Isolation and Characterization of Porcine Sapelovirus from the PDCoV-Positive Sample and Its Molecular Epidemiology in Henan Province, China

Porcine sapelovirus (PSV) is an emerging swine enteric virus that can cause various disorders including acute diarrhea, respiratory distress, reproductive failure, and polioencephalomyelitis in pigs. In this study, we isolated a PSV strain HNHB-01 from a clinical porcine deltacoronavirus- (PDCoV-) positive intestinal content of a diarrheic piglet. PSV was first identified using the small RNA deep sequencing and assembly, and further identified by the electron microscopic observation and the immunofluorescence assay. Subsequently, this virus was serially passaged in swine testis (ST) cells, and the complete genomics of PSV HNHB-01 passage 5 (P5), P30, P60, and P100 were sequenced and analyzed. 9 nucleotide mutations and 7 amino acid changes occurred in the PSV HNHB-01 P100 strain when compared with the PSV HNHB-01 P5. Pathogenicity investigation showed that orally inoculation of PSV HNHB-01 P30 could cause obvious clinical symptoms and had broad tissue tropism in 5-day-old piglets. Epidemiological investigation revealed that PSV infections and the coinfections of diarrhea coronaviruses were highly prevalent in swine herds. The complete genomes of 8 representative PSV epidemic strains were sequenced and analyzed. Phylogenetic analysis revealed that the PSV epidemic strains were closely related to other PSV reference strains that located in the Chinese clade. Furthermore, recombination analysis revealed that the recombination events were occurred in downstream of the 2C region in our sequenced PSV HNNY-02/CHN/2018 strain. Our results provided theoretical basis for future research studies of the pathogenic mechanism, evolutionary characteristics, and the development of vaccines against PSV.

Evaluating the Effect of SARS-CoV-2 Spike Mutations by Causal Inference (preprint)

Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, which necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a principled framework of causal inference for evaluating Spike mutations. In the context of large-scale genomes of SARS-CoV-2, it estimates the contribution of mutations to viral fitness across lineages and validates mutational effects on the Spike stability, receptor-binding affinity, and potential for immune escape. Key fitness-enhancing mutations and protein regions are recognized and studied. The transmission capacity of any new variant possessing these mutations can be predicted based on our model, solely based on the viral sequence. This research produces an innovative and systematic insight into SARS-CoV-2 and promotes functional studies of its key mutations.

Susceptibility to mice and potential evolutionary characteristics of porcine deltacoronavirus.

Porcine deltacoronavirus (PDCoV) is a novel coronavirus that causes diarrhea in suckling piglets and has the potential for cross-species transmission, posing a threat to animal and human health. However, the susceptibility profile of different species of mice to PDCoV infection and its evolutionary characteristics are still unclear. In the current study, we found that BALB/c and Kunming mice are susceptible to PDCoV. Our results showed that there were obvious lesions in intestinal and lung tissues from the infected mice. PDCoV RNAs were detected in the lung, kidney, and intestinal tissues from the infected mice of both strains, and there existed wider tissue tropism in the PDCoV-infected BALB/c mice. The RNA and protein levels of aminopeptidase N from mice were relatively high in the kidney and intestinal tissues and obviously increased after PDCoV infection. The viral-specific IgG and neutralizing antibodies against PDCoV were detected in the serum of infected mice. An interesting finding was that two key amino acid mutations, D138H and Q641K, in the S protein were identified in the PDCoV-infected mice. The essential roles of these two mutations for PDCoV-adaptive evolution were confirmed by cryo-electron microscope structure model analysis. The evolutionary characteristics of PDCoV among Deltacoronaviruses (δ-CoVs) were further analyzed. δ-CoVs from multiple mammals are closely related based on the phylogenetic analysis. The codon usage analysis demonstrated that similar codon usage patterns were used by most of the mammalian δ-CoVs at the global codon, synonymous codon, and amino acid usage levels. These results may provide more insights into the evolution, host ranges, and cross-species potential of PDCoV.

Feasibility of Specimen Self-collection in Young Children Undergoing SARS-CoV-2 Surveillance for In-Person Learning.

