Flattening the Curve is Imperative: When China Relaxes the Dynamic Zero COVID-19 Policy

Since December 7, 2022, China relaxed the strict dynamic zero COVID-19 policy. Here we quantitatively analyze its potential impacts on COVID-19 trend with the epidemiological model SUVQC using the population and parameter settings of Beijing as a case. Our results indicate that if non-pharmacological interventions are completely ceased, the ICU bed demand number will peak in 26 days at [~]23.88 thousand, which is 18 times the total number of ICU beds in Beijing. COVID-19 Omicron will cause 31,817 deaths in Beijing in the first year. We urge that the flattening curve strategy is necessary to slow down the infection and avoid overwhelming the healthcare system.

Genomic epidemiology of SARS-CoV-2 in Pakistan

Pakistan has been severely affected by the COVID-19 pandemic. To investigate the initial introductions and transmissions of the SARS-CoV-2 in the country, we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected before June 1, 2020. We identified a total of 347 variants, 29 of which were over-represented in Pakistan. Meanwhile, we found over one thousand intra-host single-nucleotide variants. Several of them occurred concurrently, indicating possible interactions among them. Some of the hypermutable positions were not observed in the polymorphism data, suggesting strong purifying selections. The genomic epidemiology revealed five distinctive spreading clusters. The largest cluster consisted of 74 viruses which were derived from different geographic locations and formed a deep hierarchical structure, indicating an extensive and persistent nation-wide transmission of the virus that was probably contributed by a signature mutation of this cluster. Twenty-eight putative international introductions were identified, several of which were consistent with the epidemiological investigations. No progenies of any of these 150 viruses have been found outside of Pakistan, most likely due to the nonphmarcological intervention to control the virus. This study has inferred the introductions and transmissions of SARS-CoV-2 in Pakistan, which could provide a guidance for an effective strategy for disease control.

Genetic Mutation Analysis in Small Cell Lung Cancer by a Novel NGS-Based Targeted Resequencing Gene Panel and Relation with Clinical Features.

BACKGROUND: Small cell lung cancer (SCLC) is an aggressive and invasive malignancy that presents at advanced clinical stage with no more effective treatments. Development of a method for its early detection would be useful, also new therapeutic target need to be discovered; however, there is a lack of information about its oncogenic driver gene mutations. OBJECTIVES: We aim to identify the SCLC-related genomic variants that associate with clinical staging and serum protein biomarkers observed in other types of lung cancer. METHODS: We screened formalin-fixed paraffin-embedded (FFPE) biopsy tissues of 32 Chinese SCLC patients using the 303 oncogenic driver gene panel generated by Tiling PCR amplification sequencing (tPAS) and analyzed the patients' corresponding serum protein levels of CYFRA21-1 CEA, NSE, and SCCA. RESULTS: In total, we found 147 SCLC-related mutant genes, among these, three important genes (TP53, RB1, KMT2D) as well as five novel genes LRRK2, BRCA1, PTCH1, ARID2, and APC that altogether occurred in 90% of patients. Furthermore, increased mutations to 6 genes (WT1, NOTCH1, EPHA3, KDM6A, SETD2, ACVR1B) significantly associated with higher serum NSE levels (P = 0.0016) and higher clinical stages II + III compared to stage I (P = 0.06). CONCLUSIONS: Our panel is relatively reliable in detecting the oncogenic mutations of Chinese SCLC patients. Based on our findings, it may be possible to combine SCLC-related mutations and serum NSE for a simple detection of clinical staging.

Will the Large-scale Vaccination Succeed in Containing the COVID-19 Epidemic and How Soon?

The availability of vaccines provides a promising solution to containing the COVID-19 pandemic. Here, we develop an epidemiological model to quantitatively analyze and predict the epidemic dynamics of COVID-19 under vaccination. The model is applied to the daily released numbers of confirmed cases of Israel and United States of America to explore and predict the trend under vaccination based on their current epidemic status and intervention measures. For Israel, of which 53.83% of the population was fully vaccinated, under the current intensity of NPIs and vaccination scheme, the pandemic is predicted to end between May 14, 2021 to May 16, 2021 depending on an immunity duration between 180 days and 365 days; Assuming no NPIs after March 24, 2021, the pandemic will ends later, between July 4, 2021 to August 26, 2021. For USA, if we assume the current vaccination rate (0.268% per day) and intensity of NPIs, the pandemic will end between February 3, 2022 and August 17, 2029 depending on an immunity duration between 180 days and 365 days. However, assuming an immunity duration of 180 days and with no NPIs, the pandemic will not end, and instead reach an equilibrium state with a proportion of the population remaining actively infected. Overall the daily vaccination rate should be chosen according to the vaccine efficacy and the immunity duration to achieve herd immunity. In some situations, vaccination alone cannot stop the pandemic, and NPIs are necessary both to supplement vaccination and accelerate the end of the pandemic. Considering that vaccine efficacy and duration of immunity may be reduced for new mutant strains, it is necessary to remain cautiously optimistic about the prospect of the pandemic under vaccination.

