Immunities Specific to Both of the M Protein Ectodomain and RBD Synergize to Confer Cross-protection against SARS-CoV-2 Infections (preprint)

The effectiveness of the prototypic SARS-CoV-2 vaccine largely decreased overtime against the emerging virus strains, necessitating the universal vaccine development. The most abundant structural membrane (M) protein is highly conserved in amino acid sequence, which arouses our research interests in developing a universal immunogen based on it. Serological analysis showed that IgG responses specific to its N-terminal peptides can be strongly detected in many serum samples from both convalescent patients and vaccinees receiving inactivated vaccines, indicating the potential existence of human B-cell epitopes in reactive peptides. Microneutralization assays showed that the N-terminal peptide S2M2-30-specific hyperimmune serum was capable of cross-neutralizing the authentic viruses including wild-type HKU-001a, B.1.617.2/Delta, and Omicron subvariant BQ.1.1, and synergized with RBD-specific serum in reinforcing antiviral activities. Strong S2M2-30-specific immunities elicited in hACE2-transgenic mice could effectively inhibit B.1.1.7/Alpha (UK) infections. Our results suggest the potentiality of conserved M peptides as vaccine targets for conferring cross-protections against sarbecoviruses.

Human Early Syncytiotrophoblasts Are Highly Susceptible to SARS-CoV-2 Infection (preprint)

The ongoing and devastating pandemic of coronavirus disease 2019 (COVID-19) has led to a global public health crisis. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and can potentially pose a serious risk to maternal and neonatal health. Cases of abnormal pregnancy and vertical transmission of SARS-CoV-2 from mother to foetus have been reported but no firm conclusions are drawn. Trophoblasts are the major constituents of the placenta to protect and nourish the developing foetus. However, direct in vivo investigation of trophoblast susceptibility to SARS-CoV-2 and of COVID-19 and pregnancy is challenging. Here we report that human early syncytiotrophoblasts (eSTBs) are highly susceptible to SARS-CoV-2 infection in an angiotensin-converting enzyme 2 (ACE2)-dependent manner. From human expanded potential stem cells (hEPSCs), we derived bona fide trophoblast stem cells (TSCs) that resembled those originated from the blastocyst and the placenta in generating functional syncytiotrophoblasts (STBs) and extravillus trophoblasts (EVTs) and in low expression of HLA-A/B and amniotic epithelial (AME) cell signature. The EPSC-TSCs and their derivative trophoblasts including trophoblast organoids could be infected by SARS-CoV-2. Remarkably, eSTBs were highly susceptible to SARS-CoV-2. They expressed high levels of ACE2 and produced substantially higher amounts of virion than Vero E6 cells which are widely used in SARS-CoV-2 research and vaccine production. These findings provide experimental evidence for the clinical observations that opportunistic SARS-CoV-2 infection during pregnancy can occur. At low concentrations, two well characterized antivirals, remdesivir and GC376, effectively eliminated infection of eSTBs by SARS-CoV-2 and middle east respiratory syndrome-related coronavirus (MERS-CoV), and rescued their developmental arrest caused by the virus infection. Several human cell lines have been used in coronavirus research. However, they suffer from genetic and/or innate immune defects and have some of the long-standing technical challenges such as cell transfection and genetic manipulation. In contrast, hEPSCs are normal human stem cells that are robust in culture, genetically stable and permit efficient gene-editing. They can produce and supply large amounts of physiologically relevant normal and genome-edited human cells such as eSTBs for isolation, propagation and production of coronaviruses for basic research, antiviral drug tests and safety evaluation.

The evolution of structural resilience of global oil and gas resources trade network

This paper establishes anetwork resilience evaluation framework of the global oil and gas resourcetrade network in 2010, 2015 and 2020. The results are as follows: The links of the oil trade network present a gradually shrinking trend, and the gas tradenetwork presents a trend of close connection first and then reduced. In termsof network density, network centrality, network connectivity and network size, the structural resilience of the oil and gas resource trade network displays ashrinking trend, and the gas trade network is superior. Concerninginvulnerability and recovery, the resilience of the oil trade network issuperior to the natural gas trade network. In simulated attacks, the oil tradenetwork reveals a higher resilience towards intentional attacks, and the gastrade network shows a higher resilience towards random attacks. The Strait ofHormuz and the Strait of Malacca are critical chokepoints in the networks.

