Analysis on traditional Chinese medicine syndrome characteristics of patients infected with severe acute respiratory syndrome coronavirus 2 omicron variant in a shelter hospital in Shanghai

Objective: To analyze the characteristics of traditional Chinese medicine (TCM) syndromes of patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant in a shelter hospital in Shanghai. Methods: A total of 621 patients infected with SARS-CoV-2 omicron variant from Apr. 4 to May 24, 2022 in a shelter hospital in Shanghai were enrolled. The data of the patients, including the general information and common clinical syndromes (such as fever, headache, stuffy nose, runny nose, cough, and sputum), were collected on admission by TCM syndrome electronic scale, and core syndrome characteristics were analyzed base on the proportion of each symptom. The syndromes were divided according to the symptom score of patients, and the differences of disease course among the syndromes were compared. Results: The proportion of patients aged 30 to 49 years old was the highest among 621 patients infected with omicron variant (49.76%, 309/621). The most prominent symptoms were cough and expectoration, accounting for 62.32% (387/621) and 68.12% (423/621), respectively. The more common symptoms included sore throat, stuffy nose, runny nose, fatigue, muscle pain, and headache. White sputum was mostly seen in the expectoration and clear mucus was mostly seen in runny nose. According to the clinical symptoms, the core syndrome characteristic of patients infected with omicron variant was cold epidemic constraint in the lung featuring dampness and toxins. The main syndrome was plague invading the defensive exterior, accounting for 40.10% (249/621). The second and third ones were heat toxin attacking the lung syndrome (29.95%, 186/621) and dampness obstructing (17.55%, 109/621), while the least common syndrome was deficiency of qi and yin (7.73%, 48/621). The course of qi and yin deficiency was longer than the other 3 syndromes (P < 0.05). Conclusion: The core TCM syndrome characteristic of patients infected with SARS-CoV-2 omicron variant is cold epidemic constraint in the lung featuring dampness and toxins. The main syndrome is plague invading the defensive exterior. The pattern tends to convert into qi and yin deficiency along the long course.

Rapid determination of SARS-CoV-2 nucleocapsid proteins based on 2D/2D MXene/P-BiOCl/Ru(bpy)32+ heterojunction composites to enhance electrochemiluminescence performance.

At the end of 2019, the novel coronavirus disease 2019 (COVID-19), a cluster of atypical pneumonia caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been known as a highly contagious disease. Herein, we report the MXene/P-BiOCl/Ru(bpy)32+ heterojunction composite to construct an electrochemiluminescence (ECL) immunosensor for SARS-CoV-2 nucleocapsid protein (CoVNP) determination. Two-dimensional (2D) material ultrathin phosphorus-doped bismuth oxychloride (P-BiOCl) is exploited and first applied in ECL. 2D architectures MXene not only act as "soft substrate" to improve the properties of P-BiOCl, but also synergistically work with P-BiOCl. Owing to the inimitable set of bulk and interfacial properties, intrinsic high electrochemical conductivity, hydrophilicity and good biocompatible of 2D/2D MXene/P-BiOCl/Ru(bpy)32+, this as-exploited heterojunction composite is an efficient signal amplifier and co-reaction accelerator in the presence of tri-n-propylamine (TPA) as a coreactant. The proposed MXene/P-BiOCl/Ru(bpy)32+-TPA system exhibits a high and stable ECL signal and achieves ECL emission quenching for "signal on-off" recognition of CoVNP. Fascinatingly, the constructed ECL biosensor towards CoVNP allows a wide linear concentration range from 1 fg/mL to 10 ng/mL and a low limit of detection (LOD) of 0.49 fg/mL (S/N = 3). Furthermore, this presented strategy sheds light on designing a highly efficient ECL nanostructure through the combination of 2D MXene architectures with 2D semiconductor materials in the field of nanomedicine. This ECL biosensor can successfully detect CoVNP in human serum, which can promote the prosperity and development of diagnostic methods of SARS-CoV-2.

