread throughout China. This study uses survey data from the end of April 2020 to analyze the status of COVID-19-infected cases, the group differences, and influencing factors in college students in Wuhan. The sample size was made up 4355 participants, including 70 COVID-19-infected students. We found that during the COVID-19 outbreak in early 2020, college students in Wuhan were primarily infected during off-campus events after winter break or infected in their hometowns after leaving Wuhan; the percentage of college students with severe cases was relatively low, and most had mild cases; however, a large proportion of asymptomatic cases may exist; there were significant group differences in gender, age and place of residence; and the risk of infection was closely related to the campus environment, in which the population density and number of faculty and students on campus had a significant impact. The results indicated that the infection of students did not occur at random, thus strengthening student health education and campus management can help curb the spread of COVID-19 among students.


Subject(s)
China/epidemiology , Humans , Students , Surveys and Questionnaires
13.
Front Med ; 2021 Mar 09.
Article in English | MEDLINE | ID: covidwho-1122810

ABSTRACT

Tocilizumab has been reported to attenuate the "cytokine storm" in COVID-19 patients. We attempted to verify the effectiveness and safety of tocilizumab therapy in COVID-19 and identify patients most likely to benefit from this treatment. We conducted a randomized, controlled, open-label multicenter trial among COVID-19 patients. The patients were randomly assigned in a 1:1 ratio to receive either tocilizumab in addition to standard care or standard care alone. The cure rate, changes of oxygen saturation and interference, and inflammation biomarkers were observed. Thirty-three patients were randomized to the tocilizumab group, and 32 patients to the control group. The cure rate in the tocilizumab group was higher than that in the control group, but the difference was not statistically significant (94.12% vs. 87.10%, rate difference 95% CI-7.19%-21.23%, P = 0.4133). The improvement in hypoxia for the tocilizumab group was higher from day 4 onward and statistically significant from day 12 (P = 0.0359). In moderate disease patients with bilateral pulmonary lesions, the hypoxia ameliorated earlier after tocilizumab treatment, and less patients (1/12, 8.33%) needed an increase of inhaled oxygen concentration compared with the controls (4/6, 66.67%; rate difference 95% CI-99.17% to-17.50%, P = 0.0217). No severe adverse events occurred. More mild temporary adverse events were recorded in tocilizumab recipients (20/34, 58.82%) than the controls (4/31, 12.90%). Tocilizumab can improve hypoxia without unacceptable side effect profile and significant influences on the time virus load becomes negative. For patients with bilateral pulmonary lesions and elevated IL-6 levels, tocilizumab could be recommended to improve outcome.

14.
Virol Sin ; 2021 Mar 04.
Article in English | MEDLINE | ID: covidwho-1117772

ABSTRACT

Understanding the persistence of antibody in convalescent COVID-19 patients may help to answer the current major concerns such as the risk of reinfection, the protection period of vaccination and the possibility of building an active herd immunity. This retrospective cohort study included 172 COVID-19 patients who were hospitalized in Wuhan. A total of 404 serum samples were obtained over six months from hospitalization to convalescence. Antibodies in the specimens were quantitatively analyzed by the capture chemiluminescence immunoassays (CLIA). All patients were positive for the anti-SARS-CoV-2 IgM/IgG at the onset of COVID-19 symptoms, and the IgG antibody persisted in all the patients during the convalescence. However, only approximately 25% of patients can detect the IgM antibodies, IgM against N protein (N-IgM) and receptor binding domain of S protein (RBD-IgM) at the 27th week. The titers of IgM, N-IgM and RBD-IgM reduced to 16.7%, 17.6% and 15.2% of their peak values respectively. In contrast, the titers of IgG, N-IgG and RBD-IgG peaked at 4-5th week and reduced to 85.9%, 62.6% and 87.2% of their peak values respectively at the end of observation. Dynamic behavior of antibodies and their correlation in age, gender and severity groups were investigated. In general, the COVID-19 antibody was sustained at high levels for over six months in most of the convalescent patients. Only a few patients with antibody reducing to an undetectable level which needs further attention. The humoral immune response against SARS-CoV-2 infection in COVID-19 patients exhibits a typical dynamic of acquired immunity.

15.
Genome Med ; 13(1): 30, 2021 02 22.
Article in English | MEDLINE | ID: covidwho-1097198

ABSTRACT

BACKGROUND: Since early February 2021, the causative agent of COVID-19, SARS-CoV-2, has infected over 104 million people with more than 2 million deaths according to official reports. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. METHODS: Using high-throughput sequencing of metatranscriptomic and hybrid captured libraries, we characterized consensus genomes and intra-host single nucleotide variations (iSNVs) of serial samples collected from eight patients with COVID-19. The distribution of iSNVs along the SARS-CoV-2 genome was analyzed and co-occurring iSNVs among COVID-19 patients were identified. We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT). RESULTS: The 32 consensus genomes revealed the co-existence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in a single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparing allele frequencies of the iSNVs revealed a clear genetic differentiation between intra-host populations from the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events during intra-host migrations. Compared to RT populations, the GIT populations showed a better maintenance and rapid development of viral genetic diversity following the suspected intra-host bottlenecks. CONCLUSIONS: Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses and other RNA viruses.


