Fast de novo antibody structure prediction with atomic accuracy

Background: In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2 (AF2), a breakthrough in the field of structural biology, provides a solution to this protein structure prediction problem by learning a deep learning model. However, the computational efficiency and undesirable prediction accuracy on antibody, especially on the complementarity-determining regions limit its applications in de novo antibody design. Method(s): To learn informative representation of antibodies, we trained a deep antibody language model (ALM) on curated sequences from observed antibody space database via a well-designed transformer model. We also developed a novel model named xTrimoABFold++ to predict antibody structure from antibody sequence only based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame aligned point loss. Result(s): xTrimoABFold++ outperforms AF2 and OmegaFold, HelixFold-Single with 30+% improvement on RMSD. Also, it is 151 times faster than AF2 and predicts antibody structure in atomic accuracy within 20 seconds. In recently released antibodies, for example, cemiplimab of PD1 (PDB: 7WVM) and cross-neutralizing antibody 6D6 of SARS-CoV-2 (PDB: 7EAN), the RMSD of xTrimoABFold++ are 0.344 and 0.389 respectively. Conclusion(s): To the best of our knowledge, xTrimoABFold++ achieved the state-of-the-art in antibody structure prediction. Its improvement on both accuracy and efficiency makes it a valuable tool for de novo antibody design, and could make further improvement in immuno-theory.

Relay activism and the flows of contentious publicness on WeChat: a case study of COVID-19 in China

This paper explores a case of public contention against the censoring of a feature article about a COVID-19 whistleblower on the Chinese social media, WeChat. Moving beyond the normative theory of the public sphere and publics, we draw on Kavada and Poell's theory of 'contentious publicness' which is flexible enough to capture the complexity, diversity and hybridity of digital contention in the context of China. Through a combination of textual analysis and participatory observation, this article analyses how citizens challenged the censorship system and attempted to keep Dr Fen's story online through what we call 'relay activism'. Informed by the three dimensions of 'contentious publicness', we analyse the materiality of the communication infrastructure of WeChat and the temporal and spatial relations of the public contention (focusing primarily on WeChat and GitHub). In doing this, the paper contributes a more comprehensive approach to examining the social, structural and participatory characteristics of the contestation of censorship in China.

Visual analysis of mask sales data based on crawler

The outbreak of COVID-19 makes people feel distant from each other, and masks have become one of the indispensable articles in People's Daily life. At present, there are many brands of masks with various types and uneven quality. In order to understand the current market of masks and the sales of different brands, users can choose masks with perfect quality. This paper uses Python web crawler technology, based on the input of the word "mask", crawl JD website sales data, through data visualization technology drawing histogram, pie chart, the word cloud, etc., for goods compared with the relationship between price, average price of all brands, brands, average distribution of analysis and evaluation of user information, In this way, the sales situation, price distribution and quality evaluation of each store of the product can be visually displayed. At the same time, it also provides some reference for other users who need to buy the product. © The Authors. Published under a Creative Commons Attribution CC-BY 3.0 License.

Disease X Testing: The results of an international external quality assessment exercise

The United Nations Secretary-General Mechanism (UNSGM) for investigation of the alleged use of chemical and biological weapons is the only established international mechanism of this type under the UN. The UNGSM may launch an international investigation, relying on a roster of expert consultants, qualified experts, and analytical laboratories nominated by the member states. Under the framework of the UNSGM, we organized an external quality assurance exercise for nominated laboratories, named the Disease X Test, to improve the ability to discover and identify new pathogens that may cause possible epidemics and to determine their animal origin. The "what-if" scenario was to identify the etiological agent responsible for an outbreak that has tested negative for many known pathogens, including viruses and bacteria. Three microbes were added to the samples, Dabie bandavirus, Mammarenavirus, and Gemella spp., of which the last two have not been taxonomically named or published. The animal samples were from Rattus norvegicus, Marmota himalayana, New Zealand white rabbit, and the tick Haemaphysalis longicornis. Of the 11 international laboratories that participated in this activity, six accurately identified pathogen X as a new Mammarenavirus, and five correctly identified the animal origin as R. norvegicus. These results showed that many laboratories under the UNSGM have the capacity and ability to identify a new virus during a possible international investigation of a suspected biological event. The technical details are discussed in this report.Copyright © 2022