Long-Acting Protective Ocular Surface by Instilling Adhesive Dual-Antiviral Nanoparticles.

The eye is susceptible to viral infections, causing severe ocular symptoms or even respiratory diseases. Methods capable of protecting the eye from external viral invasion in a long-term and highly effective way are urgently needed but have been proved to be extremely challenging. Here, a strategy of forming a long-acting protective ocular surface is described by instilling adhesive dual-antiviral nanoparticles. Taking pseudotyped severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a model virus, antiviral agent-loaded nanoparticles are coated with a "double-lock" hybrid cell membrane abundant with integrin-ß1 and angiotensin converting enzyme II (ACE2). After instillation, the presence of integrin-ß1 endows coated nanoparticles with steady adhesion via specific binding to Arg-Gly-Asp sequence on the fibronectin of ocular epithelium, achieving durable retention on the ocular surface. In addition to loaded inhibitors, the exposure of ACE2 can trap SARS-CoV-2 and subsequently neutralize the associated spike protein, playing a dual antiviral effect of the resulting nanoparticles. Adhesive dual-antiviral nanoparticles enabled by coating with a "double-lock" hybrid cell membrane could be a versatile platform for topical long-acting protection against viral infection of the eye.

Chiral-Selective Antigen-Presentation by Supramolecular Chiral Polymer Micelles.

Chirality is ubiquitous in biological systems, which is closely related to biological functions, life process, and even pathogenesis of diseases. However, the interface between the chirality of synthetic materials and organisms, particularly the immune system, remains poorly understood. Here, supramolecular chiral polymer micelles (SCPMs) are prepared by complexing antigenic proteins with chiral amino acid modified polyethyleneimine. The introduction of chirality not only reduces the toxicity of cationic polymer, but also benefits cell uptake and antigen presentation. Especially, D-chirality presents the lowest cytotoxicity, while promotes the highest expression level of costimulatory molecules on dendritic cells compared to L-chirality and achirality. The superiority of D-chirality to stimulate dendritic cell maturation is supported by immunization with D-SCPMs, which achieves significant antigen-specific proliferation of T cells in the spleen, lymph nodes and tumor of mice. Chirality-mediated antigen processing and presentation is demonstrated by D-SCPMs self-assembled from chiral alkaline histidine or neutral phenylalanine modified polyethyleneimine and tumor associated ovalbumin or severe acute respiratory syndrome coronavirus 2 spike 1 antigenic protein. Immunoactivation enabled by D-chirality opens a window to prepare potent nanotherapeutics for disease prevention and treatment. This article is protected by copyright. All rights reserved.

The Cholesterol-Binding Sequence in Monomeric C-Reactive Protein Binds to the SARS-CoV-2 Spike Receptor-Binding Domain and Blocks Interaction With Angiotensin-Converting Enzyme 2.

The receptor-binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the human angiotensin-converting enzyme 2 (ACE2) receptor, which is a prerequisite for the virus to enter the cell. C-reactive protein (CRP) is an important marker of inflammation and is a putative soluble pattern recognition receptor. Clinical elevation of CRP levels in patients with COVID-19 is one of the characteristics of the disease; however, whether CRP is involved in COVID-19 pathogenesis is unknown. Here, we report that monomeric CRP (mCRP) can bind to the SARS-CoV-2 spike RBD and competitively inhibit its binding to ACE2. Furthermore, truncated mutant peptide competition assays and surface plasmon resonance binding experiments showed that the cholesterol-binding sequence (CBS, amino acids 35-47) in mCRP was critical for mediating the binding of mCRP to spike RBD. In a cell model of spike RBD and ACE2 interaction, the CBS motif effectively reduced the binding of spike RBD to ACE2 overexpressed on the cell surface. Thus, this study highlights the pattern recognition function of mCRP in innate immunity and provides a preliminary theoretical basis for the development of the CBS motif in mCRP into a functional peptide with both diagnostic significance and potential therapeutic capabilities.

