Genomic analysis of SARS-CoV-2 in forensic autopsy cases of COVID-19.
SARS-CoV-2
forensic autopsy
mutation
viral genome
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
revised:
25
06
2023
received:
24
04
2023
accepted:
14
07
2023
medline:
7
8
2023
pubmed:
4
8
2023
entrez:
4
8
2023
Statut:
ppublish
Résumé
Numerous genomic analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been conducted, highlighting its variations and lineage transitions. Despite the importance of forensic autopsy in investigating deaths due to coronavirus disease 2019 (COVID-19), including out-of-hospital deaths, viral genomic analysis has rarely been reported due in part to postmortem changes. In this study, various specimens were collected from 18 forensic autopsy cases with SARS-CoV-2 infection. Reverse-transcription quantitative polymerase chain reaction revealed the distribution of the virus in the body, primarily in the respiratory organs. Next-generation sequencing determined the complete genome sequences in 15 of the 18 cases, although some cases showed severe postmortem changes or degradation of tissue RNA. Intrahost genomic diversity of the virus was identified in one case of death due to COVID-19. The accumulation of single-nucleotide variations in the lung of the case suggested the intrahost evolution of SARS-CoV-2. Lung of the case showed diffuse alveolar damage histologically and positivity for SARS-CoV-2 by immunohistochemical analysis and in situ hybridization, indicating virus-associated pneumonia. This study provides insights into the feasibility of genomic analysis of SARS-CoV-2 in forensic autopsy cases and the potential for uncovering important information in COVID-19 deaths, including out-of-hospital deaths.
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e28990Informations de copyright
© 2023 Wiley Periodicals LLC.
Références
Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20:533-534.
Sperhake JP. Autopsies of COVID-19 deceased? Absolutely! Leg Med. 2020;47:101769.
Bösmüller H, Matter M, Fend F, Tzankov A. The pulmonary pathology of COVID-19. Virchows Arch. 2021;478:137-150.
Ackermann M, Verleden SE, Kuehnel M, et al. Pulmonary vascular endothelialitis, thrombosis, and angiogenesis in Covid-19. N Engl J Med. 2020;383:120-128.
Edler C, Schröder AS, Aepfelbacher M, et al. Dying with SARS-CoV-2 infection-an autopsy study of the first consecutive 80 cases in Hamburg, Germany. Int J Legal Med. 2020;134:1275-1284.
Youd E, Moore L. COVID-19 autopsy in people who died in community settings: the first series. J Clin Pathol. 2020;73:840-844.
Tao K, Tzou PL, Nouhin J, et al. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet. 2021;22:757-773.
Davies NG, Jarvis CI, Edmunds WJ, Jewell NP, Diaz-Ordaz K, Keogh RH. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature. 2021;593:270-274.
Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ. 2021;372:n579.
Becerra-Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract. 2020;74:e13525.
Toyoshima Y, Nemoto K, Matsumoto S, Nakamura Y, Kiyotani K. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet. 2020;65:1075-1082.
Gabbrielli M, Gandolfo C, Anichini G, et al. How long can SARS-CoV-2 persist in human corpses? Int J Infect Dis. 2021;106:1-2.
Bonelli M, Rosato E, Locatelli M, et al. Long persistence of severe acute respiratory syndrome coronavirus 2 swab positivity in a drowned corpse: a case report. J Med Case Rep. 2022;16:72.
Gagliardi S, Poloni ET, Pandini C, et al. Detection of SARS-CoV-2 genome and whole transcriptome sequencing in frontal cortex of COVID-19 patients. Brain Behav Immun. 2021;97:13-21.
Hoy Marbjerg L, Jacobsen C, Fonager J, et al. Possible involvement of central nervous system in COVID-19 and sequence variability of SARS-CoV-2 revealed in autopsy tissue samples: a case report. Clin Pathol. 2021;14:2632010X211006096.
Pardo-Seco J, Bello X, Gómez-Carballa A, Martinón-Torres F, Muñoz-Barús JI, Salas A. A timeframe for SARS-CoV-2 genomes: a proof of concept for postmortem interval estimations. Int J Mol Sci. 2022;23:12899.
Adachi T, Chong JM, Nakajima N, et al. Clinicopathologic and immunohistochemical findings from autopsy of patient with COVID-19, Japan. Emerging Infect Dis. 2020;26:2157-2161.
Shirato K, Nao N, Katano H, et al. Development of genetic diagnostic methods for detection for novel coronavirus 2019(nCoV-2019) in Japan. Jpn J Infect Dis. 2020;73:304-307.
Katano H, Kano M, Nakamura T, Kanno T, Asanuma H, Sata T. A novel real-time PCR system for simultaneous detection of human viruses in clinical samples from patients with uncertain diagnoses. J Med Virol. 2011;83:322-330.
Itokawa K, Sekizuka T, Hashino M, et al. nCoV-2019 sequencing protocol for illumina; 2021. https://protocols.io/view/ncov-2019-sequencing-protocol-for-illumina-b2msqc6e
Tyson JR, James P, Stoddart D, et al. Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore. bioRxiv; 2020. doi:10.1101/2020.1109.1104.283077
Josh Q. nCoV-2019 sequencing protocol v3 (LoCost); 2020. https://protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8ye
Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265-269.
Sekizuka T, Itokawa K, Hashino M, et al. A genome epidemiological study of SARS-CoV-2 introduction into Japan. mSphere. 2020;5:e00786-20.
DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 2011;43:491-498.
Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-576.
Aksamentov I, Roemer C, Hodcroft E, Neher R. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773.
O'Toole Á, Scher E, Underwood A, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7:veab064.
Chen AT, Altschuler K, Zhan SH, Chan YA, Deverman BE. COVID-19 CG enables SARS-CoV-2 mutation and lineage tracking by locations and dates of interest. eLife. 2021;10:e63409.
Yamada S, Fukushi S, Kinoshita H, et al. Assessment of SARS-CoV-2 infectivity of upper respiratory specimens from COVID-19 patients by virus isolation using VeroE6/TMPRSS2 cells. BMJ Open Respir Res. 2021;8:e000830.
Matsuyama S, Nao N, Shirato K, et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc Natl Acad Sci USA. 2020;117:7001-7003.
Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Prot Sci. 2018;27:135-145.
Sievers F, Wilm A, Dineen D, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:539.
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111-120.
Bittar C, Possebon FS, Ullmann LS, et al. The emergence of the new P.4 lineage of SARS-CoV-2 with spike L452R mutation in Brazil. Front Public Health. 2021;9:745310.
Hisner RBA.2.3 Sublineage with 10 highly convergent S1 mutations (5 seqs, 3xSingapore, 1xAustralia, 1xUSA) #1013; GitHub. 2022. https://github.com/cov-lineages/pango-designation/issues/1013
Stein SR, Ramelli SC, Grazioli A, et al. SARS-CoV-2 infection and persistence in the human body and brain at autopsy. Nature. 2022;612:758-763.
Deinhardt-Emmer S, Wittschieber D, Sanft J, et al. Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage. eLife. 2021;10:e60361.
Karthik G, Alaa AL, Julia M, et al. Japan Variant Report. outbreak info. 2023. https://outbreak.info/location-reports?loc=JