Impact of coronavirus disease on the HIV testing and health care delivery at a university hospital in Taiwan, 2020-2021

Background To contain the coronavirus disease 2019 (Covid-19) pandemic, non-pharmacologic interventions, including lockdown and social distancing, may have adverse impact on access to HIV testing and care. This study investigated the impact of Covid-19 on HIV testing and care at a major hospital in Taiwan in 2020-2021. Methods The numbers of clients seeking anonymous HIV voluntary counseling and testing were compared 2 years before (2018-2019) and 2 years after Covid-19 outbreak (2020-2021). People living with HIV (PLWH) who sought care at the hospital during 2018-2021 were included to examine the status of HIV care delivery and disposition. Results The annual number of HIV screening tests performed had significantly decreased from 2,507 and 2,794 in 2018 and 2019, respectively, to 2,161 and 1,737 in 2020 and 2021, respectively. The rate of discontinuation of HIV care among PLWH was 3.7% in 2019, which remained unchanged in 2020 (3.7%) and 2021 (3.8%). The respective percentage of annual plasma HIV RNA testing <2 times increased from 8.4% and 7.8% in 2018 and 2019 to 7.0% and 10.7% in 2020 and 2021, so was that of annual syphilis testing <2 times (10.1% and 8.8% to 7.9% and 12.0%). The rates of plasma HIV RNA <200 copies/ml ranged from 97.0% to 98.1% in 2018-2021. Conclusions During the Covid-19 pandemic, access to HIV counseling and testing was significantly limited. While the number of HIV-related testing decreased, the impact of Covid-19 on the continuity of antiretroviral therapy and viral suppression among PLWH appeared to be minimal in Taiwan.

Investigation of a family cluster outbreak of coronavirus disease 2019 in Xi-an. (Special Issue: Spatio-temporal dynamics analysis, risk assessment and emergency management for COVID-19 epidemic.) [Chinese]

Objective: To investigate the transmission characteristics of a family cluster outbreak of coronavirus disease 2019 (COVID-19) in Xi-an, in order to provide reference for prevention and control efforts.

Epidemiologic Features, Radiological Findings andClinical Outcomes of 19 Patients with COVID-19in a Single Center in Beijing, China.

ObjectiveTo describe the epidemiologic, clinical, laboratory, and radiological characteristics and prognoses of COVID-19 confirmed patients in a single center in Beijing, China. Methods The study retrospectively included 19 patients with nucleic acid-confirmed SARS-CoV-2 infection at our hospital from January 20 to March 5, 2020. The final follow-up date was March 14, 2020. The epidemiologic and clinical information was obtained through direct communication with the patients or their family members. Laboratory results retrieved from medical records and radiological images were analyzed both qualitatively by two senior chest radiologists as well as quantitatively via an artificial intelligence software. Results We identified 5 family clusters (13/19, 68.4%) from the study cohort. All cases had good clinical prognoses and were either mild (3/19) or moderate (16/19) clinical types. Fever (15/19, 78.9%) and dry cough (11/19, 57.9%) were common symptoms. Two patients received negative results for more than three consecutive viral nucleic acid tests. The longest interval between an initial CT abnormal finding and a confirmed diagnosis was 30 days. One patient's nucleic acid test turned positive on the follow-up examination after discharge. The presence of radiological abnormalities was non-specific for the diagnosis of COVID-19. Conclusions COVID-19 patients with mild or no clinical symptoms are common in Beijing, China. Radiological abnormalities are mostly non-specific and massive CT examinations for COVID-19 screening should be avoided. Analyses of the contact histories of diagnosed cases in combination with clinical, radiological and laboratory findings are crucial for the early detection of COVID-19. Close monitoring after discharge is also recommended.