Platinum-Decorated Gold Nanoparticle-Based Microfluidic Chip Immunoassay for Ultrasensitive Colorimetric Detection of SARS-CoV-2 Nucleocapsid Protein.

Gold nanoparticle-based point-of-care tests (POCT) are one of the most widely used diagnostic tools for SARS-CoV-2 screening. However, the limitation of their insufficient sensitivity often leads to false negative results in early disease diagnostics. The ongoing pandemic of COVID-19 makes diagnostic tools that are more accurate, sensitive, simple, and affordable in high demand. In this work, we develop a platinum-decorated gold nanoparticle (Au@Pt NP)-based microfluidic chip immunoassay with a sensitivity surpassing that of paper-based detection of nucleocapsid (N) protein, one of the most conserved biomarkers of COVID-19. The synthesized Au@Pt NPs show high stability and catalytic activity in complex environments. The catalytic amplification of Au@Pt NPs enables naked-eye detection of N protein in the low femtogram range (ca. 0.1 pg/mL) and the detection of throat swab samples in under 40 min. This microfluidic chip immunoassay is easy for operation and readout without instrument assistance, making it more suitable for on-site detection and future pathogen surveillance.

The Cholesterol-Binding Sequence in Monomeric C-Reactive Protein Binds to the SARS-CoV-2 Spike Receptor-Binding Domain and Blocks Interaction With Angiotensin-Converting Enzyme 2

The receptor-binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the human angiotensin-converting enzyme 2 (ACE2) receptor, which is a prerequisite for the virus to enter the cell. C-reactive protein (CRP) is an important marker of inflammation and is a putative soluble pattern recognition receptor. Clinical elevation of CRP levels in patients with COVID-19 is one of the characteristics of the disease;however, whether CRP is involved in COVID-19 pathogenesis is unknown. Here, we report that monomeric CRP (mCRP) can bind to the SARS-CoV-2 spike RBD and competitively inhibit its binding to ACE2. Furthermore, truncated mutant peptide competition assays and surface plasmon resonance binding experiments showed that the cholesterol-binding sequence (CBS, amino acids 35-47) in mCRP was critical for mediating the binding of mCRP to spike RBD. In a cell model of spike RBD and ACE2 interaction, the CBS motif effectively reduced the binding of spike RBD to ACE2 overexpressed on the cell surface. Thus, this study highlights the pattern recognition function of mCRP in innate immunity and provides a preliminary theoretical basis for the development of the CBS motif in mCRP into a functional peptide with both diagnostic significance and potential therapeutic capabilities.

Ultrasensitive Detection of COVID-19 Virus N Protein Based on p-Toluenesulfonyl Modified Fluorescent Microspheres Immunoassay.

The pandemic of new coronary pneumonia caused by the COVID-19 virus continues to ravage the world. Large-scale population testing is the key to controlling infection and related mortality worldwide. Lateral flow immunochromatographic assay (LFIA) is fast, inexpensive, simple to operate, and easy to carry, very suitable for detection sites. This study developed a COVID-19 N protein detect strip based on p-toluenesulfonyl modified rare earth fluorescent microspheres. The p-toluenesulfonyl-activated nanomaterials provide reactive sulfonyl esters to covalently attach antibodies or other ligands containing primary amino or sulfhydryl groups to the nanomaterial surface. Antibodies are immobilized on these nanomaterials through the Fc region, which ensures optimal orientation of the antibody, thereby increasing the capture rate of the target analyte. The use of buffers with high ionic strength can promote hydrophobic binding; in addition, higher pH could promote the reactivity of the tosyl group. The detection limit of the prepared COVID-19 N protein strips can reach 0.01 ng/mL, so it has great application potential in large-scale population screening.

Research on adaptive transmission and controls of COVID-19 on the basis of a complex network.

COVID-19 has caused massive disruption on the global economy and presents a considerable risk to human lives. Some countries have successfully controlled the pandemic by adopting strict measures, such as lockdown and travel restriction, but such methods are difficult to be applied widely due to their huge costs. To explore available and low-cost solutions, this study proposes an adaptive transmission model on the basis of a complex network, and gives control simulation method of COVID-19. The suggested model considers adaptive changes such as travel network and people's travel intention to form a three-level adaptive network transmission model among cities, communities, and people. The improved susceptible-exposed-infectious-recovered-dead transmission process is integrated into the network. Simulation experiments under high-, low-, and conventional-cost controls are performed. In these experiments, the travel restriction and closing cities are considered, and sensitivity analyses of the parameters are conducted to explore low-cost measures. Meanwhile, time duration and application conditions of different controls are discussed. Results show that lockdown is the most effective way, and the contact and infection rates are the two most important factors to control the pandemic. Low-cost combined control measures are feasible and effective for most countries. Finally, several suggestions are given for national and urban preventions and controls of COVID-19 and other infectious diseases in the future.

SARS-CoV-2 immunity and functional recovery of COVID-19 patients 1-year after infection.

The long-term immunity and functional recovery after SARS-CoV-2 infection have implications in preventive measures and patient quality of life. Here we analyzed a prospective cohort of 121 recovered COVID-19 patients from Xiangyang, China at 1-year after diagnosis. Among them, chemiluminescence immunoassay-based screening showed 99% (95% CI, 98-100%) seroprevalence 10-12 months after infection, comparing to 0.8% (95% CI, 0.7-0.9%) in the general population. Total anti-receptor-binding domain (RBD) antibodies remained stable since discharge, while anti-RBD IgG and neutralization levels decreased over time. A predictive model estimates 17% (95% CI, 11-24%) and 87% (95% CI, 80-92%) participants were still 50% protected against detectable and severe re-infection of WT SARS-CoV-2, respectively, while neutralization levels against B.1.1.7 and B.1.351 variants were significantly reduced. All non-severe patients showed normal chest CT and 21% reported COVID-19-related symptoms. In contrast, 53% severe patients had abnormal chest CT, decreased pulmonary function or cardiac involvement and 79% were still symptomatic. Our findings suggest long-lasting immune protection after SARS-CoV-2 infection, while also highlight the risk of immune evasive variants and long-term consequences for COVID-19 survivors.

Association of sleep quality before and after SARS-CoV-2 infection with clinical outcomes in hospitalized patients with COVID-19 in China.

Sleep is believed to benefit the host defense against pathogens. We aimed to investigate the association of sleep quality with clinical outcomes among hospitalized patients with COVID-19. We conducted a prospective cohort study in 205 adult hospitalized patients with diagnosed moderate COVID-19, with follow-up until hospital discharge or death. Pittsburgh Sleep Quality Index (PSQI) assessed sleep quality before and after infection. The primary outcome was the incidence of severe or critical pneumonia, and the secondary outcomes were duration of hospital stay and laboratory measurements during the follow up. Among the 205 included hospitalized patients, 185 (90.2 %) experienced poorer sleep quality after infection than before according to the PSQI score, and 25 (12.2 %) developed severe or critical pneumonia during follow-up. In Cox regression models, the adjusted hazard ratio of developing severe or critical pneumonia associated with each 1 score increment in the PSQI score before and after infection was 1.23 (95% CI: 1.09, 1.39) and 1.35 (95 % CI: 1.08, 1.67), respectively. Poorer sleep quality was also significantly associated with a prolonged hospital stay and more serious dysregulations in immune system indicated by several laboratory markers. Poorer sleep quality, either in the daily time or after infection with SARS-CoV-2, was associated with worse clinical outcomes. These findings highlight the importance of good sleep in confronting the emerging pandemic of COVID-19.

Hypertension in Patients Hospitalized with COVID-19 in Wuhan, China.

