Case clustering, contact stratification, and transmission heterogeneity of SARS-CoV-2 Omicron BA.5 variants in Urumqi, China: An observational study

Background

From August to September 2022, Urumqi, the capital of the Xinjiang Uygur Autonomous Region in China, faced its largest COVID-19 outbreak caused by the emergence of the SARS-CoV-2 Omicron BA.5.2 variants. Although the superspreading of COVID-19 played an important role in triggering large-scale outbreaks, little was known about the superspreading potential and heterogeneity in the transmission of Omicron BA.5 variants.

Methods

In this retrospective observational, contact tracing study, we identified 1139 laboratory-confirmed COVID-19 cases of Omicron BA.5.2 variants, and 51 323 test-negative close contacts in Urumqi from 7 August to 7 September 2022. By using detailed contact tracing information and exposure history of linked case-contact pairs, we described stratification in contact and heterogeneity in transmission across different demographic strata, vaccine statuses, and contact settings. We adopted beta-binomial models to characterise the secondary attack rate (SAR) distribution among close contacts and modelled COVID-19 transmission as a branching process with heterogeneity in transmission governed by negative binomial models.

Results

After the city lockdown, the mean case cluster size decreased from 2.0 (before lockdown) to 1.6, with decreased proportions of contacts in workplace and community settings compared with household settings. We estimated that 14% of the most infectious index cases generated 80% transmission, whereas transmission in the community setting presented the highest heterogeneity, with 5% index cases seeding 80% transmission. Compared with zero, one, and two doses of inactivated vaccine (Sinopharm), index cases with three doses of vaccine had a lower risk of generating secondary cases in terms of the reproduction number. Contacts of female cases, cases with ages 0-17 years, and household settings had relatively higher SAR.

Conclusions

In the context of intensive control measures, active case detection, and relatively high vaccine coverage, but with an infection-naive population, our findings suggested high heterogeneity in the contact and transmission risks of Omicron BA.5 variants across different demographic strata, vaccine statuses, and contact settings. Given the rapid evolution of SARS-CoV-2, investigating the distribution of transmission not only helped promote public awareness and preparedness among high-risk groups, but also highlighted the importance of continuously monitoring the transmission characteristics of genetic variants of SARS-CoV-2.

Prediction Model of hospitalization time of COVID-19 patients based on Gradient Boosted Regression Trees

When an outbreak of COVID-19 occurs, it will cause a shortage of medical resources and the surge of demand for hospital beds. Predicting the length of stay (LOS) of COVID-19 patients is helpful to the overall coordination of hospital management and improves the utilization rate of medical resources. The purpose of this paper is to predict LOS for patients with COVID-19, so as to provide hospital management with auxiliary decision-making of medical resource scheduling. We collected the data of 166 COVID-19 patients in a hospital in Xinjiang from July 19, 2020, to August 26, 2020, and carried out a retrospective study. The results showed that the median LOS was 17.0 days, and the average of LOS was 18.06 days. Demographic data and clinical indicators were included as predictive variables to construct a model for predicting the LOS using gradient boosted regression trees (GBRT). The MSE, MAE and MAPE of the model are 23.84, 4.12 and 0.76 respectively. The importance of all the variables involved in the prediction of the model was analyzed, and the clinical indexes creatine kinase-MB (CK-MB), C-reactive protein (CRP), creatine kinase (CK), white blood cell count (WBC) and the age of patients had a higher contribution to the LOS. We found our GBRT model can accurately predict the LOS of COVID-19 patients, which will provide good assistant decision-making for medical management.

Impact of antibody-level on viral shedding in B.1.617.2 (Delta) variant-infected patients analyzed using a joint model of longitudinal and time-to-event data

Knowledge of viral shedding remains limited. Repeated measurement data have been rarely used to explore the influencing factors. In this study, a joint model was developed to explore and validate the factors influencing the duration of viral shedding based on longitudinal data and survival data. We divided 361 patients infected with Delta variant hospitalized in Nanjing Second Hospital into two groups (≤ 21 days group and > 21 days group) according to the duration of viral shedding, and compared their baseline characteristics. Correlation analysis was performed to identify the factors influencing the duration of viral shedding. Further, a joint model was established based on longitudinal data and survival data, and the Markov chain Monte Carlo algorithm was used to explain the influencing factors. In correlation analysis, patients having received vaccination had a higher antibody level at admission than unvaccinated patients, and with the increase of antibody level, the duration of viral shedding shortened. The linear mixed-effects model showed the longitudinal variation of logSARS-COV-2 IgM sample/cutoff (S/CO) values, with a parameter estimate of 0.193 and a standard error of 0.017. Considering gender as an influencing factor, the parameter estimate of the Cox model and their standard error were 0.205 and 0.1093 (P = 0.608), the corresponding OR value was 1.228. The joint model output showed that SARS-COV-2 IgM (S/CO) level was strongly associated with the risk of a composite event at the 95% confidence level, and a doubling of SARS-COV-2 IgM (S/CO) level was associated with a 1.38-fold (95% CI: [1.16, 1.72]) increase in the risk of viral non-shedding. A higher antibody level in vaccinated patients, as well as the presence of IgM antibodies in serum, can accelerate shedding of the mutant virus. This study provides some evidence support for vaccine prevention and control of COVID-19 variants.

Superspreading potentials of SARS-CoV-2 Delta variants across different contact settings in Eastern China: A retrospective observational study

OBJECTIVES

As the genetic variants of SARS-CoV-2 continuously pose threats to global health, evaluating superspreading potentials of emerging genetic variants is of importance for region-wide control of COVID-19 outbreaks.

METHODS

By using detailed epidemiological contact tracing data of test-positive COVID-19 cases collected between July and August 2021 in Nanjing and Yangzhou, China, we assessed the superspreading potential of outbreaks seeded by SARS-CoV-2 Delta variants. The transmission chains and case-clusters were constructed according to the individual-based surveillance data. We modelled the disease transmission as a classic branching process with transmission heterogeneity governed by negative binomial models. Subgroup analysis was conducted by different contact settings and age groups.

RESULTS

We reported a considerable heterogeneity in the contact patterns and transmissibility of Delta variants in eastern China. We estimated an expected 14% (95% CI: 11-16%) of the most infectious cases generated 80% of the total transmission.

CONCLUSIONS

Delta variants demonstrated a significant potential of superspreading under strict control measures and active COVID-19 detecting efforts. Enhancing the surveillance on disease transmissibility especially in high-risk settings, along with rapid contact tracing and case isolations would be one of the key factors to mitigate the epidemic caused by the emerging genetic variants of SARS-CoV-2.

Transmission Characteristics and Inactivated Vaccine Effectiveness Against Transmission of SARS-CoV-2 Omicron BA.5 Variants in Urumqi, China

Importance

In 2022, Omicron variants circulated globally, and Urumqi, China, experienced a COVID-19 outbreak seeded by Omicron BA.5 variants, resulting in the highest number of infections in the city's record before the exit of the zero COVID-19 strategy. Little was known about the characteristics of Omicron variants in mainland China.

Objective

To evaluate transmission characteristics of Omicron BA.5 variants and the effectiveness of inactivated vaccine (mainly BBIBP-CorV) against their transmission.

Design, Setting, and Participants

This cohort study was conducted using data from an Omicron-seeded COVID-19 outbreak in Urumqi from August 7 to September 7, 2022. Participants included all individuals with confirmed SARS-CoV-2 infections and their close contacts identified between August 7 and September 7, 2022 in Urumqi.

Exposures

A booster dose was compared vs 2 doses (reference level) of inactivated vaccine and risk factors were evaluated.

Main Outcomes and Measures

Demographic characteristics, timeline records from exposure to laboratory testing outcomes, contact tracing history, and contact setting were obtained. The mean and variance of the key time-to-event intervals of transmission were estimated for individuals with known information. Transmission risks and contact patterns were assessed under different disease-control measures and in different contact settings. The effectiveness of inactivated vaccine against the transmission of Omicron BA.5 was estimated using multivariate logistic regression models.

Results

Among 1139 individuals diagnosed with COVID-19 (630 females [55.3%]; mean [SD] age, 37.4 [19.9] years) and 51 323 close contacts who tested negative for COVID-19 (26 299 females [51.2%]; mean [SD] age, 38.4 [16.0] years), the means of generation interval, viral shedding period, and incubation period were estimated at 2.8 days (95% credible interval [CrI], 2.4-3.5 days), 6.7 days (95% CrI, 6.4-7.1 days), and 5.7 days (95% CrI, 4.8-6.6 days), respectively. Despite contact tracing, intensive control measures, and high vaccine coverage (980 individuals with infections [86.0%] received ≥2 doses of vaccine), high transmission risks were found in household settings (secondary attack rate, 14.7%; 95% CrI, 13.0%-16.5%) and younger (aged 0-15 years; secondary attack rate, 2.5%; 95% CrI, 1.9%-3.1%) and older age (aged >65 years; secondary attack rate, 2.2%; 95% CrI, 1.5%-3.0%) groups. Vaccine effectiveness against BA.5 variant transmission for the booster-dose vs 2 doses was 28.9% (95% CrI, 7.7%-45.2%) and 48.5% (95% CrI, 23.9%-61.4%) for 15-90 days after booster dose. No protective outcome was detected beyond 90 days after the booster dose.

