Clinical and Immunological Characteristics in COVID-19 Convalescent Patients (preprint)

Objective: The immune responses of COVID-19 convalescent patients have not been well described. Methods Blood from thirty COVID-19 convalescent patients who were virus-free were collected. Their clinical laboratory findings and SARS-CoV-2-specific humoral and cellular immunity were detected. Results At 283 days after diagnosis of SARS-CoV-2 infection, the levels of clinical laboratory indicators and lymphocyte subtypes returned to normal levels. However, the ratio of memory/naive CD4+ T lymphocytes cells was greater in COVID-19 convalescent patients and severe COVID-19 convalescent patients, when compared with that in healthy blood donors (P=0.0135) and non-severe patients (P=0.0431), respectively. The levels of anti-SARS-CoV-2-IgM (P=0.014), S1-IgM (P=0.0004) and RBD-IgM (P=0.0002) in severe COVID-19 patients were all significantly greater than those in non-severe COVID-19 patients. When the serums of COVID-19 convalescent patients were diluted as 1:125, the predictive of serum neutralization capabilities were persistent in all patients. SARS-CoV-2-specific T cells were generated and maintained in majority of tested convalescent COVID-19 patients, regardless of the severity of disease in acute phase. Conclusion At 283 days after diagnosis of SARS-CoV-2 infection, specific cellular and humoral immunity against SARS-CoV-2 could be detectable. The severity of disease in acute phase cannot affect the strength of cellular and humoral immunity in convalescent phase.

A bioactive peptide from the pearl has dual roles in resisting SARS-CoV-2 infection and its complications (preprint)

Angiotensin-converting enzyme 2 (ACE2) is a critical receptor for the entry of the SARS-CoV-2 virus into cells. Moreover, a decrease in ACE2 level and its activity due to SARS-CoV-2 infection is considered a crucial reason for the development of Covid-19-associated complications. Here, we report a bioactive peptide derived from the seawater pearl oyster Pinctada fucata, named SCOL polypeptide, which binds strongly to ACE2 and effectively inhibits 65% of the binding of the SARS-CoV-2 S protein to ACE2; thus, this peptide can be used as a blocker to enable cells to resist SARS-CoV-2 infection. The SCOL polypeptide also increases ACE2 enzyme activity by 3.76 times. Previous studies have shown that ACE2 deficiency is associated with inflammation, pain, cardiovascular diseases, insulin resistance, and nervous system injury. Therefore, the SCOL polypeptide can be used to treat or alleviate complications such as lung inflammation, pain, diabetes, cardiovascular diseases, and loss of taste or smell caused by SARS-CoV-2 infection. Thus, the SCOL polypeptide can play a dual role in resisting SARS-CoV-2 infection.

Discrimination of influenza A virus subtypes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Influenza is a contagious respiratory illness caused by influenza viruses which possess the enormous threat to older people and young children. Rapid and precise discrimination of virus subtypes are quite crucial for the early therapy, prophylaxis and the prevention of epidemic outbreaks. Herein, a universal strategy, with influenza A virus (IAV) as a model, is proposed for the discrimination of virus subtypes based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Reference library based on nine IAVs subtypes (i.e., H1N1, H3N2, H4N8, H5N8, H6N6, H7N7, H9N2, H10N8, and H11N8) was set up for matching various IAVs subtypes. The simulative test spectra from IAVs showed that the corresponding IAVs subtypes could be distinguished in 90 min, accurately. Furthermore, the principal component analysis results also show that nine virus subtypes can be reliably distinguished. More importantly, this strategy provides an alternative method for identifying and distinguishing other viruses with high variability characteristics, such as SARS-CoV-2, which could be helpful for implementing public health strategies to counter pandemics.

Monkeypox virus quadrivalent mRNA vaccine induces antibody responses and cellular immunity and protects mice against Vaccinia virus (preprint)

There is an urgent need for efficient and safe vaccines against the monkeypox virus (MPXV) in response to the rapidly spreading monkeypox epidemic. In the age of COVID-19, mRNA vaccines have been highly successful and emerged as platforms enabling rapid development and large-scale preparation. Here, we have developed two MPXV quadrivalent mRNA vaccines, named mRNA-A-LNP and mRNA-B-LNP, based on two IMVs (A29L and M1R) and two EEVs (A35R and B6R). By administering mRNA-A-LNP and mRNA-B-LNP intramuscularly twice, mice have induced MPXV-specific IgG antibodies and potent Vaccinia virus (VACV)-specific neutralizing antibodies. Additionally, it elicited durable MPXV-specific killer memory T-cell immunity as well as memory B-cell immunity in mice. Furthermore, the passive transfer of sera from mRNA-A-LNP and mRNA-B-LNP-immunized mice protected nude mice against the VACV challenge. In addition, two doses of mRNA-A-LNP and mRNA-B-LNP were also protective against the VACV challenge in mice. Overall, our results demonstrated that mRNA-A-LNP and mRNA-B-LNP appear to be safe and effective vaccine candidates against monkeypox epidemics, as well as against outbreaks caused by other orthopoxviruses, including the smallpox virus.

Dynamic changes in production of antibodies against SARS-CoV-2 based on three serological kits

We wished to understand the dynamic changes in production of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies in sera collected from coronavirus disease 19 (COVID-19) patients. Fifty-eight serum samples from 33 patients confirmed to have COVID-19 in Gansu Province, China, were tested for three types of SARS-CoV-2-specific antibodies: immunoglobulin (Ig) M, IgG, and total antibodies. The positive rate of IgM, IgG and total antibodies increased gradually with COVID-19 progression. Within the first 3 days, the positive rate of detection of SARS-CoV-2-specific antibody using the three kits was 13.6%-31.8%. whereas, within 4-7 days, it was 36.4%-45.5%, within 8-14 days it was 55.6%-77.8%, and after 15 days, it was 100%. In addition, the three kits were used to measure antibodies from serum samples collected from healthy people, and the specificity was 99%-100%. Statistical analyses indicated no significant difference among the results of the three kits (P > 0.05 for all). In summary, the three SARS-CoV-2 antibody-detection kits had good sensitivity and specificity for detection of antibodies against SARS-CoV-2, and could aid the clinical diagnosis of COVID-19. The dynamic characteristics of production of SARS-CoV-2- specific antibodies could provide important scientific bases for epidemiologic investigations.

Innovative technology-enhanced social work service during COVID-19: How ‘Garden on the Balcony’ promoted resilience, community bonds and a green lifestyle

The ongoing COVID-19 pandemic has motivated social workers to reckon with and transform traditions in service delivery. The development, application, and evaluation of technology-enhanced practices have become more vital than ever. Garden on the Balcony (GOB) was an innovative internet-based social work service designed to respond rapidly to the COVID-19 outbreak in Beijing. This paper introduces the underlying perspectives and design of GOB and reports participants’ reflections on the program to understand its mechanisms and implications. Interview data from GOB participants were collected 4 months after the program ended. Thematic analysis generated three major themes, suggesting that GOB had (a) promoted individual resilience and family cohesion;(b) built online and offline community bonds;and (c) cultivated a green lifestyle and spiritual reflection on life. This study demonstrates a practical example of the effective use of technology-enhanced practice. [ FROM AUTHOR] Copyright of Qualitative Social Work is the property of Sage Publications, Ltd. 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 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 . (Copyright applies to all s.)

Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2 (preprint)

Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to the poor stability, most current mRNA delivery platforms need to be stored at -20 {degrees}C or -70 {degrees}C. Here we present lyophilized thermostable mRNA loaded lipid nanoparticles, which could be stored at room temperature with long-term stability. We demonstrate the applicability of lyophilization techniques to different mRNA sequences and lipid components. Three lyophilized vaccines targeting wild-type, Delta and Omicron SARS-CoV-2 variant were prepared and demonstrated to be able induce high-level of IgG titer and neutralization response. In the Delta challenge in vivo experiment, the lyophilized mRNA vaccine successfully protected the mice from infection and clear the virus. This lyophilization platform could significantly improve the accessibility of mRNA vaccine or therapeutics, particularly in remote regions.