Ongoing natural selection drives the evolution of SARS-CoV-2 genomes

SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in late December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 is actively evolving, and driven by adaptation to the new host and environments is still unknown. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating 22,078 SARS-CoV-2 genome sequences of 84 countries, we demonstrate with convincing evidence that (i) SARS-CoV-2 genomes are overall conserved under purifying selection. (ii) Ongoing positive selection is actively driving the evolution of specific genes. Notably, genes related to coronavirus infection and host immune system defense are under adaptive evolution while genes related to viral RNA replication, transcription and translation are under purifying selection. A spatial and temporal landscape of 54 critical mutants is constructed based on their divergence among viral haplotype clusters, of which multiple mutants potentially conferring viral transmissibility, infectivity and virulence of SARS-CoV-2 are highlighted.

Ancient familial Mediterranean fever mutations in human pyrin and resistance to Yersinia pestis.

Familial Mediterranean fever (FMF) is an autoinflammatory disease caused by homozygous or compound heterozygous gain-of-function mutations in MEFV, which encodes pyrin, an inflammasome protein. Heterozygous carrier frequencies for multiple MEFV mutations are high in several Mediterranean populations, suggesting that they confer selective advantage. Among 2,313 Turkish people, we found extended haplotype homozygosity flanking FMF-associated mutations, indicating evolutionarily recent positive selection of FMF-associated mutations. Two pathogenic pyrin variants independently arose >1,800 years ago. Mutant pyrin interacts less avidly with Yersinia pestis virulence factor YopM than with wild-type human pyrin, thereby attenuating YopM-induced interleukin (IL)-1ß suppression. Relative to healthy controls, leukocytes from patients with FMF harboring homozygous or compound heterozygous mutations and from asymptomatic heterozygous carriers released heightened IL-1ß specifically in response to Y. pestis. Y. pestis-infected MefvM680I/M680I FMF knock-in mice exhibited IL-1-dependent increased survival relative to wild-type knock-in mice. Thus, FMF mutations that were positively selected in Mediterranean populations confer heightened resistance to Y. pestis.

Modeling the Epidemic Dynamics and Control of COVID-19 Outbreak in China

BackgroundThe coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures. MethodWe develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models. ResultsThe SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30th, 2020, all these regions except Beijing had a reproductive number R > 1, and after January 30th, all regions had a reproductive number R < 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but jumps to 0.3229 after Feb 12th when clinical evidence was adopted in new diagnosis guidelines. The number of un-quarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21th, 2020. After fitting the model with data as of February 21th, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty. ConclusionWe suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries in a high risk of outbreak, such as South Korea, Japan, Italy and Iran.

Effect of dexmedetomidine on JAK2/STAT3 signaling pathway in lung tissues in a rat model of cardiopulmonary bypass / 中华麻醉学杂志

Objective:To evaluate the effect of dexmedetomidine on Janus kinase 2/signal transducer and activator of transcription 3 (JAK2/STAT3) signaling pathway in lung tissues in a rat model of cardiopulmonary bypass (CPB).Methods:Twenty-four clean-grade healthy male Sprague-Dawley rats, weighing 320-350 g, aged 12-16 weeks, were randomly divided into sham operation group (group S), CBP group, and dexmedetomidine group (group Dex), with 8 rats in each group.In group Dex, dexmedetomidine was intravenously infused in a dose of 5 μg/kg starting from 15 min before CPB followed by infusion of 5 μg·kg -1·h -1 during CPB.Blood samples were collected at 2 h after the end of CPB for blood gas analysis, and oxygenation index (OI) and respiratory index (RI) were calculated.Then the rats were sacrificed by bloodletting.The lung tissues were removed for microscopic examination of the pathological changes which were scored and for determination of wet/dry weight ratio (W/D ratio), contents of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6)(by enzyme-linked immunosorbent assay), and expression of JAK2, STAT3, phosphorylated JAK2 (p-JAK2) and phosphorylated STAT3 (p-STAT3) (by Western blot). The p-JAK2/JAK2 and p-STAT3/STAT3 ratios were calculated. Results:Compared with group S, the lung injury score, W/D ratio and RI were significantly increased, OI was decreased, the contents of TNF-α and IL-6, p-JAK2/JAK2 ratio and p-STAT3/STAT3 ratio were increased in the other two groups ( P<0.05). Compared with group CPB, the lung injury score, W/D ratio and RI were significantly decreased, OI was increased, the contents of TNF-α and IL-6, p-JAK2/JAK2 ratio and p-STAT3/STAT3 ratio were decreased in group Dex ( P<0.05). Conclusion:The mechanism by which dexmedetomidine attenuates CPB-induced lung injury may be related to inhibiting JAK2/STAT3 signaling pathway and reducing inflammatory responses in lung tissues of rats.