Conclusions and Relevance

This cohort study revealed key transmission characteristics of SARS-CoV-2 as they evolved, as well as vaccine effectiveness against variants. These findings suggest the importance of continuously evaluating vaccine effectiveness against emerging SARS-CoV-2 variants.

The Association Between Clinical Severity and Incubation Period of SARS-CoV-2 Delta Variants: Retrospective Observational Study

BACKGROUND

As of August 25, 2021, Jiangsu province experienced the largest COVID-19 outbreak in eastern China that was seeded by SARS-CoV-2 Delta variants. As one of the key epidemiological parameters characterizing the transmission dynamics of COVID-19, the incubation period plays an essential role in informing public health measures for epidemic control. The incubation period of COVID-19 could vary by different age, sex, disease severity, and study settings. However, the impacts of these factors on the incubation period of Delta variants remains uninvestigated.

OBJECTIVE

The objective of this study is to characterize the incubation period of the Delta variant using detailed contact tracing data. The effects of age, sex, and disease severity on the incubation period were investigated by multivariate regression analysis and subgroup analysis.

METHODS

We extracted contact tracing data of 353 laboratory-confirmed cases of SARS-CoV-2 Delta variants' infection in Jiangsu province, China, from July to August 2021. The distribution of incubation period of Delta variants was estimated by using likelihood-based approach with adjustment for interval-censored observations. The effects of age, sex, and disease severity on the incubation period were expiated by using multivariate logistic regression model with interval censoring.

RESULTS

The mean incubation period of the Delta variant was estimated at 6.64 days (95% credible interval: 6.27-7.00). We found that female cases and cases with severe symptoms had relatively longer mean incubation periods than male cases and those with nonsevere symptoms, respectively. One-day increase in the incubation period of Delta variants was associated with a weak decrease in the probability of having severe illness with an adjusted odds ratio of 0.88 (95% credible interval: 0.71-1.07).

CONCLUSIONS

In this study, the incubation period was found to vary across different levels of sex, age, and disease severity of COVID-19. These findings provide additional information on the incubation period of Delta variants and highlight the importance of continuing surveillance and monitoring of the epidemiological characteristics of emerging SARS-CoV-2 variants as they evolve.

A study on the factors influencing the transfer of COVID-19 severe illness patients out of the ICU based on generalized linear mixed effect model

The clinical data of 76 severe illness patients with novel coronavirus SARS-CoV-2 from July to August, 2020 admitted to the ICU Intensive Care Unit ward in a hospital in Urumqi were collected in the paper. By using the Laplace approximation parameter estimation method based on maximum likelihood estimation, the generalized linear mixed effect model (GLMM) was established to analyze the characteristics of clinical indicators in critical patients, and to screen the main influencing factors of COVID-19 critical patients' inability to be transferred out of the ICU in a short time: age, C-reactive protein, serum creatinine and lactate dehydrogenase.

[A clinical study of haploidentical hematopoietic stem cell transplantation in the treatment of pediatric patients with acquired severe aplastic anemia: single center experience]

目的

探讨单倍型造血干细胞移植（haplo-HSCT）治疗儿童获得性重型再生障碍性贫血（SAA）的疗效。

方法

回顾性分析2011年12月1日至2017年12月1日接受haplo-HSCT的59例SAA患者。

结果

①全部59例SAA患儿中男37例、女22例，中位年龄4.5（1.2~14.8）岁，中位体重43（12~80）kg；SAA-Ⅰ型47例，SAA-Ⅱ型12例，26例为极重型再生障碍性贫血（VSAA）；首次移植56例，二次移植3例。②预处理选用白消安+环磷酰胺+抗胸腺细胞球蛋白（ATG）方案或白消安+氟达拉滨+环磷酰胺+ATG方案；采用环孢素A（CsA）+霉酚酸酯+甲氨蝶呤方案预防急性GVHD；回输单个核细胞中位数为15.60（7.74~21.04）×10⁸/kg，CD34⁺细胞中位数为4.86（3.74~7.14）×10⁶/kg。③全部59例患儿均获得中性粒细胞和血小板植入。中性粒细胞植入中位时间为13（10~19）d，血小板植入中位时间为19（9~62）d。④Ⅰ~Ⅱ、Ⅲ/Ⅳ度急性GVHD发生率分别为45.76%（27/59）、13.56%（8/59），慢性GVHD发生率为8.47%（5/59）。巨细胞病毒血症发生率为59.32%（35/59）、EB病毒血症发生率为28.81%（17/59）。⑤中位随访时间30（8~80）个月，57例无病存活，2例死亡（均死于GVHD），5年总生存率、无失败生存率均为（96.4±2.5）%。

