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1.
BMC Pulm Med ; 22(1): 108, 2022 Mar 27.
Article in English | MEDLINE | ID: covidwho-1808360

ABSTRACT

BACKGROUND: The clinical treatment of patients suspected of pulmonary infections often rely on empirical antibiotics. However, preliminary diagnoses were based on clinical manifestations and conventional microbiological tests, which could later be proved wrong. In this case, we presented a patient whose initial diagnosis was lung abscess, but antibiotic treatments had no effect, and metagenomic Next-Generation Sequencing (mNGS) indicated presence of neoplasm. CASE PRESENTATION: A 62-year-old female was diagnosed with lung abscess at three different health facilities. However, mNGS of bronchoalveolar lavage fluid did not support pulmonary infections. Rather, the copy number variation analysis using host DNA sequences suggested neoplasm. Using H&E staining and immunohistochemistry of lung biopsy, the patient was eventually diagnosed with lung squamous cell carcinoma. CONCLUSIONS: mNGS not only detects pathogens and helps diagnose infectious diseases, but also has potential in detecting neoplasm via host chromosomal copy number analysis. This might be beneficial for febrile patients with unknown or complex etiology, especially when infectious diseases were initially suspected but empirical antibiotic regimen failed.


Subject(s)
Carcinoma, Squamous Cell , Lung Neoplasms , Carcinoma, Squamous Cell/diagnosis , Carcinoma, Squamous Cell/genetics , DNA Copy Number Variations , Female , High-Throughput Nucleotide Sequencing , Humans , Lung , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Middle Aged , Sensitivity and Specificity
2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-332339

ABSTRACT

Many patients with COVID-19 experience a range of debilitating symptoms months after being infected, a syndrome termed long-haul COVID. A 68-year-old male presented with lung opacity, fatigue, physical and cognitive weaknesses, loss of smell and lymphocytopenia. After rounds of therapeutic plasma exchange (TPE), the patient returned to normal activities and work. Mechanistically in the patient’s peripheral blood mononuclear cells (PBMCs), markers of inflammatory macrophages diminished and markers of lymphocytes, including natural killer (NK) cells and cytotoxic CD8 T-cells, increased. Circulating inflammatory proteins diminished, while positive regulators of tissue repair increased. This case study suggests that TPE has the capacity to treat long-haul COVID.

3.
Virol J ; 19(1): 57, 2022 03 28.
Article in English | MEDLINE | ID: covidwho-1765455

ABSTRACT

BACKGROUND: Abnormalities of lymphocyte subsets and cytokine profiles have been observed in most patients with coronavirus disease (COVID-19). Here, we explore the role of lymphocyte subsets and cytokines on hospital admission in predicting the severity of COVID-19. METHODS: This study included 214 patients with COVID-19 who were treated at Chongqing University Three Gorges Hospital from January 19, 2020 to April 30, 2020. Any mutants were not detected in the studied patients. Patients were divided into non-intensive care unit (ICU) (mild/moderate) group and ICU (severe/critical) group, according to the severity of the disease. Clinical and laboratory data, including peripheral lymphocyte subsets and cytokines, were analyzed and compared. Logistic regression was used to analyze the predictive factors for ICU admission. Receiver operating characteristic (ROC) curves were drawn to evaluate the predictive value of selected indicators for the severity of COVID-19. RESULTS: Of the 214 patients enrolled, 161 were non-ICU patients and 53 were ICU patients. Lymphopenia was observed in nearly all of ICU patients (96.2%) and 84.5% of non-ICU patients on hospital admission. The absolute number of lymphocytes, CD3+ T cells, CD4+ T cells, CD8+ T cells, CD19+ B cells, and natural killer (NK) cells were lower in ICU group (659.00 × 106/L, 417.00 × 106/L, 261.00 × 106/L, 140.00 × 106/L, 109.00 × 106/L, 102.00 × 106/L, respectively) than in non-ICU group (1063.00 × 109/L, 717.00 × 106/L, 432.00 × 106/L, 271.00 × 106/L, 133.00 × 106/L, 143.00 × 106/L, respectively). Interleukin (IL)-6 was significantly higher in ICU patients than in non-ICU patients (18.08 pg/mL vs. 3.13 pg/mL, P < 0.001). Multivariate logistic regression analysis showed that age (odds ratio: 1.067 [1.034-1.101]), diabetes mellitus (odds ratio: 9.154 [2.710-30.926]), CD3+ T cells (odds ratio: 0.996 [0.994-0.997]), and IL-6 (odds ratio: 1.006 [1.000-1.013]) were independent predictors for the development of severe disease. ROC curve analysis showed that the area under the ROC curve (AUC) of CD3+ T cells and IL-6 was 0.806 (0.737-0.874) and 0.785 (0.705-0.864), respectively, and the cutoff values were 510.50 × 106/L (sensitivity, 71.7%; specificity, 79.5%) and 6.58 pg/mL (77.4%, 74.5%), respectively. There were no statistical differences among all tested indicators of lymphocyte subsets and cytokines between severe group (n = 38) and critical group (n = 15) on hospital admission or ICU admission, respectively. CONCLUSIONS: The levels of lymphocyte subsets decreased and the level of IL-6 increased significantly in ICU COVID-19 patients compared with non-ICU COVID-19 patients. Therefore, the number of CD3+ T cells and the level of IL-6 on hospital admission may serve as predictive factors for identifying patients with wild-type virus infection who will have severe disease.


