Journal of Biosafety and Biosecurity最新文献

{"title":"Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China","authors":"Yamin Sun ,&nbsp;Min Wang ,&nbsp;Wenchao Lin ,&nbsp;Wei Dong ,&nbsp;Jianguo Xu","doi":"10.1016/j.jobb.2023.01.002","DOIUrl":"10.1016/j.jobb.2023.01.002","url":null,"abstract":"<div><p>On December 7, 2022, China adjusted public health control measures, there have been widespread of SARS-CoV-2 infections in Chinese mainland. As the number of infected people increased, the mutation probability of SARS-CoV-2 is also raised. Therefore, it is of great importance to monitor SARS-CoV-2 variants and its mutations in China. In this current study, 665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants; to determine the composition of variants in China across different provinces; and analyze specific mutation frequency, focusing on 12 immune escape residues. The results showed that no new mutations were generated on the 12 immune escape residues. The evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites, officially named BF.7.14 by PANGO. This variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in China. The evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants, named BA.5.2.48 and BA.5.2.49 by PANGO, respectively. This variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic transmission. Finally, this study showed that current epidemic variants in China were already circulating in other countries, and there were no additional mutations on immune escape residues that could pose a threat to other countries.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"5 1","pages":"Pages 14-20"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9876032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9325915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WITHDRAWN: The WHO and the ICTV rename viruses such as monkeypox.","authors":"Jiaxuan Gao","doi":"10.1016/j.jobb.2022.11.003","DOIUrl":"10.1016/j.jobb.2022.11.003","url":null,"abstract":"<p><p>This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.</p>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9721292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10795222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vaccination with CanSinoBIO’s inhaled COVID-19 vaccine has begun in China","authors":"Jiaxuan Gao","doi":"10.1016/j.jobb.2022.12.002","DOIUrl":"10.1016/j.jobb.2022.12.002","url":null,"abstract":"","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Page 163"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9791787/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10465487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"“Mutation blacklist” and “mutation whitelist” of SARS-CoV-2","authors":"Yamin Sun ,&nbsp;Min Wang ,&nbsp;Wenchao Lin ,&nbsp;Wei Dong ,&nbsp;Jianguo Xu","doi":"10.1016/j.jobb.2022.06.006","DOIUrl":"10.1016/j.jobb.2022.06.006","url":null,"abstract":"<div><p>Over the past two years, scientists throughout the world have completed more than 6 million SARS-CoV-2 genome sequences. Today, the number of SARS-CoV-2 genomes exceeds the total number of all other viral genomes. These genomes are a record of the evolution of SARS-CoV-2 in the human host, and provide information on the emergence of mutations. In this study, analysis of these sequenced genomes identified 296,728 <em>de novo</em> mutations (DNMs), and found that six types of base substitutions reached saturation in the sequenced genome population. Based on this analysis, a “mutation blacklist” of SARS-CoV-2 was compiled. The loci on the “mutation blacklist” are highly conserved, and these mutations likely have detrimental effects on virus survival, replication, and transmission. This information is valuable for SARS-CoV-2 research on gene function, vaccine design, and drug development. Through association analysis of DNMs and viral transmission rates, we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate, and these DNMs where classified as the “mutation whitelist” of SARS-CoV-2. The mutations on the “mutation whitelist” are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new variants. The occurrence of mutations and the evolution of viruses are dynamic processes. To more effectively monitor the mutations and variants of SARS-CoV-2, we built a SARS-CoV-2 mutation and variant<!--> <!