Global Pandemic Trends of COVID-19 in 2020 (preprint)

Background: The novel coronavirus pneumonia (COVID-19) has been global threaten to public health. This paper provides perspective to the decision-making for public health control of the pandemic or the spread of epidemic.Methods: According to the WHO global reported database, we developed and used the number of cumulative cases, and the number of cumulative deaths to calculate and analyze rates of incidence, mortality, and fatality by country, with respect to the 30 highest outbreak (Top 30) countries.Results： As of December 31, 2020, of the global population of 7.585 billion, the cumulative number of reported cases was 81,475,053, and the cumulative number of deaths was 1,798,050. The incidence rate of COVID-19 was 1074.13 per 100,000 population, the mortality rate was 23.70 per 100,000, and the case fatality rate was 2.21%. Among the Top 30 countries, the five countries with the highest number of reported cumulative cases were, in rank, the United States (19,346,790 cases), India (10,266,674), Brazil (7,563,551), Russia (3,159,297) and France (2,556,708), and the five countries with the highest number of cumulative deaths were the United States (335,789 cases), Brazil (192,681), India (148,738), Mexico (123,845) and Italy (73,604). Globally, the countries with the highest incidence rate were, in rank, Andorra, Luxembourg, Montenegro, San Marino, and Czechia; the countries with the highest mortality rate were, in rank, San Marino, Belgium, Slovenia, Italy, and North Macedonia. The highest fatality rate was found in Yemen, Mexico, Montserrat, Isle of Man, and Ecuador, respectively. In China, 96,673 cases of COVID-19 and 4788 deaths were reported in 2020, ranking the 78th and the 43rd, respectively, in the world. The incidence rate and mortality rate were 6.90/105 and 0.34/105, respectively, ranking 207th and 188th in the world. The case fatality rate was 4.95%, ranking 11th in the world.Conclusions： The COVID-19 prevalence is still on the rise, and the turning points of incidence and mortality are not yet forecasted. Personal protection, anti-epidemic measures and efforts from public health personnel, medical professionals, biotechnology R&D personnel, effectiveness of the vaccination programs and the governments, are the important factors to determine the future prevalence of this coronavirus disease.

Combined chest CT and IL-6 detection for the initial diagnosis of patients with COVID-19

Objective To explore the feasibility of evaluation of patients with COVID-19 using combined chest CT presentations and interleukin-6(IL-6) levels for classification after initial diagnosis. Methods A retrospective analysis of medical records of 59 confirmed cases of COVID-19(moderate and severe) was conducted using the semi-quantitative scoring of chest CT presentation and the blood IL-6 count.The Spearman correlation was used to compare the association between the IL-6 counts and the CT scores in the moderate group with IL abnormality and in the severity group.By evaluating IL-6 count, CT scores and combined IL-6 count + CT scores, the area under curve(AUC) and the 95% confidence interval of the receiver operator characteristic(ROC) curve and logistic regression analysis were computed to predict the probability of the severe COVID-19 and to calculate the sensitivity and specificity. Results Among moderate patients, 9 showed normal IL-6 counts while 20 with abnormal values.The range of the IL-6 counts was 7.6-37.1 pg/ml with a mean of (20.07±9.79)pg/ml.The chest CT images were characterized by the domination of glass shadow of the lungs with or without consolidation.The CT scores were from 5 to 12 points with a mean of(8.85±1.71)points.For severe patients,30 demonstrated abnormal IL-6 counts.The range was(38.33-100.3)pg/ml and the mean was 58.53 pg/ml.From chest CT images,multiple presentations of both lungs could be seen.The range of CT scores was from 8 to 16 points with a mean of(13.00±2.61)points.The IL-6 counts [58.53(38.33-100.3)pg/ml]and CT scores[(13.00±2.61)points]of the severe patients were both significantly higher than that of the moderate patients.Within the group of severe patients,the IL-6 counts were positively correlated with the CT scores(r=0.658,P<0.05;r=0.397,P<0.05),whereas no correlation was found in the group of moderate patients.The results of ROC curve showed that the best cut-off values of IL-6 count and CT score were 33.9 pg/ml and 11 points,respectively,in the diagnosis for severe patients using the combination of the two measures.The sensitivity was 96.70% and the specificity was 89.70%,both of which were better than those when using IL-6 count or CT score alone. Conclusions The chest CT of moderate and severe COVID-19 patients after initial diagnosis exhibited distinct imaging features.Combining chest CT presentations and IL-6 levels is helpful for the classification of COVID-19 patients after initial diagnosis.