Subject(s)
CD8-Positive T-Lymphocytes , COVID-19 , Humans , Interleukin-6 , Killer Cells, Natural , Lymphocyte Subsets , Prognosis
4.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-330390

ABSTRACT

Purpose: To investigate the impact of COVID-19 on the treatment of children with congenital diaphragmatic hernia (CDH). Methods: We retrospectively collected and compared the data of patients with CDH admitted between January 1, 2020 and December 31, 2021 with the CDH patients admitted before the pandemic between January 1, 2018 and December 31, 2019 (control group). Results: During the pandemic, 41 patients with CDH diagnosed prenatally were transferred to our hospital, and 40 underwent surgical repair. The number of patients treated in our hospital increased by 24.2% compared with that before the pandemic. During the pandemic, the overall survival rate, postoperative survival rate and recurrence rate were 85.4%, 87.5% and 7.3%, respectively, and there were no significant differences compared with the control group. The average length of hospital stay in patients admitted during the pandemic was longer than that in the control group, and the incidence of nosocomial infection was higher than that in the control group. Conclusions: CDH patients confirmed to be SARS-CoV-2 infection-free can receive routine treatment. Our data indicate that the implementation of protective measures during the COVID-19 pandemic, along with appropriate screening and case evaluation, do not have a negative impact on the prognosis of children.

5.
Sustainability ; 14(6):3417, 2022.
Article in English | MDPI | ID: covidwho-1742702

ABSTRACT

The COVID-19 pandemic affected how people interact with the built environment and ways of human habitation are facing significant challenges. However, the existing literature has not adequately addressed how the built environment affected the early prevalence of the pandemic. This research aims to extend the existing literature by relating the initial stage pandemic conditions with more comprehensive measures of the built environment including density, diversity, road network, and accessibility at the county level across the United States and conducting bi-weekly comparisons. We collected infection, death, and mortality data in 3141 counties between 1 March to 8 June 2020 and collected seventeen built environment attributes. Our results show that: (1) Road density and street intersection density were significantly associated with the infection rate;(2) Population density only maintained a positive correlation to the prevalence of COVID-19 during the first two weeks, after which the relationship became negative;and (3) Transit accessibility also contributed significantly to the pandemic and the accessibility of transit-oriented jobs was highly correlated to the infection rate in the first two weeks. The study provides valuable insights for policymakers and stakeholders to adopt resource allocation strategies for context-specific conditions.