Construction of a potent pan-vaccine based on the evolutionary tendency of SARS-CoV-2 spike protein. (preprint)

SARS-CoV-2 continued to spread globally along with different variants. Here, we systemically analyzed viral infectivity and immune-resistance of SARS-CoV-2 variants to explore the underlying rationale of viral mutagenesis. We found that the Beta variant harbors both high infectivity and strong immune resistance, while the Delta variant is the most infectious with only a mild immune-escape ability. Remarkably, the Omicron variant is even more immune-resistant than the Beta variant, but its infectivity increases only in Vero E6 cells implying a probable preference for the endocytic pathway. A comprehensive analysis revealed that SARS-CoV-2 spike protein evolved into distinct evolutionary paths of either high infectivity plus low immune resistance or low infectivity plus high immune resistance, resulting in a narrow spectrum of the current single-strain vaccine. In light of these findings and the phylogenetic analysis of 2674 SARS-CoV-2 S-protein sequences, we generated a consensus antigen (S6) taking the most frequent mutations as a pan-vaccine against heterogeneous variants. As compared to the ancestry SWT vaccine with significantly declined neutralizations to emerging variants, the S6 vaccine elicits broadly neutralizing antibodies and full protections to a wide range of variants. Our work highlights the importance and feasibility of a universal vaccine strategy to fight against antigen drift of SARS-CoV-2.

SARS-CoV-2 ORF8 encoded protein contains a histone mimic, disrupts chromatin regulation, and enhances replication (preprint)

SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this new virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for the ability of a cell to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of the ARKS motif in histone 3. Orf8 is associated with chromatin, binds to numerous histone-associated proteins, and is itself acetylated within the histone mimic site. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) including H3K9ac, H3K9me3, and H3K27me3 and promotes chromatin compaction while Orf8 lacking the histone mimic motif does not. Further, SARS-CoV-2 infection in human cell lines and postmortem patient lung tissue cause these same disruptions to chromatin. However, deletion of the Orf8 gene from SARS-CoV-2 largely blocks its ability to disrupt host-cell chromatin indicating that Orf8 is responsible for these effects. Finally, deletion of the ORF8 gene affects the host-cell transcriptional response to SARS-CoV-2 infection in multiple cell types and decreases the replication of SARS-CoV-2 in human induced pluripotent stem cell-derived lung alveolar type 2 (iAT2) pulmonary cells. These findings demonstrate a novel function for the poorly understood ORF8-encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Finally, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.

Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China (preprint)

At the end of 2019 Wuhan witnessed an outbreak of “atypical pneumonia” that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus - SARS-CoV-2. Herein, to provide a snapshot of the pathogens in pneumonia-associated respiratory samples from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid samples from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their “total infectome”, including viruses, bacteria and fungi. Consequently, we identified 37 pathogen species, comprising 15 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (12.8%). However, SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen – Chlamydia psittaci . Samples from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of individual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more diverse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016-2017.

Broad neutralizing nanobody against SARS-CoV-2 engineered from pre-designed synthetic library (preprint)

SARS-CoV-2 infection is initiated with Spike glycoprotein binding to the receptor of human angiotensin converting enzyme 2 via its receptor binding domain. Blocking this interaction is considered as an effective approach to inhibit virus infection. Here we report the discovery of a neutralizing nanobody, VHH60, directly produced from a humanized synthetic nanobody library. VHH60 competes with human ACE2 to bind the receptor binding domain of the Spike protein with a KD of 2.56 nM, inhibits infections of both live SARS-CoV-2 and pseudotyped viruses harboring wildtype, escape mutations and prevailing variants at nanomolar level. VHH60 also suppresses SARS-CoV-2 infection and propagation 50-fold better and protects mice from death two times longer than that of control group after live virus inoculation on mice. VHH60 therefore is a powerful synthetic nanobody with a promising profile for disease control against COVID19.

Discussion on the change of cold-dampness and retained fluid blocking lung with fire deficiency of mingmen (the gate of life) in severe patients with Coronavirus disease 2019

Traditional Chinese Medicine (TCM) practitioners have deepened their understanding of the disease theory with the gradually increasing degree of clinical intervention of coronavirus disease 2019 (COVID-19). Especially, "Dampness Toxin" as the core of TCM pathogenesis has reached consensus. However, the comprehension on the pathogenesis and transmission laws of COVID-19 still need to be quickly improved in order to promote optimization to form a more effective common regimen for diagnosis and treatment of TCM on COVID-19. The author's team based on first-line clinical and academic data verified the cause and proposed that "cold-dampness and retained fluid blocking lung with fire deficiency of Mingmen" be important pathogenesis of severe patients with COVID-19. And the treatment principle should follow "ruling water with fire, and treating tri-jiao simultaneously". The prescription should refer to Shegan Mahuang Decoction, Zhenwu Decoction, Fuzi Lizhong Decoction and other formulas to warm tri- jiao, which aims to consolidate the essence of human body. "Detoxification, dredging six-Fu organs and diuresis" also need to be considered to alleviate the symptoms at the same time. This regimen reflects the consideration of both the symptoms and causes, the combination of cold and warm medicinal herbs, tonification and purgation in combination, flexibility in syndrome differentiation and prescription and careful grasp of the balance of the property of herbs, which can provide a reference for clinical diagnosis and treatment on COVID-19.

