Effect of human aminopeptidase N (hAPN) on porcine deltacoronavirus infecting HEK293 cells

HEK293 cells were used as the cell model to investigate the role of human aminopeptidase N (hAPN) in the invasion of porcine deltacoronavirus (PDCoV) into human cells. The proliferation of PDCoV on HEK293 cells was firstly identified by RT-qPCR/RT-PCR. And then, hAPN knockout cell line was constructed by CRISPR/Cas9 technology and cell viability of HEK293 hAPN knockout and wild-type cells was verified by CCK-8 assay. Effect of hAPN knockout and overexpression on PDCoV replication was detected by RT-qPCR and Western blot. Meanwhile, interaction of PDCoV S protein and hAPN protein was analyzed by homology modeling and molecular docking. Results showed that PDCoV virus copies rapidly increased at 12-36 h and reached peak level at 36 h, it could propagate at least for passage 2 on HEK293 cells. There was no significant difference in cell viability between hAPN knockout cells and wild-type cells. Knockout of hAPN inhibit PDCoV replication and overexpression of hAPN enhance PDCoV replication. Homology modeling and molecular docking analysis showed S1 protein could bind hAPN domain II. Residues TYR92, THR51, THR48, PHE16 and MET14of S1 protein receptor binding motif 1 (RBM1) can form hydrogen bonds with residues PHE490, GLN531, ARG528 and SER529 of hAPN. This study indicates that hAPN plays a critical role in HEK293 cells during PDCoV infection, which provides new theoretical evidence for further studies on the mechanism of PDCoV entry into host cells and cross-species transmission.

Real-world uptake of COVID-19 vaccination among individuals expressing vaccine hesitancy: a registry-linkage study (preprint)

Background: Uptake of COVID-19 vaccination remains suboptimal in the United States and other settings. Though early reports indicated that a strong majority of people were interested in receiving the COVID-19 vaccine, the association between vaccine intention and uptake is not yet fully understood. Methods: During 24 February-5 December 2021, we enrolled California residents receiving molecular tests for SARS-CoV-2 infection who had not yet received any COVID-19 vaccine doses. Unvaccinated participants provided information on their intentions to receive COVID-19 vaccination in a telephone-administered survey. We matched study participants with a state-wide immunization registry and fit a Cox proportional hazards model comparing time to vaccination among those unvaccinated at study enrollment by vaccination intention (willing, unsure, or unwilling). Findings: Among 864 participants who were unvaccinated at the time of interview, 272 (31%) had documentation of receipt of COVID-19 vaccination later; including 194/423 (45.9%) who had initially reported being willing to receive vaccination, 41/185 (22.2%) who reported being unsure about vaccination, and 37/278 (13.3%) who reported unwillingness to receive vaccination. Adjusted hazard ratios (aHRs) for registry-confirmed COVID-19 vaccination were 0.49 (95% confidence interval: 0.32-0.76) and 0.21 (0.12-0.36) for participants expressing uncertainty and unwillingness to receive vaccination, respectively, as compared with participants who reported being willing to receive vaccination. Time to vaccination was shorter among participants from higher-income households (aHR 3.30 [2.02-5.39]) and who reported co-morbidities or immunocompromising conditions (aHR 1.54 [1.01-2.36]); time to vaccination was longer among participants who tested positive for SARS-CoV-2 infection (aHR 0.60 [0.43-0.84]). Sensitivity of self-reported COVID-19 vaccination status was 82% (80-85%) overall, and 98% (97-99%) among those referencing vaccination records; specificity was 87% (86-89%). Interpretation: Reported willingness to receive COVID-19 vaccination was an imperfect predictor of real-world vaccine receipt. Improving messaging about the importance of COVID-19 vaccination, regardless of previous SARS-CoV-2 infection status, may improve vaccine uptake among populations who express hesitancy to initiate vaccination.

An Evaluation of the Petroleum Investment Environment in African Oil-Producing Countries Based on Combination Weighting and Uncertainty Measure Theory

Recognizing that the evaluation of the overseas petroleum investment environment is affected by many uncertain factors and that there are problems with current evaluation methods, this paper proposes a mathematical evaluation model of an overseas oil resources investment environment, based on a combination of the weighting and uncertainty measure theory. Combining international investment environment theory with the characteristics of the petroleum industry, this paper establishes an evaluation index system for the overseas petroleum investment environment and the linear uncertainty measure function of each index. Using the subjective weight obtained using an analytic hierarchy process together with the objective weight obtained using the entropy weight method, the optimal weight of each evaluation index was obtained using minimum relative information entropy. A multi-index evaluation matrix of the top 12 oil-producing countries in Africa was calculated. Finally, the credible degree recognition criterion was used to judge the order and level of the oil investment environment. This model provides an effective method for the evaluation of the overseas petroleum investment environment. The results show that Nigeria and Angola have the best investment climate, followed by Algeria, Egypt, and Libya. In general, Africa is an important strategic partner of China and is rich in oil resources. Although Africa’s oil industry is fraught with complex challenges and headwinds, challenges also present opportunities.

Susceptibility of cell lines from different animal species to Porcine Deltacoronavirus

[Objective] To explore whether porcine deltacoronavirus (PDCoV) can infect and proliferate in different animal species-derived cell lines. [Methods] The Sichuan isolate CHN-SC2015of PDCoV was inoculated in twelve cell lines derived from hamster,poultry,monkey, human and swine. After at least five blindly passages in each cell line, the virus was identified by RT-PCR,RT-q PCR, indirect immunofluorescence assay (IFA), and sequencing. [Results] PDCoV caused distinct cytopathic effect (CPE) in Vero,PAM,PK15,ST, and LLC-PK1 cells at the 1st passage (P1) and proliferated to various degrees in PAM,PK15,ST, and LLC-PK1 cells, while the CPE gradually disappeared during subsequent passages in Vero and PAM cells. Except that in the three susceptible cell lines (PK15,LLC-PK1, and ST), the viral copies of the infected cell lines gradually decreased with the increase in passages, and PDCoV could not be detected at P4 or P5 of DEF,Marc-145,HEK-293,ZYM-SIEC02, and PAM cells. PCR results showed that PDCoV could be detected only in CEF and Vero cells at P5. The IFA results showed that PDCoV could infect other cell lines except BHK-21 and ZYM-SIEC02, and specific immunofluorescence was observed in PK15,LLC-PK1, and ST cells at P1,P3, and P9. Therefore, only three cell lines (PK15,LLC-PK1, and ST) were suitable for serial passage, with the virus titers up to 107.11,107.00, and 107.37 TCID50/mL at P9,respectively. After passage in different cell lines,CHN-SC2015 accumulated 14 nucleotide mutations corresponding to 12 amino acid mutations. [Conclusion] This study indicates that PDCoV can infect a variety of cells in vitro, suggesting that it may have the potential of cross-species transmission.

Phylogeny, Evolution, and Transmission Dynamics of Canine and Feline Coronaviruses: A Retro-Prospective Study

Canine coronavirus (CCoV) and feline coronavirus (FCoV) are endemic in companion animals. Due to their high mutation rates and tendencies of genome recombination, they pose potential threats to public health. The molecular characteristics and genetic variation of both CCoV and FCoV have been thoroughly studied, but their origin and evolutionary dynamics still require further assessment. In the present study, we applied a comprehensive approach and analyzed the S, M, and N genes of different CCoV/FCoV isolates. Discriminant analysis of principal components (DAPC) and phylogenetic analysis showed that the FCoV sequences from Chinese isolates were closely related to the FCoV clusters in Netherlands, while recombination analysis indicated that of S N-terminal domain (NTD) was the most susceptible region of mutation, and recombination of this region is an important cause of the emergence of new lineages. Natural selection showed that CCoV and FCoV subgenotypes were in selection constraints, and CCoV-IIb was in strong positive selection. Phylodynamics showed that the mean evolution rate of S1 genes of CCoV and FCoV was 1.281 × 10–3 and 1.244 × 10–3 subs/site/year, respectively, and the tMRCA of CCoV and FCoV was about 1901 and 1822, respectively. Taken together, our study centered on tracing the origin of CCoV/FCoV and provided ample insights into the phylogeny and evolution of canine and feline coronaviruses.

Infective endocarditis (MRSA)with COVID-19 concomitant：a case report (preprint)

Introduction: Since 2019,the COVID-19（a1） epidemic has rapidly spread across China,and the global spread trendappeared,which not only endangered people’s health, but also had a huge impact on the social economy.Infective endocarditis (IE(a2)) is aninflammation of the inner wall of the cardiac valves or ventricle caused by direct infection of bacteria,fungi and other pathogenic microorganisms. It is related to several and the main etiological agents are the Gram-positive cocci. At present,there is limited evidence in the literature for both conditions. Case presentation Here，we report a case of Infective endocarditis concomitant with COVID-19. A blood culture results and toe secretions culture indicated MRSA（a3） strain infection.Because it has no special past history,we consider that is communityassociated (CA-MRSA )strain. TTE（a4） did not identify endocardial vegetations. TEE（a5） was then performed and outlined IE of anterior mitral valve leaflet. CT scan of the patient revealed multiple diffuse abscesses. We tried high-flow nasal cannula(HFNC（a6）) for COVID-19,and we used a combined anti-infection approach(daptomycin, Fosfomycin, linezolid). Conclusion With aggressive anti-infective therapy,our case has achieved a good treatment outcome.

Substantial changes in gaseous pollutants and chemical compositions in fine particles in the North China Plain during the COVID-19 lockdown period: anthropogenic vs. meteorological influences

The rapid response to the COVID-19 pandemic led to unprecedented decreases in economic activities, thereby reducing the pollutant emissions. A random forest (RF) model was applied to determine the respective contributions of meteorology and anthropogenic emissions to the changes in air quality. The result suggested that the strict lockdown measures significantly decreased primary components such as Cr (-67 %) and Fe (-61 %) inPM2.5 (p<0.01), whereas the higher relative humidity (RH) andNH3 level and the lower air temperature (T) remarkably enhanced the production of secondary aerosol, including SO42- (29 %), NO3- (29 %), and NH4+ (21 %) (p<0.05). The positive matrix factorization (PMF) result suggested that the contribution ratios of secondary formation (SF), industrial process (IP), biomass burning (BB), coal combustion (CC), and road dust (RD) changed from 36 %, 27 %, 21 %, 12 %, and 4 % before the COVID-19 outbreak to 44 %, 20 %, 20 %, 9 %, and 7 %, respectively. The rapid increase in the contribution ratio derived from SF to PM2.5 implied that the intermittent haze events during the COVID-19 period were characterized by secondary aerosol pollution, which was mainly contributed by the unfavorable meteorological conditions and highNH3 level.

Issue Cover

The cover image is based on the Original Article Clinical characteristics of COVID‐19 patients with hepatitis B virus infection — a retrospective study by Rui Liu et al., https://doi.org/10.1111/liv.14774.

What is required to prevent a second major outbreak of the novel coronavirus SARS-CoV-2 upon lifting the metropolitan-wide quarantine of Wuhan city, China (preprint)

Background: The Chinese government implemented a metropolitan-wide quarantine of Wuhan city on 23rd January 2020 to curb the epidemic of the coronavirus COVID-19. Lifting of this quarantine is imminent. We modelled the effects of two key health interventions on the epidemic when the quarantine is lifted. Method: We constructed a compartmental dynamic model to forecast the trend of the COVID-19 epidemic at different quarantine lifting dates and investigated the impact of different rates of public contact and facial mask usage on the epidemic. Results: We estimated that at the end of the epidemic, a total of 65,572 (46,156-95,264) individuals would be infected by the virus, among which 16,144 (14,422-23,447, 24.6%) would be infected through public contacts, 45,795 (32,390-66,395, 69.7%) through household contact, 3,633 (2,344-5,865, 5.5%) through hospital contacts (including 783 (553-1,134) non-COVID-19 patients and 2,850 (1,801-4,981) medical staff members). A total of 3,262 (1,592-6,470) would die of COVID-19 related pneumonia in Wuhan. For an early lifting date (21st March), facial mask needed to be sustained at a relatively high rate ([≥]85%) if public contacts were to recover to 100% of the pre-quarantine level. In contrast, lifting the quarantine on 18th April allowed public person-to-person contact adjusted back to the pre-quarantine level with a substantially lower level of facial mask usage (75%). However, a low facial mask usage (<50%) combined with an increased public contact (>100%) would always lead a significant second outbreak in most quarantine lifting scenarios. Lifting the quarantine on 25th April would ensure a smooth decline of the epidemics regardless of the combinations of public contact rates and facial mask usage. Conclusion: The prevention of a second epidemic is viable after the metropolitan-wide quarantine is lifted but requires a sustaining high facial mask usage and a low public contact rate.

