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Bruinen de Bruin Y, Lequarre AS, McCourt J, Clevestig P, Pigazzani F, Zare Jeddi M, Colosio C, Goulart M. Initial impacts of global risk mitigation measures taken during the combatting of the COVID-19 pandemic. Saf Sci 2020; 128:104773. [PMID: 32296266 PMCID: PMC7158845 DOI: 10.1016/j.ssci.2020.104773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 05/03/2023]
Abstract
This paper presents an analysis of risk mitigation measures taken by countries around the world facing the current COVID-19 outbreak. In light of the current pandemic the authors collated and clustered (using harmonised terminology) the risk mitigation measures taken around the globe in the combat to contain, and since March 11, 2020, to limit the spread of the SARS-CoV-2 virus known to cause the Coronavirus disease 2019 (COVID-19). This overview gathers lessons learnt, providing an update on the current knowledge for authorities, sectors and first responders on the effectiveness of said measures, and may allow enhanced prevention, preparedness and response for future outbreaks. Various measures such as mobility restrictions, physical distancing, hygienic measures, socio-economic restrictions, communication and international support mechanisms have been clustered and are reviewed in terms of the nature of the actions taken and their qualitative early-perceived impact. At the time of writing, it is still too premature to express the quantitative effectiveness of each risk mitigation cluster, but it seems that the best mitigation results are reported when applying a combination of voluntary and enforceable measures.
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Affiliation(s)
- Yuri Bruinen de Bruin
- European Commission Joint Research Centre, Italy
- Corresponding author at: European Commission, Joint Research Centre, Via E. Fermi, 2749, 21027 Ispra, VA, Italy.
| | | | | | - Peter Clevestig
- On-Site Technical Expert to the Regional EU CBRN CoE Secretariat for the Gulf Cooperation Council Countries, Abu Dhabi, United Arab Emirates
| | - Filippo Pigazzani
- Division of Molecular and Clinical Medicine, MEMO Research, University of Dundee, United Kingdom
| | - Maryam Zare Jeddi
- Unit of Biostatistics, Epidemiology, and Public Health, University of Padua, Padua, Italy
| | - Claudio Colosio
- Department of Health Sciences of the University of Milan and Occupational Health Unit of the Saints Paolo and Carlo Hospitals, Milan, Italy
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Bruinen de Bruin Y, Lequarre AS, McCourt J, Clevestig P, Pigazzani F, Zare Jeddi M, Colosio C, Goulart M. Initial impacts of global risk mitigation measures taken during the combatting of the COVID-19 pandemic. Saf Sci 2020; 128:104773. [PMID: 32296266 PMCID: PMC7158845 DOI: 10.1016/j.ssci.2020.104773%0a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 11/10/2023]
Abstract
This paper presents an analysis of risk mitigation measures taken by countries around the world facing the current COVID-19 outbreak. In light of the current pandemic the authors collated and clustered (using harmonised terminology) the risk mitigation measures taken around the globe in the combat to contain, and since March 11, 2020, to limit the spread of the SARS-CoV-2 virus known to cause the Coronavirus disease 2019 (COVID-19). This overview gathers lessons learnt, providing an update on the current knowledge for authorities, sectors and first responders on the effectiveness of said measures, and may allow enhanced prevention, preparedness and response for future outbreaks. Various measures such as mobility restrictions, physical distancing, hygienic measures, socio-economic restrictions, communication and international support mechanisms have been clustered and are reviewed in terms of the nature of the actions taken and their qualitative early-perceived impact. At the time of writing, it is still too premature to express the quantitative effectiveness of each risk mitigation cluster, but it seems that the best mitigation results are reported when applying a combination of voluntary and enforceable measures.