Identified human breastmilk compositions effectively inhibit SARS-CoV-2 and variants infection and replication

The global pandemic of COVID-19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection confers great threat to the public health. Human breastmilk is a complex with nutritional composition to nourish infants and protect them from different kinds of infectious diseases including COVID-19. Here, we identified lactoferrin (LF), mucin1 (MUC1) and α-lactalbumin (α-LA) from human breastmilk inhibit SARS-CoV-2 infection using a SARS-CoV-2 pseudovirus system and transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP). Additionally, LF and MUC1 inhibited multiple steps including viral attachment, entry and post-entry replication, while α-LA inhibited viral attachment and entry. Importantly, LF, MUC1 and α-LA possessed potent antiviral activities towards variants such as B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.1 (kappa). Taken together, our study provides evidence that human breastmilk components (LF, MUC1 and α-LA) are promising antiviral and potential therapeutic candidates warranting further development or treating COVID-19. Graphical

The SARS-CoV-2 Omicron (B.1.1.529) variant exhibits altered pathogenicity, transmissibility, and fitness in the golden Syrian hamster model (preprint)

The newly emerging SARS-CoV-2 Omicron (B.1.1.529) variant first identified in South Africa in November 2021 is characterized by an unusual number of amino acid mutations in its spike that renders existing vaccines and therapeutic monoclonal antibodies dramatically less effective. The in vivo pathogenicity, transmissibility, and fitness of this new Variant of Concerns are unknown. We investigated these virological attributes of the Omicron variant in comparison with those of the currently dominant Delta (B.1.617.2) variant in the golden Syrian hamster COVID-19 model. Omicron-infected hamsters developed significantly less body weight losses, clinical scores, respiratory tract viral burdens, cytokine/chemokine dysregulation, and tissue damages than Delta-infected hamsters. The Omicron and Delta variant were both highly transmissible (100% vs 100%) via contact transmission. Importantly, the Omicron variant consistently demonstrated about 10-20% higher transmissibility than the already-highly transmissible Delta variant in repeated non-contact transmission studies (overall: 30/36 vs 24/36, 83.3% vs 66.7%). The Delta variant displayed higher fitness advantage than the Omicron variant without selection pressure in both in vitro and in vivo competition models. However, this scenario drastically changed once immune selection pressure with neutralizing antibodies active against the Delta variant but poorly active against the Omicron variant were introduced, with the Omicron variant significantly outcompeting the Delta variant. Taken together, our findings demonstrated that while the Omicron variant is less pathogenic than the Delta variant, it is highly transmissible and can outcompete the Delta variant under immune selection pressure. Next-generation vaccines and antivirals effective against this new VOC are urgently needed.

Analysis of the clinical characteristics of novel coronavirus pneumonia and the influencing factors of severe disease progress

Objective: To analyze the clinical characteristics of patients with novel coronavirus pneumonia (COVID-19) and the factors influencing mild eases developing into severe cases, so as to provide a basis for clinical screening, prevention and treatment of potential severe cases.

Spread of COVID-19 in China: analysis from a city-based epidemic and mobility model.

Understanding the processes and mechanisms of the spatial spread of epidemics is essential for making reasonable judgments on the development trends of epidemics and for adopting effective containment measures. Using multi-agent network technology and big data on population migration, this paper constructed a city-based epidemic and mobility model (CEMM) to stimulate the spatiotemporal of COVID-19. Compared with traditional models, this model is characterized by an urban network perspective and emphasizes the important role of intercity population mobility and high-speed transportation networks. The results show that the model could simulate the inter-city spread of COVID-19 at the early stage in China with high precision. Through scenario simulation, the paper quantitatively evaluated the effect of control measures "city lockdown" and "decreasing population mobility" on containing the spatial spread of the COVID-19 epidemic. According to the simulation, the total number of infectious cases in China would have climbed to 138,824 on February 2020, or 4.46 times the real number, if neither of the measures had been implemented. Overall, the containment effect of the lockdown of cities in Hubei was greater than that of decreasing intercity population mobility, and the effect of city lockdowns was more sensitive to timing relative to decreasing population mobility.