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323880

ABSTRACT

Background: The coronavirus disease 2019 (COVID-19) that originated in Wuhan, China, is currently spreading throughout China. The majority of infected patients either traveled to Wuhan or came into contact with an infected person from Wuhan. Investigating members of the public with a travel history to Wuhan became the primary focus of the Chinese government’s epidemic prevention and control measures, but several instances of withheld histories were uncovered as localized clusters of infections broke out. This study investigated the public’s willingness and cognition toward reporting travel history to high-risk epidemic regions, to provide effective suggestions and measures for encouraging travel reporting. Methods A cross-sectional study was conducted online between February 12 and 19, 2020. Descriptive analysis, chi-squared test, and Fisher’s exact test were used to identify socio-demographic factors and cognition toward reporting, as well as their impact on the willingness to report on travel history to high-risk epidemic regions. Results Of the 1,344 respondents, 91 (6.77%) expressed an inclination to deliberately withhold travel history. Those who understood the benefits of reporting and the legal consequences for deliberately withholding information, showed greater willingness to report their history (P < 0.05);conversely, those who believed reporting would stigmatize them and feared being quarantined after reporting showed less willingness to report (P < 0.05). Conclusions As any incident of withheld history can have unpredictable outcomes, the proportion of people who deliberately withhold information deserves attention. Appropriate public risk communication and public advocacy strategies should be implemented to strengthen the understanding that reporting on travel history facilitates infection screening and prompt treatment, and to decrease the fear of potentially becoming quarantined after reporting. Additionally, social support and policies should be established, and measures should be taken to alleviate stigmatization and discrimination against potential patients and reporters of travel history. Reinforcing the legal accountability of withholding travel history and strengthening systematic community monitoring are the measures that China is currently taking to encourage reporting on travel history to high-risk epidemic regions. These non-pharmaceutical interventions are relevant for countries that are currently facing the spread of the epidemic and those at risk of its potential spread.

7.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-320346

ABSTRACT

A novel coronavirus (SARS-CoV-2) that is initially found to trigger human severe respiratory illness in Wuhan City of China in 2019, has killed 2,718 people in China by February 26, 2020, and which has been recognized as a public health emergency of international concern as well. And the virus has spread to more than 38 countries around the world. However, the drug has not yet been officially licensed or approved to treat SARS-Cov-2 infection. NSP12-NSP7-NSP8 complex of SARS-CoV-2, essential for viral replication and transcription, is generally regarded as a potential target to fight against the virus. According to the NSP12-NSP7-NSP8 complex (PDB ID: 6NUR) structure of SARS, two homologous models were established for virtual screening in the present study, namely NSP12-NSP7 interface model and NSP12-NSP8 interface model. Seven compounds (Saquinavir, Tipranavir, Lonafarnib, Tegobuvir, Olysio, Filibuvir, and Cepharanthine) were selected for binding free energy calculations based on virtual screening and docking scores. All seven compounds can combine well with NSP12-NSP7-NSP8 in the homologous model, providing drug candidates for the treatment and prevention of SARS-CoV-2.

8.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-318615

ABSTRACT

Background: To explore the changes in lymphocyte subsets and cytokine profiles in patients with coronavirus disease 2019 (COVID-19) and their relationship with disease severity. Methods: : This study included 228 patients with COVID-19 who were treated at Chongqing University Three Gorges Hospital from January 1, 2020 to February 20, 2020. The characteristics of lymphocyte subsets and cytokine profiles of severe and mild COVID-19 patients were compared. Of the 228 patients enrolled, 48 were severe patients and 180 were mild patients. Results: : Lymphocyte counts, absolute number of total T lymphocytes, CD 4+ T cells, CD 8+ T cells, and total B lymphocytes were significantly lower in severe patients (0.8×10 9 /L, 424.5×10 6 /L, 266×10 6 /L, 145.5×10 6 /L, 109.5×10 6 /L, respectively) than in mild patients (1.2×10 9 /L, 721×10 6 /L, 439.5×10 6 /L, 281.5×10 6 /L, 135×10 6 /L, respectively). A multivariate logistic regression analysis showed that age, C-reactive protein (CRP) and the neutrophil-to-lymphocyte ratio (NLR) were independent risk factors for developing into severe condition. The lymphocyte subsets decreased and cytokine profiles increased more significantly in severe patients than in mild patients. Conclusions: : CRP, NLR, and age may serve as powerful factors for early identification of severe patients.

