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Salman M, Venkateswaran D, Prakash A, Nguyen QA, Suntisukwattana R, Atthaapa W, Tantituvanont A, Songkasupa T, Deemagarn T, Bhakha K, Pengpetch N, Saenboonrueng J, Thaweerattanasinp T, Jongkaewwattana A, Nilubol D. The Comparative Full-Length Genome Characterization of African Swine Fever Virus Detected in Thailand. Animals (Basel) 2024; 14:2602. [PMID: 39272387 PMCID: PMC11394130 DOI: 10.3390/ani14172602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
African swine fever virus (ASFV) has been responsible for the globally devastating epidemics in wild and domesticated pigs. Of the 24 identified ASFV genotypes, genotype II is the primary cause for the pandemic occurring in Europe and Asia since its emergence in Georgia in 2007. The current study aimed to characterize the full-length genomic pattern of the ASFV strain from Thailand, TH1_22/CR (Accession No. PP915735), which was then compared with genomic diversity across other Asian isolates using Georgia 2007/1 (Accession No. FR682468) as the reference. Viral DNA was isolated from the pig spleen sample following library preparation and paired-end sequencing using the MiSeq Illumina platform. The sequenced TH1_22/CR isolate spanned 189,395 nucleotides encoding 193 open reading frames (ORFs), exhibiting maximum nucleotide similarity (99.99%) with Georgian (Georgia 2007/1) and Chinese (Wuhan 2019-1 and China HLJ) isolates. Based on phylogenetic analysis, the TH1_22/CR isolate (Accession No. PP915735) was characterized as genotype II, serogroup 8, and IGR-II due to the presence of three tandem repeat sequences (TRSs). Genetic variations including SNPs and single and polynucleotide indels were identified in TH1_22/CR in agreement with other Asian isolates. For comprehensive analysis, the genome was divided into four regions (I-IV) based on gene location. Overall, the TH1_22/CR isolate demonstrated eight SNPs and indels in its genome. Two unique SNPs were reported in the coding regions of the TH1_22/CR isolate, out of which, a C-591-T substitution was seen in MGF 360-4L and a C-297-T was found in A238L, and four unique SNPs were reported in non-coding regions (NCRs). Furthermore, a 29 bp deletion was observed in the IGR between MGF 110-13La and MGF 110-13Lb, as well as 52 bp deletion in the ASFV G ACD 00350 gene. This comparative analysis establishes the foundational information for future studies on the diversity and phylogeography of this regionally significant genetic sub-group of ASFV.
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Affiliation(s)
- Muhammad Salman
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Dhithya Venkateswaran
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Anwesha Prakash
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Quynh Anh Nguyen
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Roypim Suntisukwattana
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Waranya Atthaapa
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Angkana Tantituvanont
- Department of Pharmaceutic and Industrial Pharmacies, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tapanut Songkasupa
- Department of Livestock Development, National Institute of Animal Health, 50/2 Kasetklang, Phahonyothin 45-15, Chatuchak, Bangkok 10900, Thailand
| | - Taweewat Deemagarn
- Department of Livestock Development, National Institute of Animal Health, 50/2 Kasetklang, Phahonyothin 45-15, Chatuchak, Bangkok 10900, Thailand
| | - Kultyarat Bhakha
- Department of Livestock Development, National Institute of Animal Health, 50/2 Kasetklang, Phahonyothin 45-15, Chatuchak, Bangkok 10900, Thailand
| | - Nuttun Pengpetch
- Department of Livestock Development, National Institute of Animal Health, 50/2 Kasetklang, Phahonyothin 45-15, Chatuchak, Bangkok 10900, Thailand
| | - Janya Saenboonrueng
- National Center for Genetic Engineering and Biotechnology, Pathum Thani 12120, Thailand
| | | | - Anan Jongkaewwattana
- National Center for Genetic Engineering and Biotechnology, Pathum Thani 12120, Thailand
| | - Dachrit Nilubol
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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Giammarioli M, Torresi C, Biccheri R, Cammà C, Marcacci M, Dondo A, Razzuoli E, Fusco G, Casalinuovo F, Scicluna MT, Dei Giudici S, Martin AMM, Rossi E, Casciari C, Pela M, Iscaro C, Gallardo C, Marocco G, Orrico M, Feliziani F. Genetic Characterization of African Swine Fever Italian Clusters in the 2022-2023 Epidemic Wave by a Multi-Gene Approach. Viruses 2024; 16:1185. [PMID: 39205159 PMCID: PMC11360507 DOI: 10.3390/v16081185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024] Open
Abstract
The first report of African swine fever virus (ASFV) genotype II in Italy in 2022 marked the beginning of a significant invasion in at least eight Italian regions with different infection clusters. In this study, we used the multi-gene approach to investigate the epidemiological associations between ASFV strains causing cases and outbreaks in wild boar and pigs in Italy from January 2022 to the end of 2023. Our results confirm that all the tested ASFV-positive Italian samples belonged to genotype II and show high homology with genotype II ASFV sequences previously collected in Eurasian countries. Molecular characterization revealed the presence of four genetic groups in Italy. The majority of African swine fever (ASF) samples analyzed in the current study (72%) belonged to genetic group 3, which was the most representative in Europe. The results also provide evidence of the prevalence of genetic group 19 (15.9%). In addition, we identified new putative genetic groups, genetic group 25 (9.1%) and genetic group 26 (3.0%), which have never been described before. This is the first detailed report on the molecular characterization of more than 130 ASFV strains circulating in Italy.