Long-Term Clinical Sequelae and Immunological Features of COVID-19 Survivors: A Cross-Sectional Study in Wuhan, China (preprint)

Objectives: To describe the clinical sequelae and immunological features of COVID-19 survivors who have been discharged from the hospital for 5-8 months. Methods: This study is a cross-sectional study of confirmed COVID-19 patients aged ≥18 years who were discharged from hospitals in Wuhan from January to April 2020. The demographics, clinical features, and laboratory findings of the participants were collected from medical records in the hospital. The participants from the study completed an investigation of clinical sequelae, blood tests, a pulmonary function examination and an unarmed rehabilitation evaluation at Hubei Provincial Hospital of Traditional Chinese & Western Medicine. A group of volunteers who were free of COVID-19 and lived in Wuhan during the outbreak were recruited as the comparison group.Results: The average age of the 574 COVID-19 survivors was 57.7±11.4 years, and 348 (60.6%) survivors were female. The average number of days from the onset of symptoms was 241.79±16.16. The average number of days from discharge was 194.3±14.4. Clinical sequelae were common, including general symptoms (n=321, 55.9%), respiratory symptoms (n=265, 46.2%), digestive symptoms (n=84, 14.6%), nervous symptoms (n=75,13.1%) and psychosocial symptoms (n=201, 35%). A total of 190 (33.7%) survivors reported reduced exercise capacity. Through the results of pulmonary function examination, anomalies were noted in carbon monoxide diffusion capacity (DLCO)% in 110 cases (32.4%), maximal mid-expiratory flow (MMEF)% in 105 cases (30.7%), forced expired flow at 50% of forced vital capacity (FEF 50 )% in 128 cases (37.4%), and forced expired flow at 75% of forced vital capacity (FEF 75 )% in 240 cases (70.2%). The counts of T lymphocyte, CD4+ T lymphocyte counts, CD8+ T lymphocyte counts, B lymphocyte and NK cell in the survival group was significantly lower than that in the comparison group(all P < 0.05).There were 252 (43.9%) survivors whose total T lymphocyte counts had dropped, 260 (45.3%) whose CD4+T lymphocyte counts had dropped, 231 (40.2%) whose CD8+ T lymphocyte counts had dropped, 119 (20.7%) whose B lymphocyte counts had dropped, and 54 (9.4%) whose NK cell counts had dropped. But there were no statistically significant differences in the incidence of lymphocyte subsets reduction between severe and nonsevere groups (all P > 0.05). The T lymphocyte counts, CD4+ T lymphocyte counts and CD8+ T lymphocyte counts of the patients before discharge were significantly higher than those in the early stage of admission (P < 0.025). There were 319 (55.6%) survivors with positive or weakly positive IgG antibodies and 17 (2.9%) survivors with positive or weakly positive IgM antibodies.Conclusion: Even after 5 to 8 months of discharge, many survivors still have clinical sequelae, and some of them have impaired immune function. Therefore, the long-term rehabilitation of COVID-19 survivors remains a concern.Funding Statement: This study was funded by the National Key R&D Plan of China (2020YFC0841600), Guangdong Provincial Key Laboratory of Research on Emergency in TCM (2017B030314176), R&D plan in key areas of Guangdong Province (2020B1111300005), and National Administration of Traditional Chinese Medicine (2020ZYLCYJ05-11).Declaration of Interests: The authors declare that they have no competing interests.Ethics Approval Statement: This study was approved by the ethical committees of Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China (GPHCM; No. BF2020-205-01). All participants signed informed consent forms.

Ozone pollution mitigation in guangxi (south China) driven by meteorology and anthropogenic emissions during the COVID-19 lockdown.