Antibody neutralization to SARS-CoV-2 and variants after one year in Wuhan (preprint)

Most COVID-19 patients can build effective humoral immunity against SARS-CoV-2 after recovery . However, it remains unknown how long the protection can maintain and how efficiently it can protect people from the reinfection of the emerging SARS-CoV-2 variants. Here we evaluated the sera from 248 COVID-19 convalescents around one year post-infection in Wuhan, the earliest epicenter of SARS-CoV-2. We demonstrated that the SARS-CoV-2 immunoglobulin G (IgG) maintains at a high level and potently neutralizes the infection of the original strain (WT) and the B.1.1.7 variant in most patients. However, they showed varying degrees of efficacy reduction against the other variants of concern (P.1, B.1.525, and especially B.1.351) in a patient-specific manner. Mutations in RBD including K417N, E484K, and E484Q/L452R (B.1.617) remarkably impair the neutralizing activity of the convalescents' sera. Encouragingly, we found that a small fraction of patients' sera showed broad neutralization potency to multiple variants and mutants, suggesting the existence of broadly neutralizing antibodies recognizing the epitopes beyond the mutation sites. Our results suggest that the SARS-CoV-2 vaccination effectiveness relies more on the timely re-administration of the epitope-updated vaccine than the durability of the neutralizing antibodies.

Assessing the Effectiveness of Mass Testing and Quarantine in the Spread of COVID-19 in Beijing and Xinjiang, 2020

Coronavirus disease (COVID-19) cases and COVID-19-related deaths have been increasing worldwide since the outbreak in 2019. Before the mass vaccination campaign for COVID-19, the main methods for COVID-19 control in China were mass testing and quarantine. Based on the transmission mechanism of COVID-19, we constructed a dynamic model for COVID-19 transmission in two typical regions: Beijing and Xinjiang. We calculated the basic reproduction number R0, proved the global stability of COVID-19 transmission via the Lyapunov function technique, and introduced the final size. We assessed the effectiveness of mass testing and quarantine. Sensitivity analysis indicated that the more the people were tested per day, the larger is the quarantine proportionality coefficient, the earlier the source location was determined, and the better is the controlling effect. In addition, it was more effective to increase the coefficient of quarantine if the population density in the region was low. To eliminate the pandemic, the government has to expand testing and quarantine, requiring a large amount of continuous manpower, material, and financial resources. Therefore, new control measures should be developed.

An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City (preprint)

Epidemiological models can provide the dynamic evolution of a pandemic but they are based on many assumptions and parameters that have to be adjusted over the time when the pandemic lasts. However, often the available data are not sufficient to identify the model parameters and hence infer the unobserved dynamics. Here, we develop a general framework for building a trustworthy data-driven epidemiological model, consisting of a workflow that integrates data acquisition and event timeline, model development, identifiability analysis, sensitivity analysis, model calibration, model robustness analysis, and forecasting with uncertainties in different scenarios. In particular, we apply this framework to propose a modified susceptible-exposed-infectious-recovered (SEIR) model, including new compartments and model vaccination in order to forecast the transmission dynamics of COVID-19 in New York City (NYC). We find that we can uniquely estimate the model parameters and accurately predict the daily new infection cases, hospitalizations, and deaths, in agreement with the available data from NYC's government's website. In addition, we employ the calibrated data-driven model to study the effects of vaccination and timing of reopening indoor dining in NYC.