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Affiliation(s)
| | | | | | - Peter Clevestig
- On-Site Technical Expert to the Regional EU CBRN CoE Secretariat for the Gulf Cooperation Council Countries, Abu Dhabi, United Arab Emirates
| | - Filippo Pigazzani
- Division of Molecular and Clinical Medicine, MEMO Research, University of Dundee, United Kingdom
| | - Maryam Zare Jeddi
- Unit of Biostatistics, Epidemiology, and Public Health, University of Padua, Padua, Italy
| | - Claudio Colosio
- Department of Health Sciences of the University of Milan and Occupational Health Unit of the Saints Paolo and Carlo Hospitals, Milan, Italy
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Toprak S, Ersoy G, Hart J, Clevestig P. The pathology of lethal exposure to the Riot Control Agents: towards a forensics-based methodology for determining misuse. J Forensic Leg Med 2014; 29:36-42. [PMID: 25572084 DOI: 10.1016/j.jflm.2014.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 08/20/2014] [Accepted: 11/28/2014] [Indexed: 10/24/2022]
Abstract
The aim of this is to review deaths associated with the use of Riot Control Agents (RCAs) and to assess how the presenting pathologies is such cases may better inform cause of death conclusions upon autopsy. We also sought to present which additional steps should be added to the Minnesota protocol and the European harmonization of medico-legal autopsy rules in suspected cases of deaths associated with the use of RCAs. We included 10 lethal cases in our study. In three cases, RCAs were found to be the sole cause of death, in three cases RCAs were ruled a secondary cause of death due asphyxia or asthma subsequent to exposure to RCAs and in four cases RCAs were contributory factors to death. In three cases the responsible agents were identified as Chloroacetophenone (CN), Chlorobenzylidene malononitrile (CS) and Oleoresin capsicum (OC) and in the remaining 7 cases, the agent was OC alone. As there are no specific findings in suspected cases of death associated with RCA use, establishing cause of death and whether RCAs are the sole cause or only a contributory factor will be based on the elimination of other possible causes of death. For this reason, a specifically structured autopsy is essential. This specifically structured autopsy should contain basic principles of the Minnesota Protocol and the European harmonization of medico-legal autopsy rules with the following additional steps taken: examination of clothing, eyes, and skin; examination of pharyngeal, tracheobronchial, and eusophegeal mucosas; and a thorough recording of the steps taken by the party conducting the arrest, including other possible causes of in-custody death, as well as a detailed medical history of the deceased.
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Affiliation(s)
- Sadik Toprak
- Department of Forensic Medicine, Bulent Ecevit University, Zonguldak, Turkey.
| | - Gokhan Ersoy
- Istanbul University, Institute of Forensic Medicine, Istanbul, Turkey.
| | - John Hart
- Stockholm International Peace Research Institute, Signalistgatan 9, 169 70 Solna, Sweden.
| | - Peter Clevestig
- Stockholm International Peace Research Institute, Signalistgatan 9, 169 70 Solna, Sweden.
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Caridha R, Gieng K, Fried U, Lindgren S, Clevestig P, Ehrnst A. Transmitted HIV-1 variants in HIV infected mother-child pairs carrying different subtypes. Retrovirology 2012. [PMCID: PMC3442025 DOI: 10.1186/1742-4690-9-s2-p162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Pramanik L, Fried U, Clevestig P, Ehrnst A. Charged amino acid patterns of coreceptor use in the major subtypes of human immunodeficiency virus type 1. J Gen Virol 2011; 92:1917-1922. [PMID: 21525208 DOI: 10.1099/vir.0.029447-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 has several genetic subtypes and two coreceptor use phenotypes: R5 that uses CCR5, while X4 uses CXCR4. A high amino acid charge of the envelope glycoprotein 120 V3 region, common at positions 11 and 25, is important for CXCR4 use. We characterized charged V3 amino acids, retrieving all biologically phenotyped sequences from the HIV Sequence Database. Selecting individually unique ones randomly yielded 48 subtype A, 231 B, 180 C, 37 D and 32 CRF01_AE sequences; 482 were R5 and 46 were X4. Charged amino acids were conserved in both R5 and X4 with general and subtype-specific patterns. X4 viruses gained a higher charge from positive amino acids at positions other than in R5, and through the loss of negative amino acids. Other positions than 11/25 had a greater impact on charge (P<0.001). This describes how R5 evolves into X4 in a subtype-specific context, useful for computer-based predictions and vaccine design.