Antibody Cocktail Exhibits Broad Neutralization against SARS-CoV-2 and SARS-CoV-2 variants (preprint)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has precipitated multiple variants resistant to therapeutic antibodies. In this study, 12 high-affinity antibodies were generated from convalescent donors in early outbreaks using immune antibody phage display libraries. Of them, two RBD-binding antibodies (F61 and H121) showed high affinity neutralization against SARS-CoV-2, whereas three S2-target antibodies failed to neutralize SARS-CoV-2. Following structure analysis, F61 identified a linear epitope located in residues G446 - S494, which overlapped with angiotensin-converting enzyme 2 (ACE2) binding sites, while H121 recognized a conformational epitope located on the side face of RBD, outside from ACE2 binding domain. Hence the cocktail of the two antibodies achieved better performance of neutralization to SARS-CoV-2. Importantly, F61 and H121 exhibited efficient neutralizing activity against variants B.1.1.7 and B.1.351, those showed immune escape. Efficient neutralization of F61 and H121 against multiple mutations within RBD revealed a broad neutralizing activity against SARS-CoV-2 variants, which mitigated the risk of viral escape. Our findings defined the basis of therapeutic cocktails of F61 and H121 with broad neutralization and delivered a guideline for the current and future vaccine design, therapeutic antibody development, and antigen diagnosis of SARS-CoV-2 and its novel variants.

The Significance of KL-6 as Prognosis Monitoring Biomarker in Patients With Severe COVID-19 From Stabilized Stage Toward Convalescence (preprint)

Background: This study aims to identify some biomarkers for monitoring the recovery of lung injury in severe COVID-19 patients from stabilized stage toward convalescence.Methods: We enrolled participants who diagnosed with severe COVID-19 (n = 28) and health volunteers (n = 25) from Taikang Tongji (Wuhan) Hospital. The patients were in a stabilized stage and had a course of 48.1±12.8 days. We followed these patients for 90 days. The blood routine, cytokines (IL-1β, IL-2, IL-4, IL-5, IL-6, IL-10, IL-12p70, IL-17A, TNF-α, IFN-α, IFN-γ), type II alveolar epithelium injury indicators (Surfactant protein A (SP-A), Krebs von den Lungen-6 (KL-6)) and chest CT were tested on the 1, 30, 60, and 90 days after enrollment. Results: In stabilized stage, the parameters of blood routine and some cytokines (IL-1β, IL-2, IL-4, IL-12p70, TNF-α) had bounced back to normal (p>0.05). Some cytokines (IL-5, IL-6, IL-10, IL-17A, IFN-α, IFN-γ) and type II alveolar epithelium injury indicators (SP-A and KL-6) were still higher than normal (p<0.05). During the stabilized stage to convalescence, in spite of the variation of monocyte count, monocyte/lymphocyte ratio, IL-5, IL-10, IL-12p70, IL-17A, IFN-γ, IFN-α, SP-A and KL-6 were downward trend (p<0.05), only KL-6 level (p<0.05) could simultaneously reflect the lung injury volume which be measured by CT. Conclusions: Our preliminary data indicated that KL-6 could be an effective prognostic biomarker for monitoring the recovery of lung function in patients with severe COVID-19 from stabilized stage toward convalescence.

Comprehensive analysis of the host-virus interactome of SARS-CoV-2 (preprint)

Host-virus protein-protein interaction is the key component of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lifecycle. We conducted a comprehensive interactome study between the virus and host cells using tandem affinity purification and proximity labeling strategies and identified 437 human proteins as the high-confidence interacting proteins. Functional characterization and further validation of these interactions elucidated how distinct SARS-CoV-2 viral proteins participate in its lifecycle, and discovered potential drug targets to the treatment of COVID-19. The interactomes of two key SARS-CoV-2 encoded viral proteins, NSP1 and N protein, were compared with the interactomes of their counterparts in other human coronaviruses. These comparisons not only revealed common host pathways these viruses manipulate for their survival, but also showed divergent protein-protein interactions that may explain differences in disease pathology. This comprehensive interactome of coronavirus disease-2019 provides valuable resources for understanding and treating this disease.