It is unclear whether patients with hypertension are more likely to be infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) than the general population and whether there is a difference in the severity of coronavirus disease (COVID-19) pneumonia in patients who have taken ACEI/ARB drugs compared with those who have not.This observational study included data from all patients with clinically confirmed COVID-19 admitted to Hankou Hospital, Wuhan, China, between January 5 and March 8, 2020. Data were extracted from clinical and laboratory records. Follow-up was cut off on March 8, 2020.A total of 274 patients, 75 with hypertension and 199 without hypertension, were included in the analysis. Compared with patients without hypertension, patients with hypertension were older and were more likely to have preexisting comorbidities, including chronic renal insufficiency, cardiovascular disease, diabetes mellitus, and cerebrovascular disease. Moreover, patients with hypertension tended to have higher positive rate for SARS-CoV-2 PCR detection. Multivariate logistic regression analysis showed that age (P = 0.005) and gender (P = 0.019) were independent risk factors associated with the severity of pneumonia in patients on admission, whereas ACEI/ARB treatment (P = 0.184) was not.Patients with COVID-19 with hypertension were significantly older and were more likely to have underlying comorbidities, including chronic renal insufficiency, cardiovascular disease, diabetes mellitus, and cerebrovascular disease. ACEI/ARB drugs did not influence the severity of pneumonia in patients with SARS-CoV-2. In future studies, a larger sample size and multi-center clinical data would be needed to support these conclusions.

The impact of COVID-19 on China’s regional economies and industries

Scientifically assessing the economic impact of major public health emergencies, containing their negative effects, and enhancing the resilience of an economy are important national strategic needs. The new coronavirus disease (COVID-19) has, to date, been effectively contained in China, but the threat of imported cases and local risks still exist. The systematic identification of the virus’s path of influence and intensity is significant for economic recovery. This study is based on a refined multi-regional general equilibrium analysis model, which measures the economic and industrial impacts at different epidemic risk levels in China and simulates development trends and the degree of damage to industries and the economy under changes to supplies of production materials and product demand. The results show that, at the macroeconomic level, China’s GDP will decline about 0.4% to 0.8% compared to normal in 2020, with an average drop of about 2% in short-term consumption, an average drop in employment of about 0.7%, and an average increase in prices of about 0.9%. At the industry level, the epidemic will have the greatest short-term impact on consumer and laborintensive industries. For example, the output value of the service industry will fall 6.3% compared to normal. Looking at the impact of the epidemic on the industrial system, the province most affected by the epidemic is Hubei, which is the only province in China in the level-1 risk category. As the disease spread outward from Hubei, there were clear differences in the main industries that were impacted in different regions. In addition, simulation results of recovery intensity of regional economies under the two epidemic response scenarios of resumption of work and production and active fiscal stimulus policies show that an increase in fiscal stimulus policies produces a 0.3% higher rate of gross regional product growth but it causes commodity prices to rise by about 1.8%. Measures to resume work and production offer a wider scope for industrial recovery.

Epidemiological and Clinical Characteristics of 217 Cases of COVID-19 in Jiangsu Province, China.

BACKGROUND COVID-19 has become a worldwide epidemic disease and is a public health crisis. We aim to provide evidence for clinical diagnosis and assessment of severity by analyzing patients' clinical data and early laboratory results and exploring the correlation between laboratory results and clinical classification. MATERIAL AND METHODS We enrolled 283 cases of suspected and diagnosed COVID-19 from 16 hospitals in Jiangsu Province from January to April 2020. The routine laboratory blood examinations, T lymphocyte subsets, and biochemical and coagulation function among different populations were contrasted by t test and chi-square (χ²) test. RESULTS Cough, fever, and dyspnea could be helpful to diagnose COVID-19 infection (P<0.05). Patients who were older or had comorbidities tended to become severe and critical cases. Among all the patients, the most obvious abnormal laboratory results were higher neutrophil count, CRP, total bilirubin, BUN, CRE, APTT, PT, and D-dimer, and lower blood platelet and lymphocyte count. CD3⁺ T cell, CD4⁺ T cell, and CD8⁺ T cell counts gradually decreased with exacerbation of the disease (P<0.05). CONCLUSIONS Cough and fever were the most common symptom. Patients with comorbidities were in more serious condition. The detection of inflammatory indexes, coagulation function, lymphocyte subsets, and renal function can help diagnose and assess the severity of COVID-19.