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Affiliation(s)
- Lotta Pramanik
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Ulrik Fried
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Peter Clevestig
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
| | - Anneka Ehrnst
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, PO Box 280, SE-171 77 Stockholm, Sweden
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Clevestig P, Pramanik L, Leitner T, Ehrnst A. CCR5 use by human immunodeficiency virus type 1 is associated closely with the gp120 V3 loop N-linked glycosylation site. J Gen Virol 2006; 87:607-612. [PMID: 16476981 DOI: 10.1099/vir.0.81510-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) enters cells through the chemokine receptors CCR5 (R5 virus) and/or CXCR4 (X4 virus). Loss of N-linked glycans and increased net charge of the third variable loop (V3) of the gp120 envelope glycoprotein have been observed to be important steps towards CXCR4 use. All reported sequences using CCR5 or CXCR4 exclusively, or using both, were gathered from the Los Alamos HIV Database and analysed with regard to the V3 N-linked glycosylation motifs (sequons) and charge. The V3 loop glycan had a sensitivity of 0.98 and a 0.92 positive predictive value in the context of CCR5 use. The difference from X4 was remarkable (P<10(-12)). Especially, the sequon motif NNT within the V3 loop was conserved in 99.2 % of the major clades. The results suggest a close association between the V3 loop glycan and CCR5 use and may provide new insight into HIV-1 tropism and help to improve phenotype-prediction models.
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Affiliation(s)
- Peter Clevestig
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
| | - Lotta Pramanik
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Anneka Ehrnst
- Department of Laboratory Medicine, Division of Clinical Virology, Karolinska University Hospital Huddinge, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
- Microbiology and Tumor Biology Center, Karolinska Institutet, Box 280, SE-171 77 Stockholm, Sweden
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Clevestig P, Maljkovic I, Casper C, Carlenor E, Lindgren S, Navér L, Bohlin AB, Fenyö EM, Leitner T, Ehrnst A. The X4 phenotype of HIV type 1 evolves from R5 in two children of mothers, carrying X4, and is not linked to transmission. AIDS Res Hum Retroviruses 2005; 21:371-8. [PMID: 15929699 DOI: 10.1089/aid.2005.21.371] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previously, we found that emergence of the X4 viral phenotype in HIV-1-infected children was related to the presence of X4 in their mothers (C.H. Casper et al., J Infect Dis 2002; 186:914-921). Here, we investigated the origin of the X4 phenotype in the child, analyzing two mother-child pairs (Ma-Ca, Mb-Cb) where the mothers carried X4 and their children developed X4 after an initial presence of R5. We used nested polymerase chain reaction of the env V3 region to generate 203 HIV-1 clones for sequencing (Ma, n = 44; Ca, n = 73; Mb, n = 61; Cb, n = 25) from DNA of peripheral blood mononuclear cell (PBMC) lysates, altogether 167 clones, or from cDNA of plasma RNA, 36 clones. PBMC and plasma isolate sequences from each time point enabled us to assign the probable phenotype to clone sequences in a phylogenetic tree. The transmission and evolution were reconstructed using the maximum likelihood method. In mother-child pair Ma-Ca, one maternal R5 isolate clustered with the child's R5 sequences, at the earliest time when R5 was isolated in the child, confirming this as a likely source of the transmitted R5 phenotype. At age 3, an X4 population was present in the child that had evolved from the child's own R5-associated population, clearly distinct from the maternal X4 sequences. The second mother-child pair (Mb-Cb) displayed a similar pattern. Amino acid substitution patterns corroborated the conclusions from the phylogenetic tree. Thus, in both children, the X4 virus developed from their own R5 population, and was not caused by transmission of X4.
