Estimating monthly surface ozone using multi-source satellite products in China based on Deep Forest model

Surface ozone (O3), a well-recognized air pollutant, exists in the atmosphere, which has a detrimental effect on public health and the ecological environment. It is reported that surface O3 has seen a significant increase in many cities from 2019 to 2021 (COVID-19 pandemic). In this study, we applied an innovative machine learning model (Deep Forest) coupled with satellites, the Troposphere Monitoring Instrument (TROPOMI) and the Ozone Monitoring Instrument (OMI), and meteorological datasets to estimate monthly surface O3 of 1 km spatial resolution across China during this pandemic period. Our model achieved an overall R2 of 0.974, 0.963, and root mean square error (RMSE) of 6.016 μg/m3, 7.214 μg/m3 on TROPOMI-based datasets and OMI-based datasets, respectively. Also, we found the higher ozone concentration regions were in Eastern China. Simultaneously, the surface O3 concentration was high in summer(average = 110.57 ± 15.01 μg/m3). And the ozone concentration in summer 2020 (average = 107.78 ± 13.90 μg/m3) declined unprecedently than in summer 2019 (average = 110.54 ± 16.58 μg/m3). Our results indicated that TROPOMI data could provide robust data support for surface ozone concentration estimation. Furthermore, this study could enhance our comprehension of the formation mechanisms of surface O3 in China and assist air environment management decision-making.

Disparities in COVID-19 clinical studies from high-income and low-and middle-income countries.

OBJECTIVES: To examine the disparities between COVID-19 studies conducted in high-income countries (HICs) and low-and middle-income countries (LMICs). METHODS: We used the International Clinical Trials Registry Platform to identify COVID-19-related studies registered from December 31, 2019 to December 31, 2021. The World Bank definition was used to classify countries as high-, upper-middle-, lower-middle-, and low-income. The last three were considered to be LMICs. We examined the disparities in response speed, classification of medicines and vaccines, and registration and results reporting compliance between COVID-19 studies conducted in HICs and LMICs. RESULTS: We included 12,396 COVID-19 studies, with 6631 (53.5%) from HICs. HIC-registered studies reached a peak of 1039 in April 2020, whereas LMICs had only 440 studies. Of the 6969 interventional trials, those from HICs showed higher registration compliance (2199, 62.3% vs 1979, 57.6%, P <0.001) and results reporting compliance (hazard ratio 0.39, 95% confidence interval 0.28-0.55, P < 0.001) than LMICs. HICs also conducted significantly more small-molecule drug (956, 57.5% vs 868, 41.2%, P <0.001) and messenger RNA vaccine trials (135, 32.9% vs 19, 4.8%, P <0.001) than LMICs. CONCLUSION: HICs conducted COVID-19 trials with faster response speed and higher registration and publication compliance and produced more innovative pharmaceutical and vaccine products to combat COVID-19 than LMICs.

Neutralizing antibodies and T-cell responses to inactivated SARS-CoV-2 vaccine in COVID-19 convalescents one and a half years after infection.

Vaccines have been considered the most promising solution for ending the coronavirus disease 2019 (COVID-19) pandemic. Information regarding neutralizing antibodies (NAbs) and T-cell immune response in inactivated SARS-CoV-2 vaccine-immunized COVID-19 convalescent patients were either only available for a short time after illness recovered or not available at all (T-cell immunity). We evaluated SARS-CoV-2 NAbs and cellular immune responses to the SARS-CoV-2 inactivated vaccine in convalescent patients who recovered from infection for about one and a half years. We found that compared to before vaccination, SARS-CoV-2 NAbs and specific T-cell responses were significantly boosted by the inactivated vaccine in convalescent patients, which confirmed the pre-existing adaptive immunity in SARS-CoV-2 infected people. We observed that NAbs and IFN-γ-secreting T-cell response elicited by a single vaccine dose in subjects with prior COVID-19 infection were higher than after two doses of vaccine in SARS-CoV-2 naïve subjects. Both humoral and cellular immune responses elicited by one and two doses of inactivated vaccine were comparable in COVID-19-recovered persons. In conclusion, inactivated COVID-19 vaccine induced robust NAbs and T-cell responses to SARS-CoV-2 in COVID-19 convalescent patients and immune responses after one dose were equal to that after receiving two doses, which highlighted that robust humoral and cellular immune response can be reactivated by the inactivated vaccine in SARS-CoV-2 convalescent patients.

Short-term ex vivo tissue culture models help study human lung infectionsA review.

Most studies on human lung infection have been performed using animal models, formalin or other fixed tissues, and in vitro cultures of established cell lines. However, the experimental data and results obtained from these studies may not completely represent the complicated molecular events that take place in intact human lung tissue in vivo. The newly developed ex vivo short-term tissue culture model can mimic the in vivo microenvironment of humans and allow investigations of different cell types that closely interact with each other in intact human lung tissues. Therefore, this kind of model may be a promising tool for future studies of different human lung infections, owing to its special advantages in providing more realistic events that occur in vivo. In this review, we have summarized the preliminary applications of this novel short-term ex vivo tissue culture model, with a particular emphasis on its applications in some common human lung infections.

Neutralizing antibodies and cellular immune response after two doses of inactivated SARS-CoV-2 vaccine in China.

BACKGROUND: As of 2022, inactivated SARS-CoV-2 vaccines had been used in more than 91 countries. However, limited real world information was available on the immune responses of the inactivated SARS-CoV-2 vaccine. METHODS: We used SARS-CoV-2 pseudovirues to determine the neutralizing antibodies (NAbs) to wild type and several global variants and utilized enzyme-linked immunosorbent assay to investigate IFN-γ-secreting T-cell responses to SARS-CoV-2 among 240 vaccinated individuals after two doses of inactivated vaccine in China. RESULTS: A majority of the vaccinated (>90%) developed robust NAbs and T-cell responses to SARS-CoV-2 in the first two months after the second dose. After six months, only 37.0% and 44.0% of vaccinees had NAbs and T-cell immunity to SARS-CoV-2, respectively. Immune serum retained most of its neutralizing potency against the Alpha and Iota variants, but lost significant neutralizing potency against the Beta, Kappa, Delta, and Omicron variants. Only 40% of vaccine-sera retained low-level neutralization activities to Omicron, with a 14.7-fold decrease compared to the wild type. CONCLUSION: The inactivated SARS-CoV-2 vaccine stimulated robust NAbs and T-cell immune responses in the first two months after the second dose but the immune effect dropped rapidly, highlighing that a third dose or additional booster immunizations may be required to boost immunity against SARS-CoV-2.

SARS-CoV-2 Delta Variant in Jingmen City, Hubei Province, China, 2021: Children Susceptible and Vaccination Breakthrough Infection.

Background: The delta variant (B.1.617.2) of SARS-CoV-2 was the dominant viral strain causing COVID-19 in China, 2021. We reported a SARS-CoV-2 delta variant outbreak in Jingmen City, Hubei Province, China. Methods: The data of epidemiological, clinical, laboratorial, and vaccination of COVID-19 cases were collected through field investigation and analyzed. Results: During the outbreak from 4 to 20 August 2021, 58 cases of the SARS-CoV-2 delta variant (B.1.617.2) were identified with 15 (25.9%) asymptomatic and 43 (74.1%) symptomatic (mild and moderate) patients. The mean serial interval was 2.6 days (standard deviation: 2.0, 95% CI: 1.9-3.6). The median age of the patients was 39 years (ranging from 1 to 60 years) with the high proportion in children (19.0%). The secondary attack rate was 9.8% higher from parents to their children (<18 years) (46.2%, 95% CI: 14.8-77.5%) than that between spouses (36.4%, 95% CI: 14.5-58.2%), but no significant difference was observed (p > 0.05). Approximately half (27; 46.6%) of cases were vaccine breakthrough infections. In vaccine breakthrough cases (fully vaccinated), viral loads decreased 1.9-3.4-folds (p < 0.05), duration of viral shedding shortened 5 days (p < 0.05), and the risk of becoming symptomatic from asymptomatic decreased 33% (95% CI: 5-53%) (aged ≥12 years) than those in unvaccinated infections. Conclusions: Children are highly susceptible to the SARS-CoV-2 delta variant in the COVID-19 outbreak in Jingmen City in 2021. Inactivated vaccine derived from wide-type strain can effectively reduce the viral load, duration of viral shedding, and clinical severity in vaccine breakthrough cases. Our study indicates that protective measures that include full vaccination against COVID-19, especially in children, should be strengthened.

Neutralizing Antibodies and Cellular Immune Responses Against SARS-CoV-2 Sustained One and a Half Years After Natural Infection.

Background: COVID-19 has caused more than 2.6 billion infections and several million deaths since its outbreak 2 years ago. We know very little about the long-term cellular immune responses and the kinetics of neutralizing antibodies (NAbs) to SARS-CoV-2 because it has emerged only recently in the human population. Methods: We collected blood samples from individuals who were from the first wave of the COVID-19 epidemic in Wuhan between December 30, 2019, and February 24, 2020. We analyzed NAbs to SARS-CoV-2 using pseudoviruses and IgG antibodies to SARS-CoV-2 spike (S) and nucleocapsid (N) protein using enzyme-linked immunosorbent assay in patients' sera and determined SARS-CoV-2-specific T-cell responses of patients with ELISpot assays. Results: We found that 91.9% (57/62) and 88.9% (40/45) of COVID-19 patients had NAbs against SARS-CoV-2 in a year (10-11 months) and one and a half years (17-18 months), respectively, after the onset of illness, indicating that NAbs against SARS-CoV-2 waned slowly and possibly persisted over a long period time. Over 80% of patients had IgG antibodies to SARS-CoV-2 S and N protein one and a half years after illness onset. Most patients also had robust memory T-cell responses against SARS-CoV-2 one and a half years after the illness. Among the patients, 95.6% (43/45) had an IFN-γ-secreting T-cell response and 93.8% (15/16) had an IL-2-secreting T-cell response. The T-cell responses to SARS-CoV-2 were positively correlated with antibodies (including neutralizing antibodies and IgG antibodies to S and N protein) in COVID-19 patients. Eighty percent (4/5) of neutralizing antibody-negative patients also had SARS-CoV-2-specific T-cell response. After long-term infection, protective immunity was independent of disease severity, sex, and age. Conclusions: We concluded that SARS-CoV-2 infection elicited a robust and persistent neutralizing antibody and memory T-cell response in COVID-19 patients, indicating that these sustained immune responses, among most SARS-CoV-2-infected people, may play a crucial role in protection against reinfection.

SARS-CoV-2 ORF3a Induces Incomplete Autophagy via the Unfolded Protein Response.

In the past year and a half, SARS-CoV-2 has caused 240 million confirmed cases and 5 million deaths worldwide. Autophagy is a conserved process that either promotes or inhibits viral infections. Although coronaviruses are known to utilize the transport of autophagy-dependent vesicles for the viral life cycle, the underlying autophagy-inducing mechanisms remain largely unexplored. Using several autophagy-deficient cell lines and autophagy inhibitors, we demonstrated that SARS-CoV-2 ORF3a was able to induce incomplete autophagy in a FIP200/Beclin-1-dependent manner. Moreover, ORF3a was involved in the induction of the UPR (unfolded protein response), while the IRE1 and ATF6 pathways, but not the PERK pathway, were responsible for mediating the ORF3a-induced autophagy. These results identify the role of the UPR pathway in the ORF3a-induced classical autophagy process, which may provide us with a better understanding of SARS-CoV-2 and suggest new therapeutic modalities in the treatment of COVID-19.

A Tuberculosis Outbreak During the COVID-19 Pandemic - Hubei Province, China, 2020.

What is already known about topic? Multidrug-resistant tuberculosis (MDR-TB) has become a growing threat to public health. There were few reports about family-to-school MDR-TB outbreaks in China, especially during the coronavirus disease 2019 (COVID-19) pandemic. What is added by this report? A tuberculosis (TB) outbreak happened in Hubei Province during the COVID-19 pandemic. The transmission chain was probably from a father （MDR-TB case）with retreated TB history to his daughter, who then spread TB to her classmates. What are the implications for public health practice? We should enhance TB control both in schools and households, including strengthening TB/MDR-TB detection, health education, and ventilation. The TB contact screening cannot only be limited to outside school settings and should be conducted in the school when a TB student is absent from school for 2 or 3 months, or even longer especially during the COVID-19 pandemic.

Development of a Nucleocapsid Protein-Based ELISA for Detection of Human IgM and IgG Antibodies to SARS-CoV-2.

SARS-CoV-2 is the etiologic agent of COVID-19, which has led to a dramatic loss of human life and presents an unprecedented challenge to public health worldwide. The gold standard assay for SARS-CoV-2 identification is real-time polymerase chain reaction; however, this assay depends on highly trained personnel and sophisticated equipment and may suffer from false results. Thus, a serological antibody test is a supplement to the diagnosis or screening of SARS-CoV-2. Here, we develop and evaluate the diagnostic performance of an IgM/IgG indirect ELISA method for antibodies against SARS-CoV-2 in COVID-19. The ELISA was constructed by coating with a recombinant nucleocapsid protein of SARS-CoV-2 on an enzyme immunoassay plate, and its sensitivity and specificity for clinical diagnosis of SARS-CoV-2 infection was assessed by detecting the SARS-CoV-2-specific IgM and IgG antibodies in COVID-19 patient's sera or healthy person's sera. The SARS-CoV-2 positive serum samples (n = 168) were collected from confirmed COVID-19 patients. A commercial nucleocapsid protein-based chemiluminescent immunoassay (CLIA) kit and a colloidal gold immunochromatography kit were compared with those of the ELISA assay. The specificity, sensitivity, positive predictive value (PPV), and negative predictive value (NPV) of IgM were 100, 95.24, 100, and 91.84%, whereas those of IgG were 100, 97.02, 100, and 94.74%, respectively. We developed a highly sensitive and specific SARS-CoV-2 nucleocapsid protein-based ELISA method for the diagnosis and epidemiologic investigation of COVID-19 by SARS-CoV-2 IgM and IgG antibody detection.

Neutralizing and binding antibody kinetics of COVID-19 patients during hospital and convalescent phases (preprint)

Background: Knowledge of host immune response after natural SARS-CoV-2 infection is essential for the direction of vaccination and epidemiological control strategies against COVID-19. Methods: : Thirty-four COVID-19 patients were enrolled with 244 serial blood specimens (38.1% after hospital discharge) collected to explore the chronological evolution of neutralizing (NAb), total (TAb), IgM, IgG and IgA antibody in parallel. Results: : IgG titers reached a peak later (35 days postonset) than those of Nab, Ab, IgM and IgA (25 days postonset). IgM levels declined with an estimated half-life of 35 days postonset, which was more rapid than those of IgA and IgG (73-76 days postonset). All patients remained positive for NAb, IgG and IgA up to 3 months after illness onset. The relative contribution of IgM to NAb was higher than that of IgG (standardized β regression coefficient: 0.53 vs 0.48). However, the relative contribution of IgG to NAb increased and that of IgM further decreased after 6 weeks postonset. Conclusions: : This study suggests that SARS-CoV-2 infection induces robust neutralizing and binding antibody responses in patients. Humoral immunity against SARS-CoV-2 acquired by infection may persist for a relatively long time.

Seroprevalence and asymptomatic carrier status of SARS-CoV-2 in Wuhan City and other places of China.

Wuhan City (WH) in China was the first place to report COVID-19 in the world and the outbreak of COVID-19 was controlled in March of 2020 in WH. It is unclear what percentage of people were infected with SARS-CoV-2 and what percentage of population is carriers of SARS-CoV-2 in WH. We retrospectively analyzed the SARS-CoV-2 IgG and IgM antibody positive rates in 63,107 healthy individuals from WH and other places of China using commercial colloidal gold detection kits from March 6 to May 3, 2020. Statistical approaches were utilized to explore the difference and correlation for the seropositive rate of IgG and IgM antibody on the basis of sex, age group, geographic region and detection date. The total IgG and IgM antibody positive rate of SARS-CoV-2 was 1.68% (186/11,086) in WH, 0.59% (226/38,171) in Hubei Province without Wuhan (HB), and 0.38% (53/13,850) in the nation except for Hubei Province (CN), respectively. The IgM positive rate was 0.46% (51/11,086) in WH, 0.13% (51/38,171) in HB, and 0.07% (10/13,850) in CN. The incidence of IgM positive rates in healthy individuals increased from March 6 to May 3, 2020 in WH. Female and older age had a higher probability of becoming infected than males (OR = 1.34; 95% CI: 1.08-1.65) or younger age (OR = 2.25; 95% CI: 1.06-4.78). The seroprevalence of SARS-CoV-2 was relatively low in WH and other places of China, but it is significantly high in WH than other places of China; a large amount of asymptomatic carriers of SARS-CoV-2 existed after elimination of clinical cases of COVID-19 in Wuhan City. Therefore, SARS-CoV-2 may exist in a population without clinical cases for a long period.

Identification of cGAS as an innate immune sensor of extracellular bacterium Pseudomonas aeruginosa.