Anomalies of O3, CO, C2H2, H2CO, and C2H6 detected with multiple ground-based Fourier-transform infrared spectrometers and assessed with model simulation in 2020: COVID-19 lockdowns versus natural variability

Anomalies of tropospheric columns of ozone (O3), carbon monoxide (CO), acetylene (C2H2), formaldehyde (H2CO), and ethane (C2H6) are quantified during the 2020 stringent COVID-19 world-wide lockdown using multiple ground-based Fourier-transform infrared spectrometers covering urban and remote conditions. We applied an exponential smoothing forecasting approach to the data sets to estimate business-as-usual values for 2020, which are then contrasted with actual observations. The Community Atmosphere Model with chemistry (CAM-chem) is used to simulate the same gases using lockdown-adjusted and business-as-usual emissions. The role of meteorology, or natural variability, is assessed with additional CAM-chem simulations. The tropospheric column of O3 declined between March and May 2020 for most sites with a mean decrease of 9.2% ± 4.7%. Simulations reproduce these anomalies, especially under background conditions where natural variability explains up to 80% of the decline for sites in the Northern Hemisphere. While urban sites show a reduction between 1% and 12% in tropospheric CO, the remote sites do not show a significant change. Overall, CAM-chem simulations capture the magnitude of the anomalies and in many cases natural variability and lockdowns have opposite effects. We further used the long-term record of the Measurements of Pollution in the Troposphere (MOPITT) satellite instrument to capture global anomalies of CO. Reductions of CO vary highly across regions but North America and Europe registered lower values in March 2020.The absence of CO reduction in April and May, concomitant with reductions of anthropogenic emissions, is explained by a negative anomaly in the hydroxyl radical (OH) found with CAM-chem.The implications of these findings are discussed for methane (CH4), which shows a positive lifetime anomaly during the COVID-19 lockdown period. The fossil fuel combustion by-product tracer C2H2 shows a mean drop of 13.6% ± 8.3% in urban Northern Hemisphere sites due to the reduction in emissions and in some sites exacerbated by natural variability. For some sites with anthropogenic influence there is a decrease in C2H6.The simulations capture the anomalies but the main cause may be related to natural variability. H2CO declined during the stringent 2020 lockdown in all urban sites explained by reductions in emissions of precursors. Copyright: © 2023 The Author(s).

Symptom Based Models of COVID-19 Infection Using AI

Coronavirus Disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV2) has spread around the world in a global pandemic [1-4]. Early and daily detection of suspected COVID-19 patients is the most important approach not only for tracing close contacts to prevent further spread [5], but also providing crucial information for healthcare providers and officials to make resource allocation and policy decisions [6]. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2022.

Research progress of ulinastatin in treatment of COVID-19.

Coronavirus disease 2019 (COVID-19) is still spreading worldwide. At present, no specific drug has been developed for the virus. Ulinastatin plays an important role in anti-inflammatory. Clinically, it is mainly used in acute pancreatitis, shock and disseminated intravascular coagulation. It also has the effects of antioxidant stress, anticoagulation and immune regulation, which may be of great significance to reduce the severity and mortality of COVID-19. Combined with the pharmacological effect of ulinastatin and its clinical application in the treatment of COVID-19 complications such as acute respiratory distress syndrome and sepsis lung injury, this paper discusses the feasibility of its application in COVID-19, so as to provide help for the clinical treatment and new drug research and development of this disease.Copyright © 2022 Tianjin Press of Chinese Herbal Medicines. All Rights Reserved.

Exploration of potential mechanism of SARS-CoV-2 induced immune inflammatory response leading to progression of atherosclerosis and prediction of traditional Chinese medicine for preventing and treating based on bioinformatics.

Objective To explore the core targets and important pathways of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) induced atherosclerosis (AS) progression from the perspective of immune inflammation, so as to predict the potential prevention and treatment of traditional Chinese medicine (TCM). Methods Microarray data were obtained from the Gene Expression Omnibus (GEO) database for coronavirus disease 2019 (COVID-19) patients and AS patients, and the "limmar" and "Venn" packages were used to screen out the common differentially expressed genes (DEGs) genes in both diseases. The gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed on the common DEGs to annotate their functions and important pathways. The two gene sets were scored for immune cells and immune function to assess the level of immune cell infiltration. The protein-protein interaction (PPI) network was constructed by STRING database, and the CytoHubba plug-in of Cytoscape was used to identify the hub genes. Two external validation datasets were introduced to validate the hub genes and obtain the core genes. Immuno-infiltration analysis and gene set enrichment analysis (GSEA) were performed on the core genes respectively. Finally the potential TCM regulating the core genes were predicted by Coremine Medical database. Results A total of 7898 genes related to COVID-19, 471 genes related to AS progression;And 51 common DEGs, including 32 highly expressed genes and 19 low expressed genes were obtained. GO and KEGG analysis showed that common DEGs, which were mainly localized in cypermethrin-encapsulated vesicles, platelet alpha particles, phagocytic vesicle membranes and vesicles, were involved in many biological processes such as myeloid differentiation factor 88 (MyD88)-dependent Toll-like receptor signaling pathway transduction, interleukin-8 (IL-8) production and positive regulation, IL-6 production and positive regulation to play a role in regulating nicotinamide adenine dinucleotide phosphate oxidase activity, Toll-like receptor binding and lipopeptide and glycosaminoglycan binding through many biological pathways, including Toll-like receptor signaling pathways, neutrophil extracellular trap formation, complement and coagulation cascade reactions. The results of immune infiltration analysis demonstrated the state of immune microenvironment of COVID-19 and AS. A total of 5 hub genes were obtained after screening, among which Toll-like receptor 2 (TLR2), cluster of differentiation 163 (CD163) and complement C1q subcomponent subunit B (C1QB) genes passed external validation as core genes. The core genes showed strong correlation with immune process and inflammatory response in both immune infiltration analysis and GSEA enrichment analysis. A total of 35 TCMs, including Chuanxiong (Chuanxiong Rhizoma), Taoren (Persicae Semen), Danggui (Angelicae Sinensis Radix), Huangqin (Scutellariae Radix), Pugongying (Taraxaci Herba), Taizishen (Pseudostellariae Radix), Huangjing (Polygonati Rhizoma), could be used as potential therapeutic agents. Conclusion TLR2, CD163 and C1QB were the core molecules of SARS-CoV-2-mediated immune inflammatory response promoting AS progression, and targeting predicted herbs were potential drugs to slow down AS progression in COVID-19 patients.Copyright © 2023 Editorial Office of Chinese Traditional and Herbal Drugs. All rights reserved.

Maintainers of Stability: The Labor of China's Data-Driven Governance and Dynamic Zero-COVID

This paper examines the social, technological, and emotional labor of maintaining China's data-driven governance broadly, and dynamic zero-COVID management in particular. Drawing on ethnographic research in China, we examine the sociotechnical work of maintenance during the 2022 Shanghai lockdown. This labor included coordinating mass testing, quarantine, and lockdown procedures as well as implementing ad-hoc technological workarounds and managing public sentiments. We demonstrate that, far from being effected from the top down, China's data-driven governance relies on the circumscribed participation of citizens. During Shanghai's lockdown, citizens with relevant expertise helped to maintain technological stability by fixing or programming data systems, but also to ensure the ongoing production of"positive feelings"about social stability through data-driven governance. In so doing, such citizens simultaneously enacted an ambivalent and circumscribed form of agency, and maintained social and by extension political stability. This article sheds light on data-driven governance and political processes of maintenance. © 2023 ACM.