Importance: There is an urgent need to assess the feasibility of COVID-19 surveillance measures in educational settings. Objective: To assess whether young children can feasibly self-collect SARS-CoV-2 samples for surveillance testing over the course of an academic year. Design, Setting, and Participants: This prospective pilot cohort study was conducted from September 10, 2020, to June 10, 2021, at a K-8 school in San Mateo County, California. The research consisted of quantitative data collection efforts: (1) demographic data collected, (2) student sample self-collection error rates, and (3) student sample self-collection time durations. Students were enrolled in a hybrid learning model, a teaching model in which students were taught in person and online, with students having the option to attend virtually as needed. Data were collected under waiver of consent from students participating in weekly SARS-CoV-2 testing. Main Outcomes and Measures: Errors over time for self-collection of nasal swabs such as contaminated swabs and inadequate or shallow swabbing; time taken for sample collection. Results: Of 296 participants, 148 (50.0%) were boys and 148 (50.0%) were girls. A total of 87 participants (29.2%) identified as Asian; 2 (0.6%), Black or African American; 13 (4.4%), Hispanic/Latinx; 103 (34.6%), non-Hispanic White; 87 (29.2%), multiracial; and 6 (2.0%), other. The median school grade was fourth grade. From September 2020 to March 2021, a total of 4203 samples were obtained from 221 students on a weekly basis, while data on error rates were collected. Errors occurred in 2.7% (n = 107; 95% CI, 2.2%-3.2%) of student encounters, with the highest rate occurring on the first day of testing (20 [10.2%]). There was an overall decrease in error rates over time. From April to June 2021, a total of 2021 samples were obtained from 296 students on a weekly basis while data on encounter lengths were collected. Between April and June 2021, 193 encounters were timed. The mean duration of each encounter was 70 seconds (95% CI, 66.4-73.7 seconds). Conclusions and Relevance: Mastery of self-collected lower nasal swabs is possible for children 5 years and older. Testing duration can be condensed once students gain proficiency in testing procedures. Scalability for larger schools is possible if consideration is given to the resource-intensive nature of the testing and the setting's weather patterns.

Herpetic Keratitis Preceded by COVID-19 Vaccination.

The global Coronavirus Disease 2019 (COVID-19) pandemic has accelerated vaccine development at an unprecedented rate. A large population of people have received COVID-19 vaccines, while the vaccine safety data are limited. Here, we reported two cases of herpetic keratitis that occurred soon after receiving the inactivated COVID-19 vaccines. Case 1 was a 60-year-old woman who underwent penetrating keratoplasty (PKP) one year ago for corneal scarring caused by herpes simplex keratitis (HSK), and case 2 was a 51-year-old man with an unremarkable medical history. Both patients developed herpetic keratitis (HSK and varicella-zoster virus corneal endotheliitis, respectively) soon after receiving the inactivated COVID-19 vaccines (Sinovac). Herpetic keratitis was treated successfully with topical or plus oral antiviral ganciclovir. The short latency time in these two cases suggested that an inactivated COVID-19 vaccine may have a risk of triggering ocular herpes virus reactivation. Both clinicians and patients should be aware of this phenomenon. However, a causal relationship awaits confirmation.

Global Mutational Sweep of SARS-CoV-2: from Chaos to Order (preprint)

Analysis of large-scale genome sequences demonstrates the mutation of SARS-CoV-2 has been undergoing significant sweeps. Driven by emerging variants, global sweeps are accelerated and purified over time. This may prolong the pandemic with repeating epidemics, presenting challenges to the control and prevention of SARS-CoV-2.

