The causative agent of coronavirus disease 2019 (COVID-19), known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread accumulatively to 240 countries and continues to evolve. To gain a comprehensive understanding of the epidemiological characteristics of imported variants in China and their correlation with global circulating variants, genomic surveillance data from 11 139 imported COVID-19 cases submitted by Chinese provincial CDC laboratories between 2021 and 2022 were analyzed. Consensus sequences underwent rigorous quality checks, followed by amino acid mutations analysis using Nextclade. Sequences with satisfactory quality control status were classified according to the Pango nomenclature. The results showed that the dominant variants in imported cases reflected the global epidemic trend. An increase in the number of imported SARS-CoV-2 lineages monitored in China in the second half of 2022, and the circulating Omicron subvariants changed from the ancestral lineages of BA.5 and BA.2 into the lineages containing key amino acid mutations of spike protein. There was significant variation in the detection of Omicron subvariants among continents (χ2 = 321.968, p < 0.001) in the second half of 2022, with four lineages (BA.2.3.7, BA.2.2, BA.5.2.7, and XBB.1.2) identified through imported surveillance mainly prevalent respectively in Taiwan, China, Hong Kong SAR, China, Russian Federation, and Singapore. These findings revealed the alterations in circulating imported variants from 2021 to 2022 in China, reflecting the higher diversity of lineages in the second half of 2022, and revealed the predominant lineages of countries or regions that are in close contacts to China, providing new insights into the global prevalence of SARS-CoV-2.
COVID-19 , SARS-CoV-2 , Humans , China/epidemiology , COVID-19/epidemiology , COVID-19/virology , SARS-CoV-2/genetics , SARS-CoV-2/classification , Prevalence , Spike Glycoprotein, Coronavirus/genetics , Phylogeny , Mutation , Genome, Viral/genetics , Genetic Variation
Introduction: In the first half of 2023, a global shift was observed towards the predominance of XBB variants. China faced a significant epidemic between late 2022 and early 2023 due to Omicron subvariants BA.5.2 and BF.7. This study aims to depict the evolving variant distribution among provincial-level administrative divisions (PLADs) in China and explore the factors driving the predominance of XBB replacement. Methods: Sequences from local and imported coronavirus disease 2019 (COVID-19) cases recorded between January 1 and June 30, 2023, were included. The study analyzed the changing distribution of viral variants and assessed how the prior dominance of specific variants, XBB subvariants, and imported cases influenced the prevalence of the XBB replacement variant. Results: A total of 56,486 sequences were obtained from local cases, and 8,669 sequences were from imported cases. Starting in April, there was a shift in the prevalence of XBB from imported to local cases, with varying dominance among PLADs. In PLADs previously high in BF.7, the rise of XBB was delayed. A positive correlation was found between XBB proportions in imported cases from January to March and local cases in April. The distribution pattern of XBB subvariants differed between local and imported cases within the same PLAD. No significant differences were noted in the replacement rates of XBB subvariants. Conclusions: The timing of XBB dominance differed among various PLADs in China in the first half of 2023, correlating closely with the prevalence of XBB variants among imported cases.
Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated 2,431 variants over the course of its global transmission over the past 3 years. To better evaluate the genomic variation of SARS-CoV-2 before and after the optimization of coronavirus disease 2019 (COVID-19) prevention and control strategies, we analyzed the genetic evolution branch composition and genomic variation of SARS-CoV-2 in both domestic and imported cases in China (the data from Hong Kong and Macau Special Administrative Regions and Taiwan, China were not included) from September 26, 2022 to January 29, 2023. Methods: Analysis of the number of genome sequences, sampling time, dynamic changes of evolutionary branches, origin, and clinical typing of SARS-CoV-2 variants submitted by 31 provincial-level administrative divisions (PLADs) and Xinjiang Production and Construction Corps (XPCC) was conducted to assess the accuracy and timeliness of SARS-CoV-2 variant surveillance. Results: From September 26, 2022 to January 29, 2023, 20,013 valid genome sequences of domestic cases were reported in China, with 72 evolutionary branches. Additionally, 1,978 valid genome sequences of imported cases were reported, with 169 evolutionary branches. The prevalence of the Omicron variants of SARS-CoV-2 in both domestic and imported cases was consistent with that of international epidemic variants. Conclusions: This study provides an overview of the prevalence of Omicron variants of SARS-CoV-2 in China. After optimizing COVID-19 prevention and control strategies, no novel Omicron variants of SARS-CoV-2 with altered biological characteristics or public health significance have been identified since December 1, 2022.