-->monitoring and pre-warning system (MVMPS), which can monitor the occurrence and development of mutations and variants of SARS-CoV-2, as well as provide pre-warning for the prevention and control of SARS-CoV-2 (<span>https://www.omicx.cn/</span><svg><path></path></svg>). Additionally, this system could be used in real-time to update the “mutation whitelist” and “mutation blacklist” of SARS-CoV-2.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 114-120"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9273572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9181320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosafety and biosecurity in the era of biotechnology: The Middle East region","authors":"Laith AL-Eitan,&nbsp;Malek Alnemri","doi":"10.1016/j.jobb.2022.11.002","DOIUrl":"10.1016/j.jobb.2022.11.002","url":null,"abstract":"<div><p>Biotechnology became a paradigm-shifting science among all subfields of biology. The benefits of biotechnology have reached many practical fields, whether human health, animal, and/or agricultural. However, wherever there is a biotechnology practice, there is an associated biohazard with it, and its negative impact may reach all living entities including humans. Therefore, the cooperation of the leading institutions in this field has culminated in creating the concepts and applications of biosafety and biosecurity. The countries of the Middle East are considered biotechnology-practicing and have shown a clear acceptance to this field. But unfortunately, the Middle East region is one that is facing the most multi-challenges, which would constitute real and noticeable concern at the local and international levels. Such challenges represented by wars and armed conflicts, deteriorating economic conditions, the large number of refugees, and the spread of many epidemics. Thus, limiting the region's ability to deal with the surrounding biological hazards and struggling the way to the one health concept. Therefore, this article aims to shed light on the activities of the Middle East countries in the field of biotechnology and to address potential biological threats, whether natural such as the spread of viruses, or intentional such as biological attacks and bioterrorism. The article also shows the capacity of the countries of the region in the field of biosafety and biosecurity based on available information. Accordingly, some countries are lacking the required level of preparedness to face potential biological threats. Multi-institutional and international cooperation between the concerned countries will significantly enhance the capacity of the region in biosafety and biosecurity to meet the level of biological risk.</p><p><strong>Search methodology:</strong> wide range of related keywords (based on the section) combined with the name of the region, or one country individually have been searched using available search engines and databases such as google scholar and PubMed. After scanning the content of the found results, irrelevant articles have been excluded. <span>Fig. 2</span>, <span>Fig. 3</span>, <span>Fig. 4</span>, <span>Fig. 6</span>, <span>Fig. 7</span> were created by biorender.com.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 130-145"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2588933822000231/pdfft?md5=28081d8bf365563ef36e496beafc7d68&pid=1-s2.0-S2588933822000231-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49594192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disease X Testing: The results of an international external quality assessment exercise","authors":"Tian Qin ,&nbsp;Han Zheng ,&nbsp;Xuelian Luo ,&nbsp;Wen Zhang ,&nbsp;Jing Yang ,&nbsp;Yamin Sun ,&nbsp;Na Han ,&nbsp;Yuanhai You ,&nbsp;Liang Lu ,&nbsp;Xin Lu ,&nbsp;Di Xiao ,&nbsp;Shenshen Jiang ,&nbsp;Xuexin Hou ,&nbsp;Jinxing Lu ,&nbsp;Biao Kan ,&nbsp;Jianzhong Zhang ,&nbsp;Jianguo Xu","doi":"10.1016/j.jobb.2022.11.004","DOIUrl":"10.1016/j.jobb.2022.11.004","url":null,"abstract":"<div><p>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, <em>Dabie bandavirus</em>, <em>Mammarenavirus</em>, and <em>Gemella</em> spp<em>.</em>, of which the last two have not been taxonomically named or published. The animal samples were from <em>Rattus norvegicus, Marmota himalayana</em>, New Zealand white rabbit, and the tick <em>Haemaphysalis longicornis.</em> Of the 11 international laboratories that participated in this activity, six accurately identified pathogen X as a new <em>Mammarenavirus</em>, and five correctly identified the animal origin as <em>R. norvegicus</em>. 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.