Performance of Composite Filters Assembled from Multiple Layers of Basic Filtration Media

There is a severe shortage of face masks and N95 respirators due to the current COVID-19 pandemic, particularly in countries that were not well prepared in advance. In order to help ease the supply demands of these resources, a strategy of using multiple layers of basic filtration media to construct a composite filter that can match the particle collection efficiency offered by a N95 filtering facepiece respirator (FFR) is proposed. In this study, the filtration performances of four face masks and one N95 respirator using the same test protocol (as a reference) were first compared. Composite filter samples composed of multiple layers of basic face mask and MERV13 furnace media were then constructed and the filter performance of the composite filters was investigated. As expected, the minimum particle collection efficiency of the N95 respirator media sample was higher than 95% and the efficiency of the samples from the four tested face masks varied from 71.8% to 83.6%. The Figure of Merit (FOM) values of the face mask samples were generally half that of the N95 media sample. It was found that a N95-comparable collection efficiency can be achieved by combining two/three layers of face mask media but at the expense of a higher media pressure drop. Additionally, the composite filter samples made up of three/five layers of MERV13 furnace media could approach the FOM offered by the N95 media without the increased pressure drop. It was also found that the measured collection efficiency of multiple-layered filter media was not equal to the calculated in the test particle size range. Further studies are required to identify the reason(s).

Radiologic Risk Factors for Mortality of Patients with COVID-19 Pneumonia in Wuhan, China: A Retrospective Study (preprint)

Background: Computed tomography (CT) characteristics associated with critical outcomes of patients with coronavirus disease 2019 (COVID-19) have been reported. However, CT risk factors for mortality are poorly understood. We aimed to investigate the automatically quantified CT imaging predictors for COVID-19 mortality.Methods: In this retrospective study, laboratory-confirmed COVID-19 patients at Wuhan Central Hospital between December 9, 2019, and March 19, 2020, were included. A novel prognostic biomarker, V-HU score, depicting the volume of total pneumonia infection and the average Hounsfield unit (HU) value of consolidation areas was quantified from CT by an artificial intelligence (AI) system. Cox proportional hazards models were used to investigate risk factors for mortality.Findings: This study included 238 patients (126 survivors and 112 non-survivors). The V-HU marker was an independent predictor (hazard ratio [HR] 2·78, 95% CI 1·50-5·17; p=0·0012) after adjusting for several COVID-19 prognostic indicators significant in univariable analysis. The prognostic performance of the model containing clinical and outpatient laboratory factors was improved by integrating the V-HU marker (c-index: 0·695 versus 0·728; p<0·0001). Older patients (age>=65 years; HR 3·56, 95% CI 1·64-7·71; p=0·0006) and younger patients (age<65 years; HR 4·60, 95% CI 1·92-10·99; p<0·0001) could be risk-stratified by the V-HU marker.Interpretation: A combination of an increased volume of total pneumonia infection and high HU value of consolidation areas showed a strong correlation to COVID-19 mortality, as determined by AI quantified CT. The novel radiologic marker may be used for early risk assessment to prioritize critical care resources for patients at a high risk of mortality.Funding: None.Declaration of Interests: The authors declare no competing interests.Ethics Approval Statement: The study was approved by the Research Ethics Commission of Wuhan Central Hospital, and the requirement for writing informed consent was waived by the Ethics Commission for the emergence of infectious diseases.