9.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318613

ABSTRACT

Background: Abnormalities of lymphocyte subsets and cytokine profiles have been observed in most patients with coronavirus disease (COVID-19). Here, we explore the role of lymphocyte subsets and cytokines at hospital admission in predicting the severity of COVID-19. Methods: : This study included 214 patients with COVID-19 who were treated at Three Gorges Hospital Affiliated with Chongqing University from January 19, 2020 to April 30, 2020. Patients were divided into the non-intensive care unit (ICU) (mild/moderate) group and the ICU (severe/critical) group, according to the severity of the disease. Clinical and laboratory data, including peripheral lymphocyte subsets and cytokines, were analyzed and compared. Logistic regression was used to analyze the predictive factors for ICU admission. Receiver operating characteristic (ROC) curves were drawn to evaluate the predictive value of selected indicators for the severity of COVID-19. Results: : Of the 214 patients enrolled, 161 were non-ICU patients and 53 were ICU patients. At hospital admission, lymphopenia was observed in nearly all of the ICU patients (96.2%) and 84.5% of the non-ICU patients. The absolute number of lymphocytes, CD3 + T cells, CD4 + T cells, CD8 + T cells, CD19 + B cells, and natural killer (NK) cells was lower in the ICU group (659.00 × 10 6 /L, 417.00 × 10 6 /L, 261.00 × 10 6 /L, 140.00 × 10 6 /L, 109.00 × 10 6 /L, 102.00 × 10 6 /L, respectively) than in the non-ICU group (1063.00 × 10 9 /L, 717.00 × 10 6 /L, 432.00 × 10 6 /L, 271.00 × 10 6 /L, 133.00 × 10 6 /L, 143.00 × 10 6 /L, respectively). Interleukin (IL)-6 was significantly higher in the ICU patients than in the non-ICU patients (18.08 pg/mL vs. 3.13 pg/mL). Multivariate logistic regression analysis showed that age (odds ratio: 1.067 [1.034–1.101]), diabetes mellitus (odds ratio: 9.154 [2.710–30.926]), CD3 + T cells (odds ratio: 0.996 [0.994–0.997]), and IL-6 (odds ratio: 1.006 [1.000–1.013]) were independent predictors for the development of severe disease. ROC curve analysis showed that the area under the ROC curve (AUC) of CD3 + T cells and IL-6 was 0.806 (0.737–0.874) and 0.785 (0.705–0.864), respectively, and the cutoff values were 510.5 × 10 6 /L (sensitivity, 71.7%;specificity, 79.5%) and 6.58 pg/mL (77.4%, 74.5%), respectively. There were no statistical differences among all tested indicators of lymphocyte subsets and cytokines between the severe group ( n = 38) and the critical group ( n = 15) at hospital admission or ICU admission. Conclusions: : The levels of lymphocyte subsets decreased and the level of IL-6 increased significantly in the ICU patients compared with the non-ICU patients. Therefore, the number of CD3 + T cells and the level of IL-6 at hospital admission may serve as powerful factors for identifying patients who will have severe disease.

10.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318269

ABSTRACT

We present the findings of the LoResMT 2021 shared task which focuses on machine translation (MT) of COVID-19 data for both low-resource spoken and sign languages. The organization of this task was conducted as part of the fourth workshop on technologies for machine translation of low resource languages (LoResMT). Parallel corpora is presented and publicly available which includes the following directions: English$\leftrightarrow$Irish, English$\leftrightarrow$Marathi, and Taiwanese Sign language$\leftrightarrow$Traditional Chinese. Training data consists of 8112, 20933 and 128608 segments, respectively. There are additional monolingual data sets for Marathi and English that consist of 21901 segments. The results presented here are based on entries from a total of eight teams. Three teams submitted systems for English$\leftrightarrow$Irish while five teams submitted systems for English$\leftrightarrow$Marathi. Unfortunately, there were no systems submissions for the Taiwanese Sign language$\leftrightarrow$Traditional Chinese task. Maximum system performance was computed using BLEU and follow as 36.0 for English--Irish, 34.6 for Irish--English, 24.2 for English--Marathi, and 31.3 for Marathi--English.