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Affiliation(s)
- Monica Giammarioli
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Claudia Torresi
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Roberta Biccheri
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (C.C.); (M.M.)
| | - Maurilia Marcacci
- National Reference Center for Whole Genome Sequencing of Microbial Pathogens, Database and Bioinformatic Analysis, Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy; (C.C.); (M.M.)
| | - Alessandro Dondo
- Istituto Zooprofilattico Sperimentale Piemonte, Liguria e Valle d’Aosta “I. Altara”, 10154 Turin, Italy; (A.D.); (E.R.)
| | - Elisabetta Razzuoli
- Istituto Zooprofilattico Sperimentale Piemonte, Liguria e Valle d’Aosta “I. Altara”, 10154 Turin, Italy; (A.D.); (E.R.)
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, 80055 Napoli, Italy; (G.F.); (F.C.)
| | - Francesco Casalinuovo
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, 80055 Napoli, Italy; (G.F.); (F.C.)
| | - Maria Teresa Scicluna
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy;
| | - Silvia Dei Giudici
- Istituto Zooprofilattico Sperimentale della Sardegna “G. Pegreffi”, 07100 Sassari, Italy;
| | - Ana Maria Moreno Martin
- Istituto Zooprofilattico Sperimentale della Lombardia e della Emilia Romagna “Bruno Ubertini”, 25124 Brescia, Italy;
| | - Elisabetta Rossi
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Cristina Casciari
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Michela Pela
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Carmen Iscaro
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | - Carmina Gallardo
- European Union Reference Laboratory for African Swine Fever (EURL), Centro de Investigación en Sanidad Animal (CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas (CSIC), Valdeolmos, 28130 Madrid, Spain;
| | - Gaia Marocco
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
| | | | - Francesco Feliziani
- National Reference Laboratory (NRL) for Swine Fever, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.T.); (R.B.); (E.R.); (C.C.); (M.P.); (C.I.); (G.M.); (F.F.)
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Petrini S, Brutti A, Casciari C, Calderone D, Pela M, Giammarioli M, Righi C, Feliziani F. High-Pressure Processing of Different Tissue Homogenates from Pigs Challenged with the African Swine Fever Virus. Viruses 2024; 16:638. [PMID: 38675978 PMCID: PMC11053747 DOI: 10.3390/v16040638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
African swine fever (ASF) is a disease that is a growing threat to the global swine industry. Regulations and restrictions are placed on swine movement to limit the spread of the virus. However, these are costly and time-consuming. Therefore, this study aimed to determine if high-pressure processing (HPP) sanitization techniques would be effective against the ASF virus. Here, it was hypothesized that HPP could inactivate or reduce ASF virus infectivity in tissue homogenates. To test this hypothesis, 30 aliquots of each homogenate (spleen, kidney, loin) were challenge-infected with the Turin/83 strain of ASF, at a 10 7.20 median hemadsorption dose (HAD)50/mL. Subsequently, eight aliquots of each homogenate were treated with 600 millipascal (600 MPa) HPP for 3, 5, and 7 min. Six untreated aliquots were used as the controls. Virological results showed a reduction in the viral titer of more than 7-log. These results support the validity of the study hypothesis since HPP treatment was effective in inactivating ASFV in artificially prepared samples. Overall, this study suggests the need for further investigation of other ASFV-contaminated meat products.
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Affiliation(s)
- Stefano Petrini
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
| | - Andrea Brutti
- SSICA Stazione Sperimentale per l’Industria delle Conserve Alimentari, Fondazione di Ricerca Parma, 43121 Parma, Italy;
| | - Cristina Casciari
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
| | - Davide Calderone
- Associazione Industriali delle Carni e dei Salumi (ASSICA), 20089 Milan, Italy;
| | - Michela Pela
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
| | - Monica Giammarioli
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
| | - Cecilia Righi
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
| | - Francesco Feliziani
- National Reference Centre for Pestiviruses and Asfivirus, Istituto Zooprofilattico Sperimentale Umbria-Marche “Togo Rosati”, Via Gaetano Salvemini, 1, 06126 Perugia, Italy; (C.C.); (M.P.); (M.G.); (C.R.); (F.F.)