With the implementation of COVID-19 restrictions and consequent improvement in air quality due to the nationwide lockdown, ozone (O3) pollution was generally amplified in China. However, the O3 levels throughout the Guangxi region of South China showed a clear downward trend during the lockdown. To better understand this unusual phenomenon, we investigated the characteristics of conventional pollutants, the influence of meteorological and anthropogenic factors quantified by a multiple linear regression (MLR) model, and the impact of local sources and long-range transport based on a continuous emission monitoring system (CEMS) and the HYSPLIT model. Results show that in Guangxi, the conventional pollutants generally declined during the COVID-19 lockdown period (January 24 to February 9, 2020) compared with their concentrations during 2016-2019, while O3 gradually increased during the resumption (10 February to April 2020) and full operation periods (May and June 2020). Focusing on Beihai, a typical Guangxi region city, the correlations between the daily O3 concentrations and six meteorological parameters (wind speed, visibility, temperature, humidity, precipitation, and atmospheric pressure) and their corresponding regression coefficients indicate that meteorological conditions were generally conducive to O3 pollution mitigation during the lockdown. A 7.84 µg/m3 drop in O3 concentration was driven by meteorology, with other decreases (4.11 µg/m3) explained by reduced anthropogenic emissions of O3 precursors. Taken together, the lower NO2/SO2 ratios (1.25-2.33) and consistencies between real-time monitored primary emissions and ambient concentrations suggest that, with the closure of small-scale industries, residual industrial emissions have become dominant contributors to local primary pollutants. Backward trajectory cluster analyses show that the slump of O3 concentrations in Southern Guangxi could be partly attributed to clean air mass transfer (24-58%) from the South China Sea. Overall, the synergistic effects of the COVID-19 lockdown and meteorological factors intensified O3 reduction in the Guangxi region of South China.

Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations (preprint)

Recombinant neutralizing antibodies (nAbs) derived from recovered patients have proven to be effective therapeutics for COVID-19. Here, we describe the use of advanced protein engineering and modular design principles to develop tetravalent synthetic nAbs that mimic the multi-valency exhibited by IgA molecules, which are especially effective natural inhibitors of viral disease. At the same time, these nAbs display high affinity and modularity typical of IgG molecules, which are the preferred format for drugs. We show that highly specific tetravalent nAbs can be produced at large scale and possess stability and specificity comparable to approved antibody drugs. Moreover, structural studies reveal that the best nAb targets the host receptor binding site of the virus spike protein, and thus, its tetravalent version can block virus infection with a potency that exceeds that of the bivalent IgG by an order of magnitude. Design principles defined here can be readily applied to any antibody drug, including IgGs that are showing efficacy in clinical trials. Thus, our results present a general framework to develop potent antiviral therapies against COVID-19, and the strategy can be readily deployed in response to future pathogenic threats.

Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters (preprint)

COVID-19 pandemic is the third zoonotic coronavirus (CoV) outbreak of the century after severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) since 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. The FDA-approved molecule was found to inhibit multiple steps of viral replication, suggesting multiple underlying antiviral mechanisms. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Additionally, clofazimine exhibited synergy when administered with remdesivir. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. Taken together, our data provide evidence that clofazimine may have a role in the control of the current pandemic SARS-CoV-2, endemic MERS-CoV in the Middle East, and, possibly most importantly, emerging CoVs of the future.

Modified management mode for colorectal cancer during COVID-19 outbreak - a single-center experience.

During the epidemic of COVID-19, the management model of colorectal cancer has to be changed at our center due to relatively limited medical resources. Outpatient visits are reduced under well protected after appointment, and rigorous investigation of epidemiological history and clinical symptoms are needed. We prefer a simple and convenient treatment regimen, which may also be postponed appropriately. Minimally invasive CRC surgery combined with a perioperative program of enhanced recovery after surgery should be recommended. We also focus on mental health treatments and healthy lifestyle education. In addition, routine follow-up can be moderately delayed. In total, adequate doctor-patient communication is also recommended throughout the treatment.

Temporal lung changes on thin-section CT in patients with COVID-19 pneumonia (preprint)

We examined characteristics of chest CT during different time periods for patients with coronavirus disease 2019 (COVID-19) pneumonia in Huizhou, China. This study included 56 COVID-19 patients having abnormal CT acquired between January 22 and March 3, 2020. Scans of 56 patients were classified into 4 groups (Group 1-Group 4) based on the date on which scan was obtained at the 1st, 2nd, 3rd week and longer than 3 weeks after illness onset. Forty-five patients with follow-up scans were categorized into 4 groups according to extents that lesions reduced. GGO was prevalent in Groups 1-4 (58.1-82.6%). Consolidation was the more common in Group 2 (26.2%) and then declined in Group 3 and 4 (20.0%; 9.7%). The highest frequency of fibrous stripes occurred in Group 3 (46.7%) and then decreased to 35.5% in Group 4. CT scores were higher for Group 2 than others. Among 45 follow-up patients, 11 (24.4%) of them recovered with lesions reducing ≥75% and had shorter hospital durations compared with others. There were temporal patterns of lung abnormalities in COVID-19 patients, with the highest extent of lesion involvement occurring in the 2nd week. Isolation and review are required for COVID-19 patients who have been discharged from hospital.