11.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315626

ABSTRACT

The therapeutic effect of tocilizumab remains controversial. We aimed to evaluate whether tocilizumab might be beneficial in COVID-19 patients. We searched PubMed, Embase and Cochrane library from inception to June 23, 2020. Summary estimates of overall response rate (ORR) and all-cause death rate in all patients were analyzed. This study was registered with PROSPERO (CRD42020191313). We included data from 28 articles including 991 COVID-19 patients who underwent tocilizumab administration. The pooled ORR was 72% (95% CI, 66-79%) and pooled all-cause death rate was 16% (95% CI, 11-22%). The optimal timing of administration was the 7.15 day from the symptom onset and with the lowest death rate of 13.11%. 562 patients were defined as with severe infection, and the pooled ORR was 78% (95% CI, 70-85%). The pooled ORR of 56 organ transplantation recipients was 53% (95% CI, 26-78%), which was lower than non-transplant patients [75% (95% CI, 69-81%)]. Nearly all studies confirmed the safety of tocilizumab administration. Tocilizumab improves the clinical outcome of COVID-19 patients, especially in severe cases, and the optimal timing of administration may provide the guidance for management. However, tocilizumab may be used with caution in solid transplant recipients for the suboptimal efficacy.

12.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315573

ABSTRACT

The COVID-19 pandemic has accelerated the digitalisation of the global economy and industry. However, the Next Generation EU (NG-EU) plan, which aims to provide a strong economic recovery for EU member states, has been criticised for its allocation delay and increased risk of hysteresis, that is, the dependence of the state of a system on its history. Under these circumstances, this paper proposes a blockchain-based two-layer system, Next Generation Digital Currency (NGDC), to assist an accountable and transparent fund allocation process for NG-EU funds. A consortium network in layer one is designed for all EU member state central banks and the European Central Bank (ECB) to maintain a trustable and verifiable fund tracking ledger. A Prime-Coordinator PBFT (PC-PBFT) consensus mechanism-based agreement protocol is proposed to resolve discrepancies in the transaction validation process. The simulation results show that PC-PBFT can support at least 30 transactions per second (tps) with transaction processing time less than 1 second on average.

13.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315564

ABSTRACT

Background: The spread of the Coronavirus Disease 2019(COVID-19) pandemic has a great impact on people's life, study, and work. People must stay at home and cannot go out for a long time, especially when the number of infected people increases rapidly. In order to explore the changes in the behavior of people at home during the COVID-19 pandemic in March, 2020, a national survey in China was conducted on people’s anxiety, sleep quality, study/work status, daily activities and family communication with the window opening and overlooking behavior. Methods The survey was carried out by online questionnaires of SMS service. A total of 3401 valid questionnaires were received. Chi-square analysis was used to establish the relationship model of the human behavior and activities during the stay-home of the COVID-19 pandemic. Results The survey results showed that due to the influence of the COVID-19, more than 74.92% participants had anxiety. Compared with the pre-outbreak period, the sleep quality of people become worse. There was a tendency for people to study/work less, exercise less, play more game, and watch the TV. On the other hand, the family communication has been increased, and people have tried to open windows and look outside through windows to alleviate the human anxiety. Conclusions This paper has revealed COVID-19 has had a great impact on people's behavior in all sorts of ways. The response of people affected by the pandemic should be constantly identified and monitored, to assist policy formulation for future short-term or long-term pandemic.