SARS-CoV-2 protein encoded by ORF8 contains a histone mimic that disrupts chromatin regulation (preprint)

SARS-CoV-2 emerged in China at the end of 2019 and caused the global pandemic of COVID-19, a disease with high morbidity and mortality. While our understanding of this novel virus is rapidly increasing, gaps remain in our understanding of how SARS-CoV-2 can effectively suppress host cell antiviral responses. Recent work on other viruses has demonstrated a novel mechanism through which viral proteins can mimic critical regions of human histone proteins. Histone proteins are responsible for governing genome accessibility and their precise regulation is critical for a cell’s ability to control transcription and respond to viral threats. Here, we show that the protein encoded by ORF8 (Orf8) in SARS-CoV-2 functions as a histone mimic of two critical histone 3 sites containing an ARKS motif. Orf8 expression in cells disrupts multiple critical histone post-translational modifications (PTMs) while Orf8 lacking this histone mimic motif does not. Orf8 binds to numerous histone-associated proteins and to DNA, and is itself acetylated within the histone mimic site. Importantly, SARS-CoV-2 infection of multiple susceptible cell types causes the same global changes of histone post-translational modifications that are disrupted by Orf8 expression; these include induced pluripotent stem cell-derived alveolar type 2 cells (iAT2) and cardiomyocytes (iCM) and postmortem patient lung tissue. These findings demonstrate a novel function for the poorly understood SARS-CoV-2 ORF8 encoded protein and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Notably, this work provides a potential mechanism for emerging findings from human patients indicating that ORF8 deletion results in less severe illness and describes a potentially druggable pathway that may contribute to the virulence of SARS-CoV-2.

Regional Impacts of COVID-19 on Carbon Dioxide Detected Worldwide from Space (preprint)

Activity reductions in early 2020 due to the Coronavirus Disease 2019 pandemic led to unprecedented decreases in carbon dioxide (CO2) emissions. Despite their record size, the resulting atmospheric signals are smaller than and obscured by climate variability in atmospheric transport and biospheric fluxes, notably that related to the 2019-2020 Indian Ocean Dipole. Monitoring CO2 anomalies and distinguishing human and climatic causes thus remains a new frontier in Earth system science. We show, for the first time, that the impact of short-term, regional changes in fossil fuel emissions on CO2 concentrations was observable from space. Starting in February and continuing through May, column CO2 over many of the World's largest emitting regions was 0.14 to 0.62 parts per million less than expected in a pandemic-free scenario, consistent with reductions of 3 to 13 percent in annual, global emissions. Current spaceborne technologies are therefore approaching levels of accuracy and precision needed to support climate mitigation strategies with future missions expected to meet those needs.

Re-positive discharged COVID-19 patients are at low transmission risk for SARS-CoV-2 infection– a finding from recovered COVID-19 patients in Wuhan, China (preprint)

Discharged COVID-19 patients have been found to be retested positive for SARS-CoV-2 (re-positive), which has widely raised concern among the public. We investigated the prevalence and transmission risk of re-positive cases in discharged COVID-19 patients and their SARS-CoV-2-specific antibody levels in Wuhan, China. Of 1065 discharged COVID-19 patients investigated, 518 (48.64%) patients were males; the mean age was 53.29 ± 14.91 years, with a median duration of 40 (IQR: 31–47) days since discharge. 63 patients were tested re-positive for SARS-CoV-2, with the re-positive prevalence to be 5.92% (95%CI: 4.50%-7.33%). The re-positive prevalence was higher in females (7.86%, 95%CI: 5.61%-10.12%) than that in males (3.86%, 95%CI: 2.20%-5.52%, P = 0.006). Re-positive prevalence was similar in patients tested positive and negative for IgG (6.01% vs 5.56%, P = 0.821) or IgM (6.38% vs 5.07%, P = 0.394). Illness severity and duration from illness onset to retest were not associated with the risk of positive results for SARS-CoV-2 after discharge. All 196 environmental samples collected from 49 re-positive patients were tested negative for SAR-CoV-2. Only one close contact to the re-positive patient had been tested positive for SARS-CoV-2; however, he might be a previous COVID-19 case but had not been detected before. Viral culture of 6 nasopharyngeal specimens presented no cytopathic effect of Vero E6 cells. Virus sequencing of 11 nasopharyngeal specimens indicated genomic fragments of SARS-CoV-2. 898 (84.72%) patients and 705 (66.51%) patients were tested positive for SARS-CoV-2-specific IgG and IgM, respectively. Self-report symptoms at the survey were similar, regardless of the level of antibody. All the re-positive patients and their matched non-re-positive patients were tested negative for SARS-CoV-2 four months later. These findings indicate that Testing re-positive of SARS-CoV-2 is common in discharged COVID-19 patients, but no evidence showed the transmission risk of these re-positive cases. Further isolation of recovered COVID-19 patients is unnecessary. However, only 85% recovered COVID-19 patients had SARS-CoV-2-specific antibody, which suggested discharged COVID-19 patients still had potential re-infection risk.