Cyclic GMP-AMP synthase (cGAS) is reported essential for detecting intracellular bacteria. However, it remains to be determined whether and how cGAS is involved in extracellular bacterial infection. Here, we report that cGAS is essential for mediating type I interferon (IFN) production in infection by multiple extracellular pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus. In addition, the canonical cGAS-stimulator of interferon gene (STING)-IFN axis is required for protecting mice from P. aeruginosa-induced mouse acute pulmonary infection, confirmed in cGAS pathway-specific gene deficiency mouse models. cGAS -/- and STING -/- mice exhibited reduced type I IFNs production, excessive inflammatory response accompanied with decreased resistance to P. aeruginosa challenge. Unfolded protein response was also modulated by cGAS through IRF3 and type I IFNs under P. aeruginosa infection. Collectively, these findings uncover the importance of cGAS in initiating immune responses against extracellular bacterial infection.

Real-time naive case fatality rates can reflect timeliness of case confirmation during pandemics.

An objective law was observed that naive case fatality rates (CFRs) of a disease will decrease early and then gradually increase infinitely near the true CFR as time went on during an outbreak. The normal growth of naive CFR was an inherent character rather than indicating the disease was becoming more severe. According to the law, by monitoring real-time naive CFRs, it can help outbreak-controllers know if there were many cases left unconfirmed or undiscovered in the outbreak. We reflected on the use of the naive CFR in the context of COVID-19 outbreaks. The results showed that Hubei Province of China, France and South Korea had cases that were not confirmed in a timely manner during the initial stages of the outbreak. Delayed case confirmations existed for long periods of time in France, Italy, the United Kingdom, the Netherlands and Spain. Monitoring of real-time naive CFRs could be helpful for decision-makers to identify under-reporting of cases during pandemics.

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

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

Neutralizing and binding antibody kinetics of COVID-19 patients during hospital and convalescent phases (preprint)

Knowledge of the host immune response after natural SARS-CoV-2 infection is essential for informing directions of vaccination and epidemiological control strategies against COVID-19. In this study, thirty-four COVID-19 patients were enrolled with 244 serial blood specimens (38.1% after hospital discharge) collected to explore the chronological evolution of neutralizing (NAb), total (TAb), IgM, IgG and IgA antibody in parallel. IgG titers reached a peak later (approximately 35 days postonset) than those of Nab, Ab, IgM and IgA (20~25 days postonset). After peaking, IgM levels declined with an estimated average half-life of 10.36 days, which was more rapid than those of IgA (51.25 days) and IgG (177.39 days). Based on these half-life data, we estimate that the median times for IgM, IgA and IgG to become seronegative are 4.59 (IQR 4.12-5.03), 7.78 (IQR 6.71-9.16) and 42.72 (IQR 33.75-47.96) months post disease onset. The relative contribution of IgM to NAb was higher than that of IgG (standardized {beta} regression coefficient: 0.53 vs 0.48), so the rapid decline in NAb may be attributed to the rapid decay of IgM in acute phase. However, the relative contribution of IgG to NAb increased and that of IgM further decreased after 6 weeks postonset. It's assumed that the decline rate of NAb might slow down to the same level as that of IgG over time. This study suggests that SARS-CoV-2 infection induces robust neutralizing and binding antibody responses in patients and that humoral immunity against SARS-CoV-2 acquired by infection may persist for a relatively long time.

Serology characteristics of SARS-CoV-2 infection since exposure and post symptom onset

BACKGROUND: Timely diagnosis of SARS-CoV-2 infection is a prerequisite for treatment and prevention. The serology characteristics and complement diagnosis value of the antibody test to RNA test need to be demonstrated. METHOD: Serial sera of 80 patients with PCR-confirmed COVID-19 were collected at the First Affiliated Hospital of Zhejiang University, China. Total antibody (Ab), IgM and IgG antibodies against SARS-CoV-2 were detected, and the antibody dynamics during the infection were described. RESULTS: The seroconversion rates for Ab, IgM and IgG were 98.8%, 93.8% and 93.8%, respectively. The first detectible serology marker was Ab, followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 days post exposure (d.p.e) or 9, 10 and 12 days post onset (d.p.o), respectively. The antibody levels increased rapidly beginning at 6 d.p.o. and were accompanied by a decline in viral load. For patients in the early stage of illness (0-7 d.p.o), Ab showed the highest sensitivity (64.1%) compared to IgM and IgG (33.3% for both, p<0.001). The sensitivities of Ab, IgM and IgG increased to 100%, 96.7% and 93.3% 2 weeks later, respectively. When the same antibody type was detected, no significant difference was observed between enzyme-linked immunosorbent assays and other forms of immunoassays. CONCLUSIONS: A typical acute antibody response is induced during SARS-CoV-2 infection. Serology testing provides an important complement to RNA testing in the later stages of illness for pathogenic specific diagnosis and helpful information to evaluate the adapted immunity status of patients.