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 151-157"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2588933822000255/pdfft?md5=22d379b0d6c5c2d32130178dcceb4105&pid=1-s2.0-S2588933822000255-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48204183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing decontamination practices at a medical microbiology research laboratory","authors":"Merna M. Alfy,&nbsp;Sherine B. El Sayed,&nbsp;Mona El-Shokry","doi":"10.1016/j.jobb.2022.08.002","DOIUrl":"10.1016/j.jobb.2022.08.002","url":null,"abstract":"<div><p>To our knowledge, this is the first study to conduct an objective assessment of the routine decontamination practices at a medical microbiology research laboratory (MRL) a year after a biosafety training was provided to all laboratory staff. Between March 28th and June 28th, 2021, unobtrusive observations were carried out to identify-three high-touch surfaces at the MRL during different working hours. Swabbing was used to evaluate the effectiveness of the disinfectant used in the laboratory. All three high-touch surfaces were sampled before and after decontamination with 200 ppm of 5 % sodium hypochlorite (household bleach) to quantify the microbial load and identify the types of organisms residing on the laboratory surfaces. A higher concentration (500 ppm) of 5 % sodium hypochlorite was employed after refresher training was provided to housekeeping staff, and resampling of the three surfaces was carried out during a 4-week follow-up period using the same procedure. The three high-touch surfaces identified were the two sides of the workbench (22 %–24 %) and the front surface of one incubator (14 %). <em>Anthracoid bacilli</em> and <em>Staphylococcus aureus</em> were the most commonly found organisms on laboratory surfaces pre-intervention (100 % and 89 %, respectively) and post-intervention (56 % and 44 %, respectively). Other microorganisms detected included <em>Salmonella</em> spp. (27.7 %), <em>Proteus</em> spp. (5.6 %), <em>Escherichia coli</em> (5.6 %), and <em>Klebsiella</em> spp. (33.3 %). Employing a higher concentration (500 ppm) of sodium hypochlorite significantly (p ≤ 0.000) reduced the total aerobic colony count from an average of 15–250 cfu/cm² to 10–60 cfu/cm². This study demonstrated suboptimal decontamination practices at the MRL and the need to apply a higher concentration (500 ppm) of sodium hypochlorite to reduce the overall microbial load. It also demonstrated the importance of quantitative assessment to monitor decontamination practices and ensure staff compliance. More studies are needed to identify bacterial communities within the laboratory, which will help provide guidance regarding the types, proper concentrations, and appropriateness of the in -use disinfectants. Furthermore, large-scale studies on the acceptable level of residual contamination following any decontamination process are urgently recommended.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 124-129"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2588933822000218/pdfft?md5=88c0b4e1a3c5a3fc55edd6942c2cd7bf&pid=1-s2.0-S2588933822000218-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44832882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heat inactivation of monkeypox virus","authors":"Christophe Batéjat,&nbsp;Quentin Grassin,&nbsp;Maxence Feher,&nbsp;Damien Hoinard,&nbsp;Jessica Vanhomwegen,&nbsp;Jean-Claude Manuguerra,&nbsp;India Leclercq","doi":"10.1016/j.jobb.2022.08.001","DOIUrl":"10.1016/j.jobb.2022.08.001","url":null,"abstract":"<div><p>Different kinds of media spiked with monkeypox virus (MPXV) were subjected to heat inactivation at different temperatures for various periods of time. The results showed that MPXV was inactivated in less than 5 min at 70 °C and less than 15 min at 60 °C, with no difference between viruses from the West African and Central African clades. The present findings could help laboratory workers to manipulate MPXV in optimal biosafety conditions and improve their protocols.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 121-123"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9534137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9578532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2021–2022 monitoring, early warning, and forecasting of global infectious diseases","authors":"Jie Luan,&nbsp;Jianbo Ba,&nbsp;Bin Liu,&nbsp;Xiongli Xu,&nbsp;Dong Shu","doi":"10.1016/j.jobb.2022.06.001","DOIUrl":"10.1016/j.jobb.2022.06.001","url":null,"abstract":"<div><h3>Background</h3><p>COVID-19 has had a considerable impact on society since 2019, and the disease has high mortality and infection rates. There has been a particular focus on how to best manage COVID-19 and how to analyze and predict the epidemic status of infectious diseases in general.