A selectivity-enhanced colloidal crystal array for ribavirin sensing based on the synergistic effect of covalent and non-covalent interactions

Ribavirin is an important antiviral with demonstrated activity against coronaviruses such as severe acute respiratory syndrome coronavirus and coronavirus disease 2019 virus. However, abuse of ribavirin will cause great environmental damage and threaten human health owing to its reproductive toxicity and teratogenicity. Therefore, an innovative detection method is demanded for simple and sensitive detection of ribavirin. This work reports an imprinted colloidal crystal array (ICCA) for ribavirin sensing. The building blocks of the ICCA are ribavirin imprinted spheres, which possess superior binding efficiency toward ribavirin. Benefiting from the highly ordered structure, the ICCA exhibits optical properties which change upon binding ribavirin. The changes in reflectance wavelength enable a fast and label-free detection of ribavirin between 21 and 245 μmol L−1. Moreover, the sensor shows excellent selectivity for ribavirin detection in river water. Overall, all the results reported in this work demonstrate that the ICCA should be a promising detection tool for antivirals. © 2023 Society of Industrial Chemistry. © 2023 Society of Industrial Chemistry.

Epidemiological characteristics of four times of community transmission of COVID-19 in Hebei

Objective To analyze the epidemiological characteristics of community transmission of the coronavirus disease 2019 (COVID-19) caused by four imported cases in Hebei Province, and to provide a scientific basis for the prevention and control of the disease. Methods Descriptive epidemiological methods were used to analyze the epidemiological characteristics of four community-transmitted COVID-19 outbreaks reported in the China Disease Control and Prevention Information System from January 1, 2020 to December 31, 2021 in Hebei Province. Results From January 1, 2020 to December 31, 2021, four community-transmitted COVID-19 outbreaks caused by imported COVID-19 occurred in Hebei Province, respectively related of Hubei (Wuhan) Province, Beijing Xinfadi market, Overseas cases and Ejina banner of Inner Mongolia Autonomous Region. Total of 1 656 cases (1 420 confirmed cases and 236 asymptomatic cases) were reported, including 375 cases in phase A (From January 22 to April 16, 2020), and phase B (from June 14 to June 24, 2020) 27 cases were reported, with 1 116 cases reported in the third phase (Phase C, January 2 to February 14, 2021), and 138 cases reported in the fourth phase (Phase D, October 23 to November 14, 2021). The 1 656 cases were distributed in 104 counties of 11 districts (100.00%), accounting for 60.46% of the total number of counties in the province. There were 743 male cases and 913 female cases, with a male to female ratio of 0.81:1. The minimum age was 13 days, the maximum age was 94 years old, and the average age (median) was 40.3 years old. The incidence was 64.01% between 30 and 70 years old. Farmers and students accounted for 54.41% and 14.73% of the total cases respectively. Of the 1 420 confirmed cases, 312 were mild cases, accounting for 21.97%;Common type 1 095 cases (77.11%);There was 1 severe case and 12 critical cases, accounting for 0.07% and 0.85%, respectively. 7 patients died from 61.0 to 85.7 years old. The mean (median) time from onset to diagnosis was 1.9 days (0-31 days), and the mean (median) time of hospital stay was 15 days (1.5-56 days). Conclusions Four times in Hebei province COVID-19 outbreak in scale, duration, population, epidemic and type of input source, there are some certain difference, but there are some common characteristics, such as the outbreak occurs mainly during the legal holidays or after starting and spreading epidemic area is mainly in rural areas, aggregation epidemic is the main mode of transmission, etc. To this end, special efforts should be made to strengthen the management of people moving around during holidays, and strengthen the implementation of epidemic prevention and control measures in places with high concentration of people. To prevent the spread of the epidemic, we will step up surveillance in rural areas, farmers' markets, medical workers and other key areas and groups, and ensure early detection and timely response.Copyright © 2022 China Tropical Medicine. All rights reserved.

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease. IMPORTANCE COVID-19 involves a number of organ systems and can present with a wide range of symptoms. From how the virus infects cells to how it spreads between people, the available research suggests that these patterns are very similar to those seen in the closely related viruses SARS-CoV-1 and possibly Middle East respiratory syndrome-related CoV (MERS-CoV). Understanding the pathogenesis of the SARS-CoV-2 virus also contextualizes how the different biological systems affected by COVID-19 connect. Exploring the structure, phylogeny, and pathogenesis of the virus therefore helps to guide interpretation of the broader impacts of the virus on the human body and on human populations. For this reason, an in-depth exploration of viral mechanisms is critical to a robust understanding of SARS-CoV-2 and, potentially, future emergent human CoVs (HCoVs).Copyright © 2021 Rando et al.

Ground-Based MAX-DOAS Observation of Trace Gases from 2019 to 2021 in Huaibei, China

With the spread of the COVID-19 pandemic and the implementation of closure measures in 2020, population mobility and human activities have decreased, which has seriously impacted atmospheric quality. Huaibei City is an important coal and chemical production base in East China, which faces increasing environmental problems. The impact of anthropogenic activities on air quality in this area was investigated by comparing the COVID-19 lockdown in 2020 with the normal situation in 2021. Tropospheric NO2, HCHO and SO2 column densities were observed by ground-based multiple axis differential optical absorption spectroscopy (MAX-DOAS). In situ measurements for PM2.5, NO2, SO2 and O3 were also taken. The observation period was divided into four phases, the pre-lockdown period, phase 1 lockdown, phase 2 lockdown and the post-lockdown period. Ground-based MAX-DOAS results showed that tropospheric NO2, HCHO and SO2 column densities increased by 41, 14 and 14%, respectively, during phase 1 in 2021 vs. 2020. In situ results showed that NO2 and SO2 increased by 59 and 11%, respectively, during phase 1 in 2021 vs. 2020, but PM2.5 and O3 decreased by 15 and 17%, respectively. In the phase 2 period, due to the partial lifting of control measures, the concentration of pollutants did not significantly change. The weekly MAX-DOAS results showed that there was no obvious weekend effect of pollutants in the Huaibei area, and NO2, HCHO and SO2 had obvious diurnal variation characteristics. In addition, the relationship between the column densities and wind speed and direction in 2020 and 2021 was studied. The results showed that, in the absence of traffic control in 2021, elevated sources in the Eastern part of the city emitted large amounts of NO2. The observed ratios of HCHO to NO2 suggested that tropospheric ozone production involved NOX-limited scenarios. The correlation analysis between HCHO and different gases showed that HCHO mainly originated from primary emission sources related to SO2. © 2023 by the authors.

Understanding Digital Identity during the Pandemic: An Investigation of Two Chinese Spanish Teachers

During combatting the COVID-19 pandemic, the most widespread change in Spanish as a foreign language instruction is imperative online teaching. It demands that language teachers move all teaching activities to virtual platforms, facilitating the construction of their digital identities. However, there is scarce attention on Spanish teachers' professional development, given the necessity of understanding the evolvement of their identities across virtual learning platforms. Through the lens of a case study, this research explores the digital identities of Spanish as a foreign language teachers during the school lockdown in 2022. The data includes semi-structured interviews, virtual classroom discourse, lesson plans, and reflective writing. The results show that Spanish teachers formed multiple digital identities, including curriculum innovators, vulnerable actors, involuntary team workers, overseas returnees, and academic researchers. Among them, the first three are core identities, while overseas returnees and academic researchers are peripheral identities. Regardless, they were formed and negotiated under the influence of teachers' past experiences, the exercise of agency, emotional vulnerability, and social context. In addition, a contradictory belief in teaching was also identified during the formation of Chinese Spanish teachers' digital identities.