14.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315327

ABSTRACT

Background: : Coronavirus disease 2019 (COVID-19), a highly infectious disease, has been rapidly spreading all over the world and remains a great threat to global public health. Patients diagnosed with severe or critical cases have a poor prognosis. Hence, it is crucial for us to identify potentially severe or critical cases early, and give timely treatments for targeted patients. In the clinical practice of treating patients with COVID-19, we have observed that the neutrophil-to-lymphocyte ratio (NLR) of severe patients is higher than that in mild patients. We performed this systematic review and meta-analysis to evaluate the predictive values of NLR on disease severity and mortality in patients with COVID-19. Methods: : We searched PubMed, EMBASE, China National Knowledge Infrastructure (CNKI) and Wanfang databases to identify eligible studies (up to August 11, 2020). Two authors independently screened studies and extracted data. The methodological quality of the included studies was assessed by Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2). Results: : Thirteen studies involving 1579 patients reported the predictive value of NLR on disease severity. The pooled sensitivity (SEN), specificity (SPE) and area under curve (AUC) were 0.78 (95% CI 0.70-0.84), 0.78 (95% CI 0.73-0.83) and 0.85 (95% CI 0.81-0.88), respectively. Ten studies involving 2967 patients reported the predictive value of NLR on mortality. The pooled SEN, SPE and AUC were 0.83 (95% CI 0.75-0.89), 0.83 (95% CI 0.74-0.89) and 0.90 (95% CI 0.87-0.92), respectively. Conclusions: : NLR has good predictive values on disease severity and mortality in patients with COVID-19 infection. Evaluating NLR can help clinicians identify potentially severe cases early, conduct early triage and initiate effective management in time, which may reduce the overall mortality of COVID-19. Trial registration: This meta-analysis was prospectively registered on PROSPERO database (Registration number: CRD42020203612).

15.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-326267

ABSTRACT

We present the findings of the LoResMT 2021 shared task which focuses on machine translation (MT) of COVID-19 data for both low-resource spoken and sign languages. The organization of this task was conducted as part of the fourth workshop on technologies for machine translation of low resource languages (LoResMT). Parallel corpora is presented and publicly available which includes the following directions: English$\leftrightarrow$Irish, English$\leftrightarrow$Marathi, and Taiwanese Sign language$\leftrightarrow$Traditional Chinese. Training data consists of 8112, 20933 and 128608 segments, respectively. There are additional monolingual data sets for Marathi and English that consist of 21901 segments. The results presented here are based on entries from a total of eight teams. Three teams submitted systems for English$\leftrightarrow$Irish while five teams submitted systems for English$\leftrightarrow$Marathi. Unfortunately, there were no systems submissions for the Taiwanese Sign language$\leftrightarrow$Traditional Chinese task. Maximum system performance was computed using BLEU and follow as 36.0 for English--Irish, 34.6 for Irish--English, 24.2 for English--Marathi, and 31.3 for Marathi--English.

16.
Front Pharmacol ; 12: 759587, 2021.
Article in English | MEDLINE | ID: covidwho-1662607

ABSTRACT

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of coronavirus disease 2019 (COVID-19), which has resulted in a global pandemic. Methodology: We used a two-step polymerase chain reaction to detect the ACE genotype and ELISA kits to detect the cytokine factor. We also used proteomics to identify the immune pathway related to the ACE protein expression. Result: In this study, we found that the angiotensin-converting enzyme (ACE) deletion polymorphism was associated with the susceptibility to COVID-19 in a risk-dependent manner among the Chinese population. D/D genotype distributions were higher in the COVID-19 disease group than in the control group (D/D odds ratio is 3.87 for mild (p value < 0.0001), 2.59 for moderate (p value = 0.0002), and 4.05 for severe symptoms (p value < 0.0001), logic regression analysis. Moreover, genotype-specific cytokine storms and immune responses were found enriched in patients with the ACE deletion polymorphism, suggesting the contribution to the susceptibility to COVID-19. Finally, we identified the immune pathway such as the complement system related to the ACE protein expression of patients by lung and plasma proteomics. Conclusion: Our results demonstrated that it is very important to consider gene polymorphisms in the population to discover a host-based COVID-19 vaccine and drug design for preventive and precision medicine.