15-Month Health Outcomes of Hospitalized COVID-19 Patients from Onset: A Cohort Study (preprint)

Background: The long-term impact of COVID-19 on patient health has been a recent focus. This study aims to determine the persistent symptoms and psychological conditions of patients hospitalized with COVID-19 15 months after onset. The potential risk factors were also explored.Methods: A cohort of COVID-19 patients discharged from February 20, 2020 to March 31, 2020 was recruited. Follow-ups were conducted using validated questionnaires and psychological screening scales at 15 months after onset to evaluate the patients’ health status. The risk factors for long-term health impacts and their associations with disease severity was analyzed.Findings: 534 COVID-19 patients were enrolled. The median age of the patients was 62.0 years old (IQR 52.0-70.0) and 295 were female (55.2%). The median time from onset to follow-up was 460.0 (451.0-467.0) days. Sleep disturbance (18.5%, 99/534) and fatigue (17.2%, 92/534) were the most common persistent symptoms. 6.4% (34/534) of the patients had depression, 9.2% (49/534) were anxious, 13.0% (70/534) had insomnia and 4.7% (25/534) suffered from posttraumatic stress disorder (PTSD). Multivariate adjusted logistic regression analysis showed that glucocorticoid use during hospitalization (OR 3.58, 95% CI 1.12-11.44) was significantly associated with an increased risk of fatigue. The OR values for anxiety and sleep disorders were 2.36 (95% CI 1.07-5.20) and 2.16 (95% CI 1.13-4.14) in females compared with males. The OR value of PTSD was 25.6 (95% CI 3.3-198.4) in patients with persistent symptoms to those without persistent symptoms. No significant associations were observed between fatigue syndrome or adverse mental outcomes and disease severity.Interpretation: 15-month follow-up in this study aroused the need of extended rehabilitation intervention for complete recovery in COVID-19 patients. Funding: None to declare. Declaration of Interest: All the authors declare no competing interests.Ethical Approval: The Research Ethics Committee of Shanghai Changzheng Hospital approved this study (2020SL007).

Patients with COVID- 19 testing positive for nucleic acids of SARS-CoV -2 in re-examination after discharge from hospital: an analysis of three cases

Detection of the nucleic acids (NAs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the "gold standard" for diagnosis of coronavirus disease 2019 (COVID-19). Antibody detection in serum is an important auxiliary method. We undertook retrospective analyses of the results of NA detection and antibody detection in the diagnosis, treatment and isolation of COVID-19 patients at the beginning of the disease as well as upon discharge from hospital. We offered a preliminary discussion on the correlation between NA detection and antibody detection and the infectious factors of COVID-19. Our study can provide a reference for monitoring SARS -CoV-2 infection in the treatment and rehabilitation of patients with COVID-19.

COVID-19 Diagnostic Testing For All - Using Non-Dilutive Saliva Sample Collection, Stabilization and Ambient Transport Devices (preprint)

Covid-19 testing is not accessible for millions during this pandemic despite our best efforts. Without greatly expanded testing of asymptomatic individuals, contact tracing and subsequent isolation of spreaders remains unobtainable as a means for control. In an effort to increase RT-PCR assay testing for the presence of the novel beta-coronavirus SARS-CoV-2 as well as improve sample collection safety, GenTegra LLC has introduced two products for saliva collection and viral RNA stabilization: GTR-STM (GenTegra Saliva Transport Medium) and GTR-STMdk (GenTegra Saliva Transport Medium Direct to PCR). Both products contain a proprietary formulation based on GenTegra's novel "Active Chemical ProtectionTM" (ACP) technology that gives non-dilutive, error-free saliva sample collection using RNA stabilization chemicals already dried in the collection tube. GTR-STM can be used for safer saliva-based sample collection at home (or at a test site). Following saliva collection, the sample-containing GTR-STM can be kept at ambient temperature during shipment to an authorized CLIA lab for analysis. SARS-CoV-2 viral RNA in GTR-STM is stable for over a month at ambient temperature, easily surviving the longest transit times from home to lab. GTR-STM enhances patient comfort, convenience, compliance and reduces infectious virus exposure to essential medical and lab professionals. Alternatively, the GTR-STMdk direct-into-PCR product can be used to improve lab throughput and reduce reagent costs for saliva sample collection and testing at any lab site with access to refrigeration. GTR-STMdk reduces lab process time by 25% and reagent costs by 30% compared to other approaches. Since GTR-STMdk retains SARS-CoV-2 viral RNA stability for three days at ambient temperature, it is optimized for lab test site rather than at home saliva collection. SARS-COV-2 viral RNA levels as low as 0.4 genome equivalents/uL are detected in saliva samples using GTR-STMdk. This increased sensitivity of SARS-CoV-2 detection can expand Covid-19 testing to include asymptomatic individuals using pooled saliva. The formal Limit of Detection (LoD) of SARS-CoV-2 in GTR-STM and GTR-STMdk in human saliva in individual and pooled samples will shortly be known.