The emergence of inter-clade hybrid SARS-CoV-2 lineages revealed by 2D nucleotide variation mapping (preprint)

I performed whole-genome sequencing on SARS-CoV-2 collected from COVID-19 samples at Mayo Clinic Rochester in mid-April, 2020, generated 85 consensus genome sequences and compared them to other genome sequences collected worldwide. I proposed a novel illustrating method using a 2D map to display populations of co-occurring nucleotide variants for intra- and inter- viral clades. This method is highly advantageous for the new era of big-data when high-throughput sequencing is becoming readily available. Using this method, I revealed the emergence of inter-clade hybrid SARS-CoV-2 lineages that are potentially caused by homologous genetic recombination.

Methyltransferase-like 3 modulates severe acute respiratory syndrome coronavirus-2 RNA N6-methyladenosine modification and replication (preprint)

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) 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.

Immunogenicity and Safety of a SARS-CoV-2 Inactivated Vaccine in Healthy Adults Aged 18-59 years: Report of the Randomized, Double-blind, and Placebo-controlled Phase 2 Clinical Trial (preprint)

BACKGROUND The top priority for the control of COVID-19 pandemic currently is the development of a vaccine. A phase 2 trial conducted to further evaluate the immunogenicity and safety of a SARS-CoV-2 inactivated vaccine (CoronaVac). METHODS We conducted a randomized, double-blind, placebo-controlled trial to evaluate the optimal dose, immunogenicity and safety of the CoronaVac. A total of 600 healthy adults aged 18-59 years were randomly assigned to receive 2 injections of the trial vaccine at a dose of 3 g/0.5 mL or 6 g /0.5mL, or placebo on Day 0,14 schedule or Day 0,28 schedule. For safety evaluation, solicited and unsolicited adverse events were collected after each vaccination within 7 days and 28 days, respectively. Blood samples were taken for antibody assay. RESULTS CoronaVac was well tolerated, and no dose-related safety concerns were observed. Most of the adverse reactions fell in the solicited category and were mild in severity. Pain at injection site was the most frequently reported symptoms. No Grade 3 adverse reaction or vaccine related SAEs were reported. CoronaVac showed good immunogenicity with the lower 3 g dose eliciting 92.4% seroconversion under Day 0,14 schedule and 97.4% under Day 0,28 schedule. 28 days after two-dose vaccination, the Nab levels of individual schedules range from 23.8 to 65.4 among different dosage and vaccination schedules. CONCLUSIONS Favorable safety and immunogenicity of CoronaVac was demonstrated on both schedules and both dosages, which support the conduction of phase 3 trial with optimum schedule/dosage per different scenarios.

Airborne SARS-CoV-2 and the Use of Masks for Protection against Its Spread in Wuhan, China (preprint)

The outbreak of COVID-19 has caused a global public health crisis. The spread of SARS-CoV-2 by contact is widely accepted, but the relative importance of aerosol transmission for the spread of COVID-19 is controversial. Here we characterize the distribution of SARA-CoV-2 in 123 aerosol samples, 63 masks, and 30 surface samples collected at various locations in Wuhan, China. The positive percentages of viral RNA included 21% of the aerosol samples from an intensive care unit and 39% of the masks from patients with a range of conditions. A viable virus was isolated from the surgical mask of one critically ill patient while all viral RNA positive aerosol samples were cultured negative. The SARS-CoV-2 detected in masks from patients, ambient air, and respirators from health workers compose a chain of emission, transport, and recipient of the virus. Our results indicate that masks are effective in protecting against the spread of viruses, and it is strongly recommended that people throughout the world wear masks to break the chain of virus transmission and thus protect themselves and others from SARS-CoV-2.

Mycophenolate Mofetil Is Active Against SARS-CoV-2 in Vero E6 Cells (preprint)

Mycophenolate mofetil was reported to have broad in vitro activity against different viruses and had been tried in combination with IFN-β in treating MERS infection. We tested the pharmacological activity of mycophenolate mofetil using SARS-CoV-2 infected Vero cells. The half-maximal effective concentration (EC50) of mycophenolate mofetil against SARS-CoV-2 was 0.47 μM while that of remdesivir was 0.77 μM. Molecular docking results of mycophenolate mofetil to potential target proteins of COVID-19 suggested that mycophenolate mofetil might inhibit SARS-CoV-2 mainly by interacting with DHODH and IMPDH2. Furthermore, mycophenolate mofetil as an immunosuppressant may be a good therapeutic option for the management of hyperinflammation in patients with severe COVID-19. Based on its high potency against SARS-CoV-2 in Vero E6 cells, its good pharmacokinetics and clinical safety profile, mycophenolate mofetil deserves further exploration as potential treatment for COVID-19.