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MESH Headings
- Amino Acid Sequence
- Child
- Child, Preschool
- Evolution, Molecular
- Female
- HIV Envelope Protein gp120/chemistry
- HIV Envelope Protein gp120/genetics
- HIV Infections/transmission
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- Infant
- Infant, Newborn
- Infectious Disease Transmission, Vertical
- Leukocytes, Mononuclear/virology
- Molecular Sequence Data
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Phenotype
- Phylogeny
- Pregnancy
- Pregnancy Complications, Infectious/virology
- Receptors, CCR5/genetics
- Receptors, CCR5/metabolism
- Receptors, CXCR4/genetics
- Receptors, CXCR4/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
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Affiliation(s)
- P Clevestig
- Microbiology and Tumor Biology Center, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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Casper CHE, Clevestig P, Carlenor E, Leitner T, Anzén B, Lidman K, Belfrage E, Albert J, Bohlin AB, Navér L, Lindgren S, Fenyö EM, Ehrnst AC. Link between the X4 phenotype in human immunodeficiency virus type 1-infected mothers and their children, despite the early presence of R5 in the child. J Infect Dis 2002; 186:914-21. [PMID: 12232831 DOI: 10.1086/342948] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2002] [Revised: 04/24/2002] [Indexed: 11/03/2022] Open
Abstract
Coreceptor use was determined for human immunodeficiency virus type 1 (HIV-1) isolates of various subtypes from 11 women during pregnancy and their infected children. Isolates from peripheral blood mononuclear cells (n=79) and from plasma (n=59) were available. The clinical and immunological stages of HIV-1 infection were recorded. Coreceptor use was tested on human cell lines expressing CD4 and different chemokine receptors. The R5 virus predominated, and only 9 isolates from 2 mothers used CXC chemokine receptor 4. All children carried the R5 virus at the time of diagnosis of HIV-1 infection. In 2 children of mothers carrying the X4 virus, the virus switched from R5 to X4 or to R5X4 by age 18 months (child no. 9) and age 48 months (child no. 10), whereas no children followed up to a similar age whose mothers were carrying the R5 virus experienced such a switch (P=.048). This points to a link between the presence of X4 virus in the mother and the emergence of X4 virus in her child.
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Affiliation(s)
- Charlotte H E Casper
- Microbiology and Tumor Biology Center, Neonatal Unit, Department of Woman and Child Health, Karolinska Hospital, Stockholm, Sweden
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Casper C, Navér L, Clevestig P, Belfrage E, Leitner T, Albert J, Lindgren S, Ottenblad C, Bohlin AB, Fenyö EM, Ehrnst A. Coreceptor change appears after immune deficiency is established in children infected with different HIV-1 subtypes. AIDS Res Hum Retroviruses 2002; 18:343-52. [PMID: 11897036 DOI: 10.1089/088922202753519124] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Change of HIV-1 coreceptor use has been connected to progression of disease in children infected with HIV-1, presumably subtype B. It has not been possible to discern whether the appearance of new viral phenotypes precedes disease development or comes as a consequence of it. We studied the evolution of coreceptor use in HIV-1 isolates from 24 vertically infected children. Their clinical, virological, and immunological status was recorded and the env V3 subtype was determined by DNA sequencing. Coreceptor use was tested on human cell lines, expressing CD4 together with CCR5, CXCR4, and other chemokine receptors. The children carried five different env subtypes (nine A, five B, four C, three D, and one G) and one circulating recombinant form, CRF01_AE (n = 2). Of the 143 isolates, 86 originated from peripheral blood mononuclear cells (PBMCs) and 57 originated from plasma, received at 90 time points. In 52 of 54 paired plasma and PBMC isolates the coreceptor use was concordant. All 74 isolates obtained at 41 time points during the first year of life used CCR5. A change from use of CCR5 to use of CXCR4 occurred in four children infected with subtype A, D, or CRF01_AE after they had reached 1.5 to 5.8 years of age. There was a significant association with decreased CD4+ cell levels and severity of disease but, interestingly, the coreceptor change appeared months or even years after the beginning of the immunological deterioration. Thus CXCR4-using virus may emerge as a possible consequence of immune deficiency. The results provide new insights into AIDS development in children.
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Affiliation(s)
- C Casper
- Microbiology and Tumor Biology Center, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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