Shifting Trust: Examining How Trust and Distrust Emerge, Transform, and Collapse in COVID-19 Information Seeking

During crises like COVID-19, individuals are inundated with conflicting and time-sensitive information that drives a need for rapid assessment of the trustworthiness and reliability of information sources and platforms. This parallels evolutions in information infrastructures, ranging from social media to government data platforms. Distinct from current literature, which presumes a static relationship between the presence or absence of trust and people's behaviors, our mixed-methods research focuses on situated trust, or trust that is shaped by people's information-seeking and assessment practices through emerging information platforms (e.g., social media, crowdsourced systems, COVID data platforms). Our findings characterize the shifts in trustee (what/who people trust) from information on social media to the social media platform(s), how distrust manifests skepticism in issues of data discrepancy, the insufficient presentation of uncertainty, and how this trust and distrust shift over time. We highlight the deep challenges in existing information infrastructures that influence trust and distrust formation.

Will the COVID-19 Pandemic Outbreak Intensify the Resource Misallocation in China's Food Production?

Resource misallocation is one of the important manifestations of agricultural supply-side distortion and an important causal factor that hinders food production increase and affects food security. Did the COVID-19 pandemic intensify China's food production misallocation? The extent and consequences require quantitative assessment and scenario analysis. In this paper, we use a combination of input-output model and computable general equilibrium (CGE) model, and further incorporate the most important input factor in agriculture-intermediate inputs-into the model. At the same time, simulation of the pandemic impact from the demand and supply sides, respectively, and scenario analysis of the impact of the COVID-19 pandemic on China's food production. The results of the study show that: first, compared with the baseline level before the epidemic, the overall TFP growth of China's food industry chain decreased, and the TFP growth rate of the food distribution sector decreased most significantly. Second, there are significant factor misallocation distortions of capital, labor, and intermediate inputs. Third, in the short term, the period of the COVID-19 pandemic led to a decline in the vitality of the national labor market, but the return of non-farm employed labor in rural areas instead reduced the degree of labor misallocation in the food sector. Fourth, the demand side has a greater impact on China's food production, among which the consumer demand has a particularly strong impact on the resource allocation of food production, and the short-term shock will mainly have a more obvious impact on the allocation of labor factors and the allocation of intermediate input factors in the food industry chain. Accordingly, this paper proposes that in order to guarantee China's food security and adapt to the short-term characteristics of the era when the COVID-19 pandemic is rampant, China should make efforts in four areas: rational allocation of food production resources and factors, solid construction of the whole food industry chain, stable guarantee of the food market system and transfer to enhance social expectations.

The Impact of a Public Health Emergency on the Demand for Life Insurance – An Empirical Analysis Based on Severe Acute Respiratory Syndrome

We examined changes in personal life insurance purchase decisions after a public health event by incorporating perceived health risk and regret into the expected utility function. The model predicts that the epidemic will create incremental insurance demand. Based on the 2003 severe acute respiratory syndrome outbreak in China, we used a panel dataset of 30 provinces from 2000 to 2007 and applied the difference-in-differences method to confirm the prediction empirically. The results showed that the epidemic did not significantly impact the demand for life insurance in the short term but played a role in the long term. People increased their health-care expenditure and premiums for new policies after the severe acute respiratory syndrome event, suggesting that the epidemic changed people's perceived risk and triggered anticipated regret, which increased life insurance demand. Some robustness checks also supported our findings. © 2023 Institute of World Economics and Politics, Chinese Academy of Social Sciences.

[Analysis on infection sources and transmission chains of three outbreaks caused by 2019-nCoV Omicron variant in Beijing, China].