Low Serum Cholesterol Level Among Patients with COVID-19 Infection in Wenzhou, China (preprint)

Background: A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel coronavirus COVID-19. Meanwhile, as the infection progressed, a large number of cases were also diagnosed in Wenzhou, China. The objective of the study is to describe the clinical laboratory features, especially lipid profile of the patients with COVID-19 infection in Wenzhou.Methods: All cases were in a designated hospital in Wenzhou, and confirmed by positive virial nucleic acid detection through PCR assay. All clinical laboratory data were from the first test results after their admission. The unpaired t test was used for data analysis.Findings: The absolute value of white blood cells, neutrophils and lymphocytes were lower than healthy controls ( P ＜0.05), more significantly, the patients had sharply decreased total cholesterol (TC), HDL-cholesterol and LDL-cholesterol levels ( P ＜0.001), 3.70±0.09mmol/L, 1.18±0.03 mmol/L and 1.82±0.08 mmol/L respectively, and increased monocyte/HDL-cholesterol ratio (0.37±0.02 vs 0.28±0.01 in healthy control). Among the patients, the primary infection cases showed the lower HDL-cholesterol levels (1.10±0.04 mmol/L) and higher monocyte/HDL-cholesterol ratio (0.43±0.03) than the secondary infection cases by person-to-person transmission ( P ＜0.05). Compared with the female patients, the male patients had higher levels of monocytes [(0.46±0.02) ×10 9 /L], M/HDL-C ratio (0.44±0.02), and lactate dehydrogenase (LDH, 257.6±12.32 U/l).Interpretation: Low serum cholesterol level in the patients with COVID-19 in Wenzhou, China. Altered serum cholesterol provide important information, and is meaningful to understand the disease.Funding Statement: This work is funded by Natural Science Foundation of Zhejiang Province (LQ18H020005). Declaration of Interests: The authors declare no competing interests.Ethics Approval Statement: This study was authorized by Ethics Commission of Wenzhou Central Hospital.

Comparative study of the lymphocyte change between COVID-19 and non-COVID-19 pneumonia cases suggesting uncontrolled inflammation might not be the main reason of tissue injury (preprint)

Background: The corona virus disease 2019 (COVID-19) shows unusually high transmission rate and unique clinical characteristics, with key pathological mechanism remaining unclear. Here, we analysed the laboratory data based on clinical samples from COVID-19 patients, in parallel comparison with non-COVID-19 pneumonia cases, in an attempt to elucidate the key pathological features of COVID-19 during its infection of the human body. Methods: We analysed biochemical indices and lymphocyte subpopulation in COVID-19 patients, and compare these data from non-COVID-19 pneumonia cases. Correlation analysis was performed between leukocyte subgroups count and biochemical indexes in COVID-19 patients. Results: The study enrolled 110 patients, comprising 88 COVID-19 patients and 22 non-COVID-19 pneumonia cases. We observed significant differences, including abnormal biochemical indices (CRP, LDH, AST, eGFR, and sodium ion concentration) and reduced lymphocyte subsets count, between the COVID-19 patients and non-COVID-19-caused pneumonia cases. Correlation analysis indicates that the count for lymphocyte subsets-but not that for neutrophils and monocytes-exhibits a significant negative correlation with biochemical indices relating to organ injury, in the COVID-19 infected patients. Conclusions: The study indicates significantly different clinical features between 2019 novel coronavirus (2019-nCoV)-caused and non-2019-nCoV-caused pneumonia, especially in terms of lymphocytopenia and organ injury. Notably, correlation analysis demonstrates that tissue damage in COVID-19 patients is attributed to virus infection itself rather than uncontrolled inflammatory responses ("cytokine storm"). These findings provide new insights for developing efficient therapeutic strategies against COVID-19 infection.