Perceived family adaptability and cohesion and depressive symptoms: A comparison of adolescents and parents during COVID-19 pandemic.

OBJECTIVE: To compare the differences of depressive symptoms and perceived family cohesion and adaptability between adolescents and parents during the pandemic; to explore the association between depressive symptoms and family cohesion and adaptability. METHODS: A total of 8,940 adolescents (45.77% males; Mean age=15.31±0.018 years old) and their parents (24.34% males; Mean age=40.78±0.60 years old) from Shenyang, Liaoning Province, China, participated in the survey and completed several questionnaires online. We used the Patient Health Questionnaire-9 (PHQ-9) and the Family Adaptability Cohesion Scale, Second Edition, Chinese version (FACES II-CV) to evaluate depressive symptoms and family cohesion and family adaptability from the perception of parents and adolescents. RESULTS: Results indicated significant differences between adolescents' and parents' perspectives of family functions. Significant negative correlations exist between depressive symptoms and family cohesion and family adaptability from the perspectives of both adolescents and parents. In addition, regression models with demographic characteristics adjusted showed that the perceived family cohesion and adaptability of parents and adolescents and the agreements between them could be predicted by their depressive symptoms. LIMITATION: Cross-sectional study and limited population-wide are limitations. CONCLUSION: Detecting the depressive symptoms of adolescents and parents earlier and promptly providing family intervention are of great significance to promote their perceptions of family cohesion and adaptability, which contribute to the mental health development of adolescents and parents during the COVID-19 pandemic.

Mycobacterium vaccae Nebulization in the Treatment of COVID-19: A Randomized, Double-Blind, Placebo-Controlled Trial.

Background: Severe acute respiratory syndrome coronavirus 2 infection is associated with strong infectiousness and has no effective therapy. We aimed to explore the efficacy and safety of Mycobacterium vaccae nebulization in the treatment of Coronavirus Disease 2019 (COVID-19). Methods: In this randomized, double-blind, placebo-controlled clinical trial, we included 31 adult patients with moderate COVID-19 who were admitted to the Fourth People's Hospital of Nanning (Nanning, China) between January 22, 2020 and February 17, 2020. Patients were randomly divided into two groups: group A (standard care group) and group B (M. vaccae in combination with standard care group). The primary outcome was the time interval from admission to viral RNA negative conversion (oropharyngeal swabs were used in this study). Secondary outcomes included chest computed tomography (CT), mortality, length of hospital stay, complications during treatment, and so on. Patients were followed up to 4 weeks after discharge (reexamination of viral RNA, chest CT, etc.). Results: Nucleic acid test negative conversion time in group B was shorter than that in group A (2.9 days [2.7-8.7] vs. 6.8 days [3.3-13.8]; p = 0.045). No death and no conversion to severe or critical cases were observed in both groups. Two weeks after discharge, neither "relapse" nor "return to positive" cases were found. Four weeks after discharge, it was found that there was no case of " relapse " or "return to positive" in group B, and 1 patient in group A showed "return to positive", but there was no clinical manifestation and imaging progression. No adverse reactions related to M. vaccae were found during observation period. Conclusion:M. vaccae treatment might shorten the time interval from admission to viral RNA negative conversion, which might be beneficial to the prevention and treatment of COVID-19. Clinical Trial Registration: ChiCTR2000030016.

[Acute kidney injury in patients hospitalized with COVID-19 in Wuhan, China: a single-center retrospective observational study].