Objective: To investigate the infection sources and the transmission chains of three outbreaks caused by 2019-nCoV Omicron variant possibly spread through cross-border logistics in Beijing. Methods: Epidemiological investigation and big data were used to identify the exposure points of the cases. Close contacts were traced from the exposure points, and the cases' and environmental samples were collected for nucleic acid tests. Positive samples were analyzed by gene sequencing. Results: The Omicron variant causing 3 outbreaks in Beijing from January to April, 2022 belonged to BA.1, BA.1.1 and BA.2. The outbreaks lasted for 8, 12 and 8 days respectively, and 6, 42 and 32 cases infected with 2019-nCoV were reported respectively. International mail might be the infection source for 1 outbreak, and imported clothes might be the infection sources for another 2 outbreaks. The interval between the shipment start time of the imported goods and the infection time of the index case was 3-4 days. The mean incubation period (Q1, Q3) was 3 (2,4) days and the mean serial interval (Q1, Q3) was 3 (2,4)days. Conclusions: The 3 outbreaks highlighted the risk of infection by Omicron variant from international logistics-related imported goods at normal temperature. Omicron variant has stronger transmissibility, indicating that rapid epidemiological investigation and strict management are needed.

A Novel Framework to Forecast COVID-19 Incidence Based on Google Trends Search Data

The global outbreak of coronavirus disease 2019 (COVID-19) has spread to more than 200 countries worldwide, leading to severe health and socioeconomic consequences. As such, the topic of monitoring and predicting epidemics has been attracting a lot of interest. Previous work reported search volumes from Google Trends are beneficial in decoding influenza dynamics, implying its potential for COVID-19 prediction. Therefore, a predictive model using the Wiener methods was built based on epidemic-related search queries from Google Trends, along with climate variables, aiming to forecast the dynamics of the weekly COVID-19 incidence in Washington, DC, USA. The Wiener model, which shares the merits of interpretability, low computation costs, and adaptation to nonlinear fluctuations, was used in this study. Models with multiple sets of features were constructed and further optimized by the highest weight selecting strategy. Furthermore, comparisons to the other two commonly used prediction models based on the autoregressive integrated moving average (ARIMA) and long short-term memory (LSTM) were also performed. Our results showed the predicted COVID-19 trends significantly correlated with the actual (rho <inline-formula> <tex-math notation="LaTeX">$=$</tex-math> </inline-formula> 0.88, <inline-formula> <tex-math notation="LaTeX">$p $</tex-math> </inline-formula> <inline-formula> <tex-math notation="LaTeX">$<$</tex-math> </inline-formula> 0.0001), outperforming those with ARIMA and LSTM approaches, indicating Google Trends data as a useful tool in terms of COVID-19 prediction. Also, the model using 20 search queries with the highest weighting outperformed all other models, supporting the highest weight feature selection as a feasible criterion. Google Trends search query data can be used to forecast the outbreak of COVID-19, which might assist health policymakers to allocate health care resources and taking preventive strategies. IEEE

Massive-scale genomic analysis reveals SARS-CoV-2 mutation characteristics and evolutionary trends

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic resulted in significant societal costs. Hence, an in-depth understanding of SARS-CoV-2 virus mutation and its evolution will help determine the direction of the COVID-19 pandemic. In this study, we identified 296,728 de novo mutations in more than 2,800,000 high-quality SARS-CoV-2 genomes. All possible factors affecting the mutation frequency of SARS-CoV-2 in human hosts were analyzed, including zinc finger antiviral proteins, sequence context, amino acid change, and translation efficiency. As a result, we proposed that when adenine (A) and tyrosine (T) bases are in the context of AM (M stands for adenine or cytosine) or TA motif, A or T base has lower mutation frequency. Furthermore, we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection, which explains why SARS-CoV-2 prefers AT3 codons usage. In addition, we found a host-specific asymmetric dinucleotide mutation frequency in the SARS-CoV-2 genome, which provides a new basis for determining the origin of the SARS-CoV-2. Finally, we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS-CoV-2. © 2022 The Authors. mLife published by John Wiley & Sons Australia, Ltd. on behalf of Institute of Microbiology, Chinese Academy of Sciences.