Clinical features of 30 cases with novel coronavirus pneumonia / 中华传染病杂志

Objective@#To analyze the epidemiological and clinical characteristics of patients with 2019 novel coronavirus (2019-nCoV) infection in Shenyang.@*Methods@#The epidemiological and clinical characteristics of 30 patients diagnosed with 2019-nCoV infection admitted to Shenyang sixth people's hospital on January 22, 2020 and February 8, 2020 were retrospectively analyzed.@*Results@#Among the 30 cases, 21 were imported, including 17 from Hubei Province and four from other provinces. Nine cases were local infections. There were 18 men and 12 women, aging from 21 to 72 years with the median of 43 years. Eight cases had underlying diseases including hypertension, diabetes, coronary heart disease and bronchitis. On admission, two (7%) cases were mild, 19 (63%) cases were ordinary, eight (27%) cases were severe, and one (3%) case was critical. Clinical manifestations mainly include fever, with or without upper respiratory tract symptoms, normal, decreased or slightly increased white blood cell counts, mainly decreased lymphocyte counts, normal or increased c-reactive protein, and normal procalcitonin. The computed tomography (CT) of the early stage of the lungs showed that multiple patchy ground glass shadows were mainly accompanied by consolidation, which often involved both lungs or multiple lobes of one lung. At the moment, the clinical treatment mainly included respiratory support, symptomatic treatment, antiviral treatment adn anti-bacterial treatment. By February 15, a total of nine cases were cured and discharged, including one mild case, six ordinary cases, and two severe cases. In the comparisons between mild/ordinary patients and severe/critical patients, the fever duration in the severe/critical group (median 11.5 d) was significantly longer than that in the light/normal group (median 2 d) (Z=-2.292, P=0.022), and the laboratory tests indicated elevated d-dimer levels (Z=-2.669, P=0.008) and more cases with neutrophilic/lymphocyte ratio > 3 (Z=-4.071, P<0.01).@*Conclusions@#In Shenyang, the early cases with 2019-nCoV infection are mainly imported cases, and expanding local infections gradually develop. Clinical manifestations are mainly characterized by fever and cough. Lung CT performance shows multiple ground glass shadows, mainly accompanied by consolidation. CT changes in the lungs should be closely monitored during the treatment, and CT findings in the lungs may change earlier than the clinical manifestations. Prolonged fever duration, elevated d-dimer level and neutrophil/lymphocyte ratio >3 could be used as early warning indicators for severe cases.

Clinical characteristics of 28 patients with novel coronavirus pneumonia / 中华传染病杂志

Objective@#To analysis the clinical characteristics and experiences in diagnosis and treatment of the patients with novel coronavirus pneumonia (NCP).@*Methods@#Clinical data of 28 patients with NCP in Nanning Fourth People's Hospital from January 22 to February 5 in 2020 were collected. The clinical manifestations, epidemiological history, laboratory tests, imaging examinations and treatments of patients were analyzed retrospectively.@*Results@#The 28 patients with confirmed viral pneumonia included 11 males and 17 females, ranging from 11 to 68 years. They all had history of epidemiological exposure and were all positive for 2019-nCoV nucleic acid in throat swabs. There were one mild case, 25 ordinary cases and two severe cases. There were four groups of family clusters. The illness onset ranged from 1 to 12 days after exposure, and the time from the symptom onset to the positive result of the nucleic acid test was 0 to 13 days. The clinical symptoms were mainly fever and cough, which progressed rapidly in a short period of time. Since the onset of illness, the peak values of axillary temperature of the 28 patients were 36.6~39.5 ℃, while five patients had no fever throughout the course of the disease with the peak temperature of ≤37 ℃. There were two patients presented with decreased white blood cell counts, five patients with elevated C reactive protein, six patients with abnormal alanine aminotransferase, three patients with abnormal aspartate aminotransferase,10 patients with elevated creatine kinase, three patients with elevated creatine kinase isoenzyme, four patients with elevated lactate dehydrogenase, and all with normal procalcitonin levels. The chest computed tomography examinations showed that the common features were ground glass shadows (21 cases), blurred edges (18 cases), speckles and patchy shadows (17 cases), thickening and disorder of some lung textures (7 cases), and visible band shadows (7 cases). Pulmonary lesions often progressed rapidly. One 11-year-old child was treated with alpha-interferon alone, and 27 patients were treated with alpha-interferon inhalation plus lopinavir/ritonavir with 4 withdrawal due to adverse reactions. Up to February 12, nine patients had been discharged from the hospital, who were ordinary cases, without death cases.@*Conclusions@#The NCP patients mostly present with fever and cough. Pulmonary lesions often progress rapidly. Respiratory pathogen testing should be conducted as early as possible and repeatedly. Disisolation should be cautious for suspected people who are negative for 2019-nCoV nucleic acid in pharynx swabs.