BACKGROUND: Mutation in the FUT1 gene can impact the structure and function of α-(1,2)-fucosyltransferase 1 (α2FucT1). To explain the para-Bombay phenotype of a novel FUT1 allele, three-dimensional (3D) modeling and mutation effect analysis of α2FucT1 were performed by bioinformatic tools. MATERIALS AND METHODS: Blood and saliva samples were collected from a patient who was suspected to be a para-Bombay phenotype. H, A, and B antigens were determined with routine serologic methods for those samples. FUT1 and FUT2 coding regions were determined by Sanger sequencing. The novel heterozygous mutation was confirmed by cloning and sequencing. 3D model of mutant α2FucT1 was built by Phyre 2 and the mutation effect was evaluated by Chimera, PROVEAN, and Polyphen-2. RESULTS: Weak H, A, and B antigens were detected on RBCs of the proband and normal quantities of H, A, and B antigens were observed in his saliva. Cloning sequencing showed that the proband carried a novel FUT1 allele (c.889C>T, p.Leu297Phe) and a null FUT1*01N.06 allele. 3D model showed that the p.Leu297Phe variant in α2FucT1 reduced the number of hydrogen bonds and the mutation effect was predicted to be deleterious and possibly damaging, which suggested that the conformation and activity of the enzyme might be significantly damaged. CONCLUSION: A novel missense mutation led to an amino acid variant p.Leu297Phe in α2FucT1, which was a potential cause of the inactivation of the enzyme. Computational evaluation was a convenient and useful approach for the mutation effect analysis of the enzyme.
Mutation, Missense , Alleles , Genotype , Mutation , Phenotype , Humans
Objectives: The prevalence of G6PD deficiency has not been reported in Yangjiang, a western city in Guangdong province. This study aims to investigate the molecular characteristics of G6PD deficiency in this region. Methods: Blood samples were collected from adults at a local hospital to screen for G6PD deficiency. The deficient samples were subjected to further analysis using PCR and reverse dot blot to determine the specific G6PD variants. Results: Among the 3314 male subjects, 250 cases of G6PD deficiency were found using the G6PD enzyme quantitative assay, resulting in a prevalence of 7.54% (250/3314) in the Yangjiang region. The prevalence of G6PD deficiency in females was 3.42% (176/5145). Out of the 268 cases of G6PD deficiency tested for G6PD mutations, reverse dot blot identified 20 different G6PD variants. The most common G6PD variant was c.1388G>A (81/268), followed by c.1376G>T (48/268), c.95A>G (32/268), c.1024C>T (9/268), c.392G>T (7/268), and c.871G>A/c.1311C>T (6/268). It was observed that c.871G>A was always linked to the polymorphism of c.1311C>T in this population. Conclusion: This investigation into G6PD deficiency in this area is expected to significantly improve our understanding of the prevalence and molecular characterization of this condition.
The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021. It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike (S) protein than the previously circulating variants of concern (VOCs). Notably, on 15 July 2022, we monitored the first VOC / Omicron subvariant BA.2.75 in China from an imported case. Moreover, nowadays, this subvariant still is predominant in India. It has nine additional mutations in the S protein compared to BA.2, three of which (W152R, G446S, and R493Q reversion) might contribute to higher transmissibility and immune escape. This subvariant could cause wider spread and pose a threat to the global situation. Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.
Introduction: After the epidemic in Wuhan City was brought under control in 2020, local outbreaks of coronavirus disease 2019 (COVID-19) in the mainland of China were mainly due to imported COVID-19 cases. The ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to generate new variants. Some have been designated as variants of concern (VOCs) by the World Health Organization (WHO). To better assess the role of imported SARS-CoV-2 surveillance and the prevalence of VOCs in 2021, the genomic surveillance data of SARS-CoV-2 from imported COVID-19 cases of 2021 in the mainland of China were analyzed. Methods: The analyses included the number of sequence submissions, time of sequence deposition, and time of detection of the VOCs in order to determine the timeliness and sensitivity of the surveillance. The proportions of VOCs were analyzed and compared with data from the Global Initiative of Sharing All Influenza Data (GISAID). Results: A total of 3,355 sequences of imported cases were submitted from 29 provincial-level administrative divisions, with differences in the number of sequence submissions and median time of sequence deposition. A total of 2,388 sequences with more than 90% genomic coverage were used for lineage analysis. The epidemic trend from Alpha to Delta to Omicron in imported cases was consistent with that in the GISAID. In addition, VOCs from imported cases were usually identified after WHO designation and before causing local outbreaks. Conclusions: The global distribution of SARS-CoV-2 VOCs changed rapidly in 2021. Robust genomic surveillance of the imported SARS-CoV-2 in the mainland of China is of great significance.
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is one of the consolidation modalities for adult patients with T-cell lymphoblastic lymphoma (T-LBL). However, the optimal conditioning regimen needs to be explored. In the present study, 40 patients with T-LBL undergoing allo-HSCT were retrospectively analyzed, including 23/40 (57.5%) with total body irradiation (TBI)-based conditioning regimen and 17/40 (42.5%) with busulfan (BU)-based regimen. TBI-based regimen significantly increased the cumulative incidence (CI) of grade II to IV acute graft-versus-host disease (aGvHD) as compared with BU-based regimen (13.0% vs 0%, P = 0.000). The relapse risk was significantly lowered in TBI-based group with a 2-year CI of relapse (CIR) of 9.1% as compared with that of 49.6% in BU-based group (P = 0.008). The 1-year and 2-year non-relapse mortalities (NRMs) for all patients were 5.0% and 10.3%, respectively. The 1-year and 2-year NRMs were 8.9% and 16.0% in TBI-based group, and 0.00% and 0.00% in BU-based group (P = 0.140). The 2-year probabilities of overall survival (OS) and relapse-free survival (RFS) were 83.0% [95% confidence interval, 63.4%-100%] and 74.0% (95% confidence interval, 54.4%-93.6%) in TBI-based group, which were higher than that of 35.0% (95% confidence interval, 0.0%-72.2%) and 50.0% (95% confidence interval, 24.5%-75.4%) in BU-based group, respectively (P = 0.020 for OS and P = 0.081 for RFS). In multivariate analysis, TBI-based regimen significantly reduced the risk of relapse [subdistribution hazard ratio (SHR) = 0.030, 95% CI, 0.002-0.040, P = 0.000] and improved the OS [hazard ratio (HR) 0.121, 95% CI, 0.021-0.683, P = 0.017] as an independent prognostic factor. These results suggested that TBI-based regimen might be an optimal choice for adult patients with T-LBL undergoing allo-HSCT.
Graft vs Host Disease , Hematopoietic Stem Cell Transplantation , Peripheral Blood Stem Cell Transplantation , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Adult , Busulfan/therapeutic use , Graft vs Host Disease/etiology , Hematopoietic Stem Cell Transplantation/methods , Humans , Peripheral Blood Stem Cell Transplantation/adverse effects , Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Recurrence , Retrospective Studies , T-Lymphocytes , Transplantation Conditioning/methods , Whole-Body Irradiation/adverse effects
OBJECTIVES: The characteristic of glucose-6-phosphate dehydrogenase (G6PD) deficiency is red blood cell (RBC) destruction in response to oxidative stress. Patients requiring RBC transfusions may simultaneously receive oxidative medications or have concurrent infections, both of which can induce hemolysis in G6PD-deficient RBCs. We intend to investigate the incidence of G6PD deficiency in voluntary blood donors and to evaluate the transfusion risk associated with G6PD deficiency in Guangdong province. METHODS: G6PD enzyme was analyzed in 3042 donors and gene mutations were genotyped in G6PD-deficient samples. RESULTS: The G6PD-deficient prevalence of voluntary blood donors was 6.97% (212/3042), 55.19% blood donors with G6PD deficiency donated blood more than twice. Eighty-five cases of G6PD deficiency were genotyped, and the common types of G6PD mutations were c.1376 G > T, c.1388 G > A, c.95 A > G, c.1024 C > T, and c.871 G > A. CONCLUSIONS: Due to the high prevalence of G6PD deficiency in Foshan area, we recommended that the screening of G6PD deficiency should be carried out for the regular blood donors to ensure the safety of blood users.