OBJECTIVE: To assess the predictors and outcomes of acute kidney injury (AKI) among patients with coronavirus disease 2019 (COVID-19). OBJECTIVE: This retrospective observational study was conducted among patients with a confirmed diagnosis of COVID-19 admitted to Hankou Hospital between January, 5 and March 8, 2020. We evaluated the association of AKI with the demographic and biochemical parameters and clinical outcomes of the patients using univariate regression analysis. OBJECTIVE: Atotal of 287 COVID-19 patients, including 55 with AKI and 232 without AKI, were included in the analysis. Compared with the patients without AKI, the patients with AKI were older, predominantly male, and were more likely to have hypoxia and pre-existing hypertension and cerebrovascular diseases. The patients with AKI also had higher levels of white blood cells, D-dimer, aspartate aminotransferase, total bilirubin, creatine kinase, lactate dehydrogenase, procalcitonin, C-reactive protein, a higher prevalence of hyperkalemia, lower lymphocyte counts, and higher chest computed tomographic scores. The incidence of stage 1 AKI was 14.3% and that of stage 2 or 3 AKI was 4.9%. The patients with AKI had much higher mortality rate than those without AKI. OBJECTIVE: AKI is an important complication of COVID-19. An older age, a male gender, multiple pre- existing comorbidities, lymphopenia, increased infection indicators, elevated D-dimer, and impaired heart and liver functions are all potential risk factors ofAKI. COVID- 19 patients with AKI that progresses into stages 2 or 3 AKI have a high mortality rate. Prevention of AKI and monitoring kidney function is critical in the care of COVID-19 patients.

Evolutionary analysis and lineage designation of SARS-CoV-2 genomes.

The pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has caused immense global disruption. With the rapid accumulation of SARS-CoV-2 genome sequences, however, thousands of genomic variants of SARS-CoV-2 are now publicly available. To improve the tracing of the viral genomes' evolution during the development of the pandemic, we analyzed single nucleotide variants (SNVs) in 121,618 high-quality SARS-CoV-2 genomes. We divided these viral genomes into two major lineages (L and S) based on variants at sites 8782 and 28144, and further divided the L lineage into two major sublineages (L1 and L2) using SNVs at sites 3037, 14408, and 23403. Subsequently, we categorized them into 130 sublineages (37 in S, 35 in L1, and 58 in L2) based on marker SNVs at 201 additional genomic sites. This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages. We also provide a companion website (www.covid19evolution.net) that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification. Finally, we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2's evolution. These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2's genome evolution.

Deciphering the Subtype Differentiation History of SARS-CoV-2 Based on a New Breadth-First Searching Optimized Alignment Method Over a Global Data Set of 24,768 Sequences.

SARS-CoV-2 has caused a worldwide pandemic. Existing research on coronavirus mutations is based on small data sets, and multiple sequence alignment using a global-scale data set has yet to be conducted. Statistical analysis of integral mutations and global spread are necessary and could help improve primer design for nucleic acid diagnosis and vaccine development. Here, we optimized multiple sequence alignment using a conserved sequence search algorithm to align 24,768 sequences from the GISAID data set. A phylogenetic tree was constructed using the maximum likelihood (ML) method. Coronavirus subtypes were analyzed via t-SNE clustering. We performed haplotype network analysis and t-SNE clustering to analyze the coronavirus origin and spread. Overall, we identified 33 sense, 17 nonsense, 79 amino acid loss, and 4 amino acid insertion mutations in full-length open reading frames. Phylogenetic trees were successfully constructed and samples clustered into subtypes. The COVID-19 pandemic differed among countries and continents. Samples from the United States and western Europe were more diverse, and those from China and Asia mainly contained specific subtypes. Clades G/GH/GR are more likely to be the origin clades of SARS-CoV-2 compared with clades S/L/V. Conserved sequence searches can be used to segment long sequences, making large-scale multisequence alignment possible, facilitating more comprehensive gene mutation analysis. Mutation analysis of the SARS-CoV-2 can inform primer design for nucleic acid diagnosis to improve virus detection efficiency. In addition, research into the characteristics of viral spread and relationships among geographic regions can help formulate health policies and reduce the increase of imported cases.