Analysis of 8 274 cases of new coronavirus nucleic acid detection and co-infection in Wuhan / 中华检验医学杂志

Objective@#To investigate the positive rate for 2019-nCoV tests and co-infections in Wuhan district.@*Methods@#A total of 8 274 cases in Wuhan were enrolled in this cross-sectional study during January 20 to February 9, 2020, and were tested for 2019-nCoV using fluorescence quantitative PCR. Both respiratory tract samples (nasopharynx, oropharynx, sputum and alveolar lavage fluid) and non-respiratory tract samples (urine, feces, anal swabs, blood and conjunctival sac swabs) were collected. If both orf1ab and N genes are positive, they are classified as nucleic acid test positive group; if both orf1ab and N genes are negative, they are classified as negative group; if single gene target is positive, they are classified as suspicious group. Individuals were divided into male group and female group according to sex. At the same time, 316 patients were tested for 13 respiratory pathogens by multiplex PCR.@*Results@#Among the 8 274 subjects, 2 745 (33.2%) were 2019-nCoV infected; 5 277 (63.8%) subjects showed negative results in the 2019-nCoV nucleic acid test; and 252 cases (3.05%) was not definitive (inconclusive result). The age of cases with COVID-19 patients and inconclusive cases was significantly higher than that of cases without 2019-nCoV infection (40 vs 56, t=27.569, P<0.001; 52 vs 56, t=6.774, P<0.001). The positive rate of 13 respiratory pathogens multiple tests was significantly lower in 104 subjects who were positive for 2019-nCoV compared with those in subjects who were negative for 2019-nCoV test (5.77% vs 18.39%, χ2=24.105, P=0.003). Four types of respiratory tract samples and five types of non-respiratory tract samples were found to be positive for 2019-nCoV nucleic acid test.@*Conclusion@#The 2019-nCoV nucleic acid positive rate in male is higher than in female. Co-infections should be pay close attention in COVID-19 patients. 2019-nCoV nucleic acid can be detected in non-respiratory tract samples.

Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China (preprint)

COVID-19 caused by a novel coronavirus SARS-CoV-2 emerged in Wuhan, Hubei province since December 2019, and caused a rapid outbreak throughout China and globally. Cities outside Hubei are also facing great challenge and require implementing of effective and feasible strategy in precision diagnosing novel coronavirus pneumonia (NCP). We described a multicenter prospective study on diagnostic strategy of suspected NCP patients from January 22nd to February 9th, 2020 in Eastern China cities. Nasopharyngeal swabs were collected from the patients. The epidemiological characteristics, clinical symptoms, laboratory assessments, and computed tomographic (CT) scans were obtained. Pathogen screen were performed including RT-PCR, multiplex PCR, rapid flu antigen tests and mNGS. We enrolled 53 suspected NCP patients, among whom 20 were laboratory-confirmed. Fourteen (70%) and 3 (15%) patients were positive for the first and second SARS-CoV-2 RT-PCR test, respectively. All NCP patients were positive for mNGS. Chest CT images and the symptoms of early stage NCP patients were similar to other viral pneumonia patients. We identified 11 of 20 co-infections in NCP cases, including regular respiratory virus, fungi and bacteria synchronously. Genomic analysis showed that 8 of 10 cases had no mutation in virus genome, while 2 cases had only one single mutation in N gene. Our study discovered that a combination of chest CT, SARS-CoV-2 RT-PCR and multi-plex PCR is recommended in regions outside Hubei province. Co-infection of other pathogens with SARS-CoV-2 exists and should be acknowledged. Repeated sampling, change of specimen type or metagenomics sequencing could further facilitate during critical clinical cases.