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Dei Giudici S, Loi F, Ghisu S, Angioi PP, Zinellu S, Fiori MS, Carusillo F, Brundu D, Franzoni G, Zidda GM, Tolu P, Bandino E, Cappai S, Oggiano A. The Long-Jumping of African Swine Fever: First Genotype II Notified in Sardinia, Italy. Viruses 2023; 16:32. [PMID: 38257733 PMCID: PMC10820622 DOI: 10.3390/v16010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
African swine fever (ASF) is a devastating infectious disease of domestic pigs and wild boar that is spreading quickly around the world and causing huge economic losses. Although the development of effective vaccines is currently being attempted by several labs, the absence of globally recognized licensed vaccines makes disease prevention and early detection even more crucial. ASF has spread across many countries in Europe and about two years ago affected the Italian susceptible population. In Italy, the first case of ASF genotype II in wild boar dates back to January 2022, while the first outbreak in a domestic pig farm was notified in August 2023. Currently, four clusters of infection are still ongoing in northern (Piedmont-Liguria and Lombardy), central (Lazio), and southern Italy (Calabria and Campania). In early September 2023, the first case of ASFV genotype II was detected in a domestic pig farm in Sardinia, historically affected by genotype I and in the final stage of eradication. Genomic characterization of p72, p54, and I73R/I329L genome regions revealed 100% similarity to those obtained from isolates that have been circulating in mainland Italy since January 2022 and also with international strains. The outbreak was detected and confirmed due to the passive surveillance plan on domestic pig farms put in place to provide evidence on genotype I's absence. Epidemiological investigations suggest 24 August as the most probable time of ASFV genotype II's arrival in Sardinia, likely due to human activities.
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Affiliation(s)
- Silvia Dei Giudici
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
| | - Federica Loi
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Sonia Ghisu
- Diagnostic Laboratories, Istituto Zooprofilattico Sperimentale della Sardegna, 08100 Nuoro, Italy; (S.G.); (F.C.); (D.B.); (E.B.)
| | - Pier Paolo Angioi
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
| | - Susanna Zinellu
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
| | - Mariangela Stefania Fiori
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
| | - Francesca Carusillo
- Diagnostic Laboratories, Istituto Zooprofilattico Sperimentale della Sardegna, 08100 Nuoro, Italy; (S.G.); (F.C.); (D.B.); (E.B.)
| | - Diego Brundu
- Diagnostic Laboratories, Istituto Zooprofilattico Sperimentale della Sardegna, 08100 Nuoro, Italy; (S.G.); (F.C.); (D.B.); (E.B.)
| | - Giulia Franzoni
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
| | | | - Paolo Tolu
- Azienda Sanitaria Locale della Sardegna, 08100 Nuoro, Italy; (G.M.Z.); (P.T.)
| | - Ennio Bandino
- Diagnostic Laboratories, Istituto Zooprofilattico Sperimentale della Sardegna, 08100 Nuoro, Italy; (S.G.); (F.C.); (D.B.); (E.B.)
| | - Stefano Cappai
- Osservatorio Epidemiologico Veterinario Regionale della Sardegna, Istituto Zooprofilattico Sperimentale della Sardegna, 09125 Cagliari, Italy;
| | - Annalisa Oggiano
- Laboratory of Virology, Deapartment of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (S.Z.); (M.S.F.); (G.F.); (A.O.)
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Ståhl K, Boklund A, Podgórski T, Vergne T, Abrahantes JC, Papanikolaou A, Zancanaro G, Mur L. Epidemiological analysis of African swine fever in the European Union during 2022. EFSA J 2023; 21:e08016. [PMID: 37223755 PMCID: PMC10201408 DOI: 10.2903/j.efsa.2023.8016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
This report presents the epidemiological analysis of African swine fever (ASF) during 2022 based on the surveillance and pig population data submitted by the European Union (EU) affected countries and one neighbouring country. Coinciding with regulatory changes and an important decrease in ASF outbreaks in 2022 in the EU, the number of domestic pig samples tested as part of active surveillance decreased by 80%, while the number of samples from passive surveillance almost doubled compared with 2021. Most outbreaks among domestic pigs in the EU were detected by testing clinical suspicions (93% of outbreaks), followed by tracing activities (5%) and weekly testing of the first two dead pigs per establishment (2%). Although most of the wild boar samples came from hunted animals, the probability of detecting PCR-positive animals was much higher in wild boar found dead. The ASF outbreaks among domestic pigs in the EU decreased by 79% while a decrease of 40% in the wild boar cases was observed in comparison with 2021. This was strongly marked in Romania, Poland and Bulgaria, with a reduction of 50-80% compared with 2021. In many countries, an important decrease in the number of pig establishments was observed, especially of small establishments with fewer than 100 pigs. The regional between farm incidence and proportion of pigs lost due to ASF in the EU was in general very low (average of 1%) apart from some regions in Romania. The impact of ASF on wild boar populations was variable, with a decline in wild boar abundance observed in certain countries versus a stable or even increased population after ASF introduction. This supports the negative relationship observed in this report between the proportion of the country with restricted zones due to ASF in wild boar and wild boar hunting bags.
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