Glucosephosphate Dehydrogenase Deficiency , Blood Donors , China/epidemiology , Erythrocyte Transfusion , Erythrocytes/metabolism , Glucosephosphate Dehydrogenase/genetics , Glucosephosphate Dehydrogenase/metabolism , Glucosephosphate Dehydrogenase Deficiency/epidemiology , Glucosephosphate Dehydrogenase Deficiency/genetics , Humans
Low temperature and certain humidity are conducive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for long-time survival and long-distance spread during logistics and trades. Contaminated cold-chain or frozen products and outer packaging act as the carrier of SARS-CoV-2, that infects the high-risk population who works in the ports, cold storage or seafood market. Since the coronavirus disease 2019 (COVID-19) pandemic worldwide, multiple localized outbreaks caused by SARS-CoV-2 contaminated imported cold-chain products have been reported in China, which brought challenges to COVID-19 prevention and control. Here, we review the evidences of SARS-CoV-2 cold-chain transmission from six confirmed cold-chain related COVID-19 outbreaks in China, especially in terms of SARS-CoV-2 whole-genome sequencing and virus isolation. In addition, we summarize the characteristics and mode of SARS-CoV-2 cold-chain transmission from both six COVID-19 outbreaks in China and the outbreaks suspected cold-chain transmission in other countries. Finally, we analyze the underlying risks of SARS-CoV-2 cold-chain transmission and propose the preventive countermeasures.
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Disease Outbreaks , Humans , Pandemics/prevention & control , Risk Factors
Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is the dominant circulating strain worldwide. To assess the importation of SARS-CoV-2 variants in the mainland of China during the Omicron epidemic, the genomic surveillance data of SARS-CoV-2 from imported coronavirus disease 2019 (COVID-19) cases in the mainland of China during the first half of 2022 were analyzed. Methods: Sequences submitted from January to July 2022, with a collection date before June 30, 2022, were incorporated. The proportions of SARS-CoV-2 variants as well as the relationships between the origin and destination of each Omicron imported case were analyzed. Results: 4,946 sequences of imported cases were submitted from 27 provincial-level administrative divisions (PLADs), and the median submission interval was within 1 month after collection. In 3,851 Omicron sequences with good quality, 1 recombinant (XU) and 4 subvariants under monitoring (BA.4, BA.5, BA.2.12.1, and BA.2.13) were recorded, and 3 of them (BA.4, BA.5, and BA.2.12.1) caused local transmissions in the mainland of China later than that recorded in the surveillance. Omicron subvariants dominated in the first half of 2022 and shifted from BA.1 to BA.2 then to BA.4 and BA.5. The percentage of BA.2 in the imported SARS-CoV-2 surveillance data was far higher than that in the Global Initiative on Sharing All Influenza Data (GISAID). The imported cases from Hong Kong Special Administrative Region, China, accounted for 32.30% of Omicron cases sampled, and 98.71% of them were BA.2. Conclusions: The Omicron variant showed the intra-Omicron evolution in the first half of 2022, and all of the Omicron subvariants were introduced into the mainland of China multiple times from multiple different locations.
What is already known about this topic? Though coronavirus disease 2019 (COVID-19) has largely been controlled in China, several outbreaks of COVID-19 have occurred from importation of cases or of suspected virus-contaminated products. Though several outbreaks have been traced to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated on the outer packaging of cold chain products, live virus has not been obtained. What is added by this report? In September 2020, two dock workers were detected as having asymptomatic SARS-CoV-2 infection using throat swabs during routine screening in Qingdao, China. Epidemiological information showed that the two dock workers were infected after contact with contaminated outer packaging, which was confirmed by genomic sequencing. Compared to the Wuhan reference strain, the sequences from the dock workers and the package materials differed by 12-14 nucleotides. Furthermore, infectious virus from the cold chain products was isolated by cell culture, and typical SARS-CoV-2 particles were observed under electron microscopy. What are the implications for public health practice? The international community should pay close attention to SARS-CoV-2 transmission mode through cold chain, build international cooperative efforts in response, share relevant data, and call on all countries to take effective prevention and control measures to prevent virus contamination in cold-chain food production, marine fishing and processing, transportation, and other operations.