17.
Front Med (Lausanne) ; 8: 783646, 2021.
Article in English | MEDLINE | ID: covidwho-1581284

ABSTRACT

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been basically under control in China since March 2020, but the import of domestic SARS-CoV-2 has begun to increase. This study reported the first case of asymptomatic SARS-CoV-2 infection imported from Spain into Sichuan Province, China, on March 11, 2020. The infected male had a body temperature of 37.5°C, normal blood oxygen saturation levels, and a computed tomography (CT) examination showed that his lungs had no shadows. However, a throat swab from the subject tested positive for SARS-CoV-2 using qPCR assay. In this study, we conducted transcriptome sequencing on respiratory throat swabs from the subject and found that the dominant SARS-CoV-2 sequence (Gene Bank ID: MW301121) was a spike protein D614G mutant strain, which is currently popular throughout world. We downloaded and analyzed SARS-CoV-2 sequences collected from cases in China and Spain for comparison and tracing purposes. After March 11, 2020, the Chinese domestic clade was naturally divided into the imported SARS-CoV-2 D614G mutant strain and evolutionarily-related similar sequences and that of sequences collected in the original Wuhan area. The sequence reported in this study was located on a small branch, far from the evolution of Wuhan sequences. As expected, the identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain.

18.
2021.
Preprint in English | Other preprints | ID: ppcovidwho-295296

ABSTRACT

Background More than ten novel COVID-19 vaccines have been approved with protections against SARS-CoV-2 infections ranges between 52-95%. It is of great interest to the vaccinees who have received the COVID-19 vaccines, vaccine developers and authorities to identify the non-responders in a timely manner so intervention can take place by either giving additional boosts of the same vaccine or switching to a different vaccine to improve the protection against the SARS-CoV-2 infections. A robust correlation was seen between binding antibody titer and efficacy (p=0.93) in the clinic studies of 7 COVID-19 vaccines, so it is of urgency to develop a simple POCT for vaccinees to self-assess their immune response at home. Methods Using CHO cell-expressed full length SARS-CoV2 S1 protein as coating antigen on colloidal gold particles, a SARS-CoV-2 S1 IgG-IgM antibody lateral flow test kit (POCT) was developed. The test was validated with negative human sera collected prior to the COVID-19 outbreaks, and blood samples from human subjects prior, during, and post-immunization of COVID-19 vaccines. Results The specificity of the POCT was 99.0%, as examined against 947 normal human sera and 20 whole blood samples collected pre-immunization. The limit of detection was 50 IU/mL of pseudovirus neutralizing titer (PVNT) using human anti-SARS-2 neutralizing standards from convalescent sera. The sensitivity of POCT for SARS-CoV-2 S1 protein antibody IgG-IgM was compared with SARS-CoV-2 RBD antibody ELISA and determined to be 100% using 23 blood samples from vaccinated human subjects and 10 samples from non-vaccinated ones. Whole blood samples were collected from 119 human subjects (ages between 22-61 years) prior to, during, and post-vaccination of five different COVID-19 vaccines. Among them, 115 people tested positive for SARS-CoV-2 S1 antibodies (showing positive at least once) and 4 people tested negative (tested negative at least twice on different days), demonstrating 96.64% of seroconversion after full-vaccination. 92.3% (36/39) of the human subjects who were younger than 45 achieved seroconversion within 2 weeks while only 57.1% (4/7) of subjects older than 45 tested positive for S1 antibodies, suggesting that younger people develop protection much faster than older ones. Even though the S1 antibody level in 88% of human subjects vaccinated with inactivated virus dropped below 50 IU/mL two months later, one boost could quickly raise the S1 antibody titer above 50 IU/mL of PVNT, indicates that the initial vaccination was successful and immunization memory was developed. Conclusion Using the lateral flow tests of SARS-CoV2 S1 IgG+IgM, vaccinated human subjects can easily self-assess the efficacy of their vaccination at home. The vaccine developer could quickly identify those non-responders and give them an additional boost to improve the efficacy of their vaccines. Vaccinees who failed in response could switch to different types of COVID-19 vaccines since there are more than 10 COVID-19 vaccines approved using three different platform technologies. Highlights More than ten novel COVID-19 vaccines have been approved with protections against SARS-CoV-2 infections ranges between 52-95%. It is of great interest to the vaccinees who have received the COVID-19 vaccines, vaccine developers and authorities to identify the non-responders in a timely manner. A highly specific and very simple lateral flow test kit for measurement of SARS-CoV-2 S1IgG+IgM antibodies post-immunization of COVID-19 vaccine using peripheral blood was developed as a home-test assay with a limit of detection (LOD) at 50 IU/mL of pseudovirus neutralizing titer (PVNT). After full vaccinations with COVID-19 vaccines, 96.6% of the volunteers successfully achieved the seroconversion of SARS-CoV-2 S1 IgG+IgM antibody. 92.3% (36/39) of the human subjects who were younger than 45 achieved seroconversion within 2 weeks while only 57.1% (4/7) of subjects older than 45 tested positive for S1 antibodies, suggesting that younger peopl develop protection much faster than older ones. Even though the S1 antibody level in 88% of human subjects vaccinated with inactivated virus dropped below the detection 2-6 months later, one boost could quickly raise the S1 antibody titer above 50 IU/mL of PVNT, indicating that the initial vaccination was successful and immunization memory was developed.