结论

haplo-HSCT是儿童SAA疗效较好的治疗方法。

Nomogram for Predicting Time to Death After Withdrawal of Life-Sustaining Treatment in Patients With Devastating Neurological Injury

Reliable prediction of time of death after withdrawal of life-sustaining treatment in patients with devastating neurological injury is crucial to successful donation after cardiac death. Herein, we conducted a study of 419 neurocritical patients who underwent life support withdrawal at four neurosurgical centers in China. Based on a retrospective cohort, we used multivariate Cox regression analysis to identify prognostic factors for patient death, which were then integrated into a nomogram. The model was calibrated and validated using data from an external retrospective cohort and a prospective cohort. We identified 10 variables that were incorporated into a nomogram. The C-indexes for predicting the 60-min death probability in the training, external validation and prospective validation cohorts were 0.96 (0.93-0.98), 0.94 (0.91-0.97), and 0.99 (0.97-1.00), respectively. The calibration plots after WLST showed an optimal agreement between the prediction of time to death by the nomogram and the actual observation for all cohorts. Then we identified 22, 26 and 37 as cut-points for risk stratification into four groups. Kaplan-Meier curves indicated distinct prognoses between patients in the different risk groups (p < 0.001). In conclusion, we have developed and validated a nomogram to accurately identify potential cardiac death donors in neurocritical patients in a Chinese population.

Removal of fluoride from water by carbon nanotube supported alumina

This paper describes a new adsorption material carbon nanotube supported alumina, used for fluoride removal from water. The effects of calcination temperature, alumina loading and pH on fluoride removal capacity were investigated. The optimum calcination temperature for preparing the adsorbents is 450 degrees C and the largest adsorption capacity takes place at alumina loading of 30 wt%. The broad pH range of 6.0-9.0 with high adsorption capability suggests that carbon nanotube supported alumina have great potential applications in practice. The adsorption data at different pH were well fitted to the Freundlich isotherm. The kinetic studies show that the adsorption reaction of fluoride removal by carbon nanotube supported alumina can be described by a second orderrate equation.

[Treatment of 2-naphtholwastewater using air oxidation and ion exchange]

The properties of 2-naphtholwastewater were studied in details in this paper, the wastewater was characterized by the strong acidity, high buffer capability and concentrated salt. Air oxidation and anion exchange were employed for the treatment of the wastewater. Under formal pH, room temperature and 1 BV/h rate, the result showed that the removal of COD reached to 97% and the recovery of sodium naphthalensulfonate to 98%. Besides, wastewater treated can be reused for washing the sodium naphthalensulfonate.

The scaffolding protein CASK mediates the interaction between rabphilin3a and beta-neurexins

CASK, a member of the membrane-associated guanylate kinase (MAGUK) superfamily, binds to the carboxyl-terminus of beta-neurexins on the intracellular side of the presynaptic membrane. The guanylate kinase-like (GUK) domains of MAGUKs lack kinase activities, but might be important for mediating specific protein-protein interaction. By a yeast two-hybrid approach, we identified an interaction between the GUK domain of CASK and the C2B domain of rabphilin3a, a presynaptic protein involved in synaptic vesicle exocytosis. The interaction was confirmed by in vitro GST pull-down and co-immunoprecipitation assays. It was proposed that presynaptic vesicles might be guided to the vicinity of points of exocytosis defined by beta-neurexins via the interaction between rabphilin3a-CASK-beta-neurexins.

[Relationship between obese gene expressive product and simple obesity in children]

OBJECTIVE

To investigate the relationship between obese gene expressive product-obese protein (OP) and the pathogenesis and prognosis of simple obesity in 30 children with normal body weight (control group).

METHODS

Before immunoassay, OP was extracted from the whole blood samples with Sep-pak C(18) Cartridge.

RESULTS

The plasma contents of OP in the obese group were (118.53 +/- 25.02) ng/L and (197.14 +/- 26.83) ng/L (P < 0.001), respectively. In the obese group, plasma OP was not detected in three cases and was (19.90 +/- 3.94) ng/L in other three cases. These obese children with severe OP deficit not only had more increased body mass index, and levels of total cholesterol, triglyceride and low-density lipoprotein-cholesterol, but also had lower therapeutic effect (16.67%) than those with mild OP depletion (79.16%).

CONCLUSION

The children with simple obesity have OP deficit. Simple obesity may be related with the reduced plasma content of OP. The obese children with severe OP deficit have poorer curative effect and unfavorable prognosis.