Two factors, the crosslinking degree of the matrix (ν) and the size of the filler (Sz), have significant impact on the Mullins effect of filled elastomers. Herein, the result. of the two factors on Mullins effect is systematically investigated by adjusting the crosslinking degree of the matrix via adding maleic anhydride into a rubber matrix and controlling the particle size of the filler via ball milling. The dissipation ratios (the ratio of energy dissipation to input strain energy) of different filled natural rubber/butadiene rubber (NR/BR) elastomer composites are evaluated as a function of the maximum strain in cyclic loading (εm). The dissipation ratios show a linear relationship with the increase of εm within the test range, and they depend on the composite composition (ν and Sz). With the increase of ν, the dissipation ratios decrease with similar slope, and this is compared with the dissipation ratios increase which more steeply with the increase in Sz. This is further confirmed through a simulation that composites with larger particle size show a higher strain energy density when the strain level increases from 25% to 35%. The characteristic dependence of the dissipation ratios on ν and Sz is expected to reflect the Mullins effect with mathematical expression to improve engineering performance or prevent failure of rubber products.
Truffles are ectomycorrhizal species forming edible ascocarps. The Italian white truffle (Tuber magnatum Pico) is the most famous and expensive species harvested to date; it comes exclusively from natural habitats in European countries. The annual production of T. magnatum is generally insufficient to respond to the high demands making its cultivation a research hotspot. The first attempt to cultivate T. magnatum started in the 1970s without success; only recently have mycorrhized plants been successfully produced. The aims of this study were (1) to assess the persistence of T. magnatum in the soil of plantations realized with mycorrhized plants and (2) to characterize the first T. magnatum orchard that produced ascocarps outside the known natural geographic range of this species. In 2018, five orchards were sampled in France, and T. magnatum was investigated in the soil. We confirmed that T. magnatum survived in the soil 3 to 8 years after planting. The key finding of this study was the harvest of T. magnatum ascocarps in 2019 and 2020 from one orchard. The production of ascocarps started 4.5 years after planting, and the ascocarps were harvested under different trees and during two consecutive seasons. A detailed analysis of the productive orchards (i.e., soil features, soil water availability, cultivation techniques) is presented. These results demonstrate the feasibility of T. magnatum cultivation worldwide by planting mycorrhized plants. The cultivation of T. magnatum could therefore become a real opportunity for farmers and could respond to the high demand of this high-priced food.
Mycorrhizae , Ascomycota , Europe , France , Italy
After 56 days without coronavirus disease 2019 (COVID-19) cases, reemergent cases were reported in Beijing, China on June 11, 2020. Here, we report the genetic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequenced from the clinical specimens of 4 human cases and 2 environmental samples. The nucleotide similarity among six SARS-CoV-2 genomes ranged from 99.98% to 99.99%. Compared with the reference strain of SARS-CoV-2 (GenBank No. NC_045512), all six genome sequences shared the same substitutions at nt241 (C â T), nt3037 (C â T), nt14408 (C â T), nt23403 (A â G), nt28881 (G â A), nt28882 (G â A), and nt28883 (G â C), which are the characteristic nucleotide substitutions of L-lineage European branch I. This was also proved by the maximum likelihood phylogenetic tree based on the full-length genome of SARS-CoV-2. They also have a unique shared nucleotide substitution, nt6026 (C â T), which is the characteristic nucleotide substitution of SARS-CoV-2 in Beijing's Xinfadi outbreak. It is noteworthy that there is an amino acid D614G mutation caused by nt23403 substitution in all six genomes, which may enhance the virus's infectivity in humans and help it become the leading strain of the virus to spread around the world today. It is necessary to continuously monitor the genetic variation of SARS-CoV-2, focusing on the influence of key mutation sites of SARS-CoV-2 on viral transmission, clinical manifestations, severity, and course of disease.