Subject(s)
/prevention & control , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing/methods , Polymorphism, Single Nucleotide , /genetics , /virology , Gene Frequency , Genotype , Haplotypes , Host-Pathogen Interactions , Humans , Phylogeny , /physiology
16.
J Med Internet Res ; 23(3): e22219, 2021 03 02.
Article in English | MEDLINE | ID: covidwho-1088863

ABSTRACT

Coincident with the tsunami of COVID-19-related publications, there has been a surge of studies using real-world data, including those obtained from the electronic health record (EHR). Unfortunately, several of these high-profile publications were retracted because of concerns regarding the soundness and quality of the studies and the EHR data they purported to analyze. These retractions highlight that although a small community of EHR informatics experts can readily identify strengths and flaws in EHR-derived studies, many medical editorial teams and otherwise sophisticated medical readers lack the framework to fully critically appraise these studies. In addition, conventional statistical analyses cannot overcome the need for an understanding of the opportunities and limitations of EHR-derived studies. We distill here from the broader informatics literature six key considerations that are crucial for appraising studies utilizing EHR data: data completeness, data collection and handling (eg, transformation), data type (ie, codified, textual), robustness of methods against EHR variability (within and across institutions, countries, and time), transparency of data and analytic code, and the multidisciplinary approach. These considerations will inform researchers, clinicians, and other stakeholders as to the recommended best practices in reviewing manuscripts, grants, and other outputs from EHR-data derived studies, and thereby promote and foster rigor, quality, and reliability of this rapidly growing field.


Subject(s)
/epidemiology , Data Collection/methods , Electronic Health Records , Data Collection/standards , Humans , Peer Review, Research/standards , Publishing/standards , Reproducibility of Results , /isolation & purification
18.
Int J Environ Res Public Health ; 18(4)2021 02 12.
Article in English | MEDLINE | ID: covidwho-1085092

ABSTRACT

In February 2020, a novel coronavirus (SARS-COV2) broke out in Wuhan city of China. The Chinese government decisively imposed nationwide confinement. This study comprised a structured, online questionnaire, based on 40 items inquiring about socio-demographic information and anthropometric data (reporting weight and height), as well as changes in food intake, physical activity, and sleep during the COVID-19 outbreak. Questionnaires were distributed to residents of Jiangsu and other provinces from 29 March to 5 April. A total of 889 respondents were included, aged between 16 and 70 years (61% females). There was a significant increase in total food intake by 9.8% and a slight increase by 29.2% of respondents, and a significant decrease in physical activity by 31.5% and a slight decrease by 23.4% of respondents, especially in snacks and drinks, and outdoor activities. The rate of weight gain in the total population was 30.6% and the average weight gain was 0.5 ± 2.8 kg. The main factors contributing to weight gain were increased food intake and reduced physical activity. Additionally, normal-weight people were more likely to gain weight than people with overweight/obesity during the COVID-19 confinement. This study provided a good warning and educational reference value on lifestyle changes during the COVID-19 confinement.


Subject(s)
/prevention & control , Life Style , Quarantine , Weight Gain , Adolescent , Adult , Aged , China/epidemiology , Exercise , Feeding Behavior , Female , Humans , Male , Middle Aged , Pandemics , RNA, Viral , Surveys and Questionnaires , Young Adult
19.
IEEE/ACM Trans Comput Biol Bioinform ; PP2021 Feb 09.
Article in English | MEDLINE | ID: covidwho-1075747

ABSTRACT

The 2019-nCoV coronavirus protein was confirmed to be highly susceptible to various mutations, which can trigger apparent changes of virus' transmission capacity and even the pathogenic mechanism. In this article, the binding interface was obtained by analyzing the interaction modes between 2019-nCoV coronavirus and the human specific target protein ACE2. Based on the "SIFT server" and the "bubble" identification mechanism, 9 amino acid sites were selected as potential mutation-sites from the 2019-nCoV-S1-ACE2 binding interface. Subsequently, one total number of 171 mutant systems for 9 mutation-sites were optimized for binding-pattern comparsion analysis, and 14 mutations that may improve the binding capacity of 2019-nCoV-S1 to ACE2 were selected. The Molecular Dynamic Simulations were conducted to calculate the binding free energies of all 14 mutant systems. Finally, we found that most of the 14 mutations on the 2019-nCoV-S1 protein could enhance the binding ability between the 2019-nCoV coronavirus and the human protein ACE2. Among which, the binding capacities for G446R, Y449R and F486Y mutations could be increased by 20%, and that for S494R mutant increased even by 38.98%. We hope this research could provide significant help for the future epidemic detection, drug development research, and vaccine development and administration.

20.
Int J Environ Res Public Health ; 18(2)2021 01 18.
Article in English | MEDLINE | ID: covidwho-1067731

ABSTRACT

The impact of the COVID-19 pandemic on the mental health of students in locked-down colleges remains obscure. This study aimed to explore influencing factors for the psychological impact of COVID-19 on Wuhan college students, post-traumatic stress symptoms in particular, so as to inform evidence-based strategy development to ameliorate such adverse impacts. An online survey was conducted from 26 to 29 April 2020, and 4355 students enrolled in Wuhan universities and colleges participated. Post-Traumatic Stress Disorder via the Impact of Event-Scale-Revised was assessed. COVID-19 disproportionately affected older male Master's and doctoral students living in Wuhan. The overall prevalence of PTSD was 16.3%. The three-level socio-interpersonal model of PTSD was empirically validated, and college students faced individual level risks such as infection with COVID-19, close relationship level risks such as family support (infection suspicion of family members, the loss of loved ones, and the family income decrease) and online course difficulties (little interaction, disturbing learning environment, and difficulty in adaption), and distant level risks such as excessive collection of personal information, estrangement of family relatives, and harassment and insult from strangers. The findings suggest the severity of the psychological impact of COVID-19. Mental health services reducing PTSD should be provided. Students who have lost loved ones and suffered family financial loss should be given particular care.


Subject(s)
/psychology , Mental Health , Pandemics , Stress, Psychological , Students/psychology , China , Female , Humans , Male , Universities
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