19.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-292995

ABSTRACT

<ns3:p>Many patients with COVID-19 experience a range of debilitating symptoms months after being infected, a syndrome termed long-haul COVID. A 68-year-old male presented with lung opacity, fatigue, physical and cognitive weaknesses, loss of smell and lymphocytopenia. After rounds of therapeutic plasma exchange (TPE), the patient returned to normal activities and work. Mechanistically in the patient’s peripheral blood mononuclear cells (PBMCs), markers of inflammatory macrophages diminished and markers of lymphocytes, including natural killer (NK) cells and cytotoxic CD8 T-cells, increased. Circulating inflammatory proteins diminished, while positive regulators of tissue repair increased. This case study suggests that TPE has the capacity to treat long-haul COVID.

20.
Ann Med ; 53(1): 2099-2109, 2021 12.
Article in English | MEDLINE | ID: covidwho-1514452

ABSTRACT

BACKGROUND: Patients appear to maintain sequelae post-coronavirus disease 2019 (COVID-19) affecting daily life and physical health. We investigated the changes in and the effects of pulmonary rehabilitation (PR) on exercise capacity and immunology six months after COVID-19 hospitalization. METHODS: This retrospective cohort reviewed 233 COVID-19 patients admitted from 17 January 2020 to 29 February 2020. Ninety-eight patients who completed 2-week and 6-month follow-ups and tests were included. Among 98 patients, 27 completed at least five sessions of PR at the First Hospital of Changsha, China, during the 6-month convalescence were allocated to the PR group; the reminder who had not performed any PR were assigned to the control group. The primary outcome was the change in six-minute walk distance (6-MWD) between the 2-week and 6-month follow-ups, which was assessed via analysis of covariance with a covariate of propensity score that adjusted for the potential confounders. Secondary outcomes were the changes in 6-MWD, SARS-CoV-2 immunoglobulins, T-lymphocytes and blood chemistry, which were evaluated via paired tests. RESULTS: Participants' ages ranged from 19 to 84 years (M = 47, standard deviation (SD)=15) 45.9% identified as male. During the 6-month convalescence, 6-MWD increased 27.0%, with a mean [95% CI] of 113 [92-134] m (p < .001). SARS-CoV-2 IgG and IgM decreased 33.3% (p = .002) and 43.8% (p = .009), CD4+ T cells increased 7.9% (p = .04), and the majority of blood chemistry significantly changed. The patients in the PR group acquired a greater increase in 6-MWD than those in control (unadjusted, 194 [167-221] m, p < .001; adjusted, 123 [68-181] m, p < .001), dose-responsiveness of PR on 6-MWD was observed (p < .001). No differences in immunity variables and blood chemistry were observed between groups. CONCLUSIONS: These findings suggest PR may be a strategy to promote the improvement of exercise capacity after COVID-19.


Subject(s)
COVID-19/rehabilitation , Convalescence , Exercise , Hospitalization/statistics & numerical data , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/psychology , Humans , Male , Middle Aged , Quality of Life , Retrospective Studies , SARS-CoV-2 , Young Adult
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