</p><p>Methods</p><p>The present study analyzed the COVID-19 epidemic patterns and made predictions of future trends based on the statistics obtained from a global infectious disease network data monitoring and early warning system (OBN, <span>http://27.115.41.130:8888/OBN/</span><svg><path></path></svg>). The development trends of other major infectious diseases were also examined.</p><p>Results</p><p>The global COVID-19 pandemic showed periodic increases throughout 2021. At present, there is a high incidence in European countries, especially in Eastern Europe, followed by in Africa. The risk of contracting COVID-19 was divided into high, medium–high, medium, medium–low, and low grades depending on the stage of the epidemic in each examined region over the current period. The occurrence and prevalence of major infectious diseases throughout the world did not significantly change in 2021.</p><p>Conclusions</p><p>The COVID-19 pandemic has strongly impacted people’s lives and the economy. The effects of global infectious diseases can be ameliorated by strengthening monitoring and early warning systems and by facilitating the international exchange of information.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 98-104"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9270068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40532459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study and prediction of the 2022 global monkeypox epidemic","authors":"Fengying Wei ,&nbsp;Zhihang Peng ,&nbsp;Zhen Jin ,&nbsp;Jinjie Wang ,&nbsp;Ximing Xu ,&nbsp;Xinyan Zhang ,&nbsp;Jun Xu ,&nbsp;Zixiong Ren ,&nbsp;Yao Bai ,&nbsp;Xiaoli Wang ,&nbsp;Bulai Lu ,&nbsp;Zhaojun Wang ,&nbsp;Jianguo Xu ,&nbsp;Senzhong Huang","doi":"10.1016/j.jobb.2022.12.001","DOIUrl":"10.1016/j.jobb.2022.12.001","url":null,"abstract":"<div><p>The World Health Organization (WHO) declared monkeypox as a public health emergency of international concern (PHEIC) on July 23, 2022, their highest level of alert. This raised concerns about the management of the global monkeypox outbreak, as well as the scientific analysis and accurate prediction of the future course of the epidemic. This study used EpiSIX (an analysis and prediction system for epidemics based on a general SEIR model) to analyze the monkeypox epidemic and to forecast the major tendencies based on data from the USA CDC (<span>https://www.cdc.gov</span><svg><path></path></svg>) and the WHO (<span>https://www.who.int/health-topics/monkeypox</span><svg><path></path></svg>). The global outbreak of monkeypox started in the UK on May 2, 2022, which marked the beginning of an epidemic wave. As of October 28, 2022, the cumulative number of reported cases worldwide was 77,115, with 36 deaths. EpiSIX simulations predict that the global monkeypox epidemic will enter a low epidemic status on March 1, 2023 with the cumulative number of confirmed cases ranging from 85,000 to 124,000, and the total number of deaths ranging from 60 to 87. Our analysis revealed that the basic reproduction number (R0) of monkeypox virus (MPXV) is near to 3.1 and the percentage of asymptomatic individuals is 13.1 %–14.5 %, both of which are similar to the data for SARS. The vaccination efficiency against susceptibility (VEs) of individuals who have had monkeypox is ∼ 79 %, and the vaccination efficiency against infectiousness (VEi) of individuals who have had monkeypox is ∼ 76 %–82 %. The mean incubation period for monkeypox is 8 days. In total, 94.7 % of infected individuals develop symptoms within 20 days and recover within 2 weeks after the confirmation of symptoms. Simulation results using EpiSIX showed that ring vaccination was remarkably effective against monkeypox. Our findings confirmed that a 20-day isolation for close contacts is necessary.</p></div>","PeriodicalId":52875,"journal":{"name":"Journal of Biosafety and Biosecurity","volume":"4 2","pages":"Pages 158-162"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9773788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10611351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}