MicroRNA-760 Resists Ambient PM2.5-induced Lung Injury Through Upregulating Heme-oxygenase 1 Expression (preprint)

Background: PM2.5 (particles matter smaller aerodynamic diameter of 2.5 μm ) exposure, as one major environmental risk factor for the global burden of disease, is associated with high risks of respiratory diseases and lung cancer. Heme-oxygenase 1 (HMOX1) has been considered as one of the major molecular antioxidant defenses to mediate cytoprotective effects against diverse stressors, including PM2.5-induced toxicity and SARS-CoV-2 infection; however, the regulatory mechanism of HMOX1 expression still needs to be elucidated. In this study, using PM2.5 as a typical stressor, we explored whether microRNAs (miRNAs) might modulate HMOX1 expression in lung cells. Results: Systematic bioinformatics analysis showed that seven miRNAs have the potential to target HMOX1 gene. Among these, hsa-miR-760 was identified as a response miRNA to PM2.5 exposure. More importantly, we revealed a “non-conventional” miRNA function in hsa-miR-760 upregulating HMOX1 expression, by targeting the coding region and interacting with YBX1 protein. In addition, we observed that exogenous hsa-miR-760 effectively elevated HMOX1 expression, reduced the reactive oxygen agents (ROS) levels, and then rescued the lung cells from PM2.5-induced apoptosis. Conclusion: Our results revealed that hsa-miR-760 might play an important role in protecting lung cells against PM2.5-induced toxicity, by elevating HMOX1 expression, and offered new clues to elucidate the diverse function of miRNAs.

Impact of the shift to a fibrinolysis-first strategy on care and outcomes of patients with ST-segment-elevation myocardial infarction during the COVID-19 pandemic-The experience from the largest cardiovascular-specific centre in China.

BACKGROUND: The impact of fibrinolysis-first strategy on outcomes of patients with ST-segment-elevation myocardial infarction (STEMI) during the COVID-19 pandemic was unknown. METHODS: Data from STEMI patients presenting to Fuwai Hospital from January 23 to April 30, 2020 were compared with those during the equivalent period in 2019. The primary end-point was net adverse clinical events (NACE; a composite of death, non-fatal myocardial reinfarction, stroke, emergency revascularization, and bleeding over BARC type 3). The secondary outcome was a composite of recurrent ischaemia, cardiogenic shock, and exacerbated heart failure. RESULTS: The final analysis included 164 acute STEMI patients from 2020 and 240 from 2019. Eighteen patients (20.2% of those with indications) received fibrinolysis therapy in 2020 with a median door-to-needle time of 60.0 (43.5, 92.0) minutes. Patients in 2020 underwent primary PCI less frequently than their counterparts (14 [14.2%] vs. 144 [86.8%] in 2019, P < 0.001), and had a longer median door-to-balloon time (175 [121,213] minutes vs. 115 [83, 160] minutes in 2019, P = 0.009). Patients were more likely to undergo elective PCI (86 [52.4%] vs. 28 [11.6%] in 2019, P < 0.001). The in-hospital NACE was similar between 2020 and 2019 (14 [8.5%] vs. 25 [10.4%], P = 0.530), while more patients developed a secondary outcome in 2020 (20 [12.2%] vs. 12 [5.0%] in 2019, P = 0.009). CONCLUSIONS: The fibrinolysis-first strategy during the COVID-19 pandemic was associated with a lower rate of timely coronary reperfusion and increased rates of recurrent ischaemia, cardiogenic shock, and exacerbated heart failure. However, the in-hospital NACE remained similar to that in 2019.

Advantages of anti-inflammatory acupuncture in treating sepsis of coronavirus disease 2019

Background: Sepsis is one of the most serious complications and a leading cause of death in patients with coronavirus disease 2019 (COVID-19). In general, it is the result of an unregulated inflammatory cascade such as a postinfection 'cytokine storm.' The conventional treatment mainly relies on glucocorticoids, of which curative effects are not ideal, as they come with significant side effects. It is critical to seek or develop other effective therapeutics in dealing cytokine storm to fight COVID-19 with sepsis. Aims and Objectives: Raise awareness of the significance applying anti-inflammatory acupuncture in dealing COVID-19 patients with sepsis and provide an appropriate acupuncture protocol that can be easily integrated into existing medical guideline. Materials and Methods: Current evidences from animal experiments and clinical trials about acupuncture in treating infectious sepsis are reviewed, and a detailed discussion on advantages of anti-inflammatory acupuncture is followed, then the rationality on the point selection and stimulation parameters of acupuncture is analyzed to propose an appropriate acupuncture protocol. Results: Current experiments have shown that acupuncture can play a significant role to improve inflammation reaction and reduce mortality in infectious animal and patients with sepsis and its mechanisms are mainly achieved by stimulating the vagus-cholinergic anti-inflammatory pathways. Applying acupuncture in treating COVID-19 patients with sepsis has four aspects of advantages. Moreover, a simple and convenient clinical acupuncture protocol including point selection and appropriate stimulation parameters is proposed. Conclusion: Acupuncture, especially electroacupuncture, has shown potentials in effectively treating infectious sepsis of animal models and critically ill patients in small sample studies by stimulating the nervous system, but has been largely overlooked in the clinic so far. It is advised that acupuncture should be integrated into the existing medical guidelines in dealing with COVID-19 complicated with sepsis.

Evolving global and national criteria for identifying a suspected case of COVID-19.

BACKGROUND: The outbreak of coronavirus disease 2019 (COVID-19) began in December 2019 and continues to spread worldwide. Rapid and accurate identification of suspected cases is critical in slowing spread of the virus that causes the disease. We aimed to highlight discrepancies in the various criteria used by international agencies and highly impacted individual countries around the world. METHODS: We reviewed the criteria for identifying a suspected case of COVID-19 used by two international public health agencies and 10 countries across Asia, Europe, and North America. The criteria included information on the clinical causes of illness and epidemiological risk factors. Non-English language guidelines were translated into English by a co-author who is fluent in that particular language. RESULTS: Although most criteria are modifications of World Health Organization recommendations, the specific clinical features and epidemiological risks for triggering evaluation of patients with suspected COVID-19 differed widely among countries. The rationale for these differences may be related to each country's resources, politics, experience with previous outbreaks or pandemics, health insurance system, COVID-19 outbreak severity, and other undetermined factors. CONCLUSION: We found no consensus regarding the best diagnostic criteria for identifying a suspected case of COVID-19.

Predictive symptoms and comorbidities for severe COVID-19 and intensive care unit admission: a systematic review and meta-analysis.

OBJECTIVES: COVID-19 has a varied clinical presentation. Elderly patients with comorbidities are more vulnerable to severe disease. This study identifies specific symptoms and comorbidities predicting severe COVID-19 and intensive care unit (ICU) admission. METHODS: A literature search identified studies indexed in MEDLINE, EMBASE and Global Health before 5th March 2020. Two reviewers independently screened the literature and extracted data. Quality appraisal was performed using STROBE criteria. Random effects meta-analysis identified symptoms and comorbidities associated with severe COVID-19 or ICU admission. RESULTS: Seven studies (including 1813 COVID-19 patients) were included. ICU patients were older (62.4 years) than non-ICU (46 years), with a greater proportion of males. Dyspnoea was the only symptom predictive for severe disease (pOR 3.70, 95% CI 1.83-7.46) and ICU admission (pOR 6.55, 95% CI 4.28-10.0). COPD was the strongest predictive comorbidity for severe disease (pOR 6.42, 95% CI 2.44-16.9) and ICU admission (pOR 17.8, 95% CI 6.56-48.2), followed by cardiovascular disease and hypertension. CONCLUSIONS: Dyspnoea was the only symptom predictive for severe COVID-19 and ICU admission. Patients with COPD, cardiovascular disease and hypertension were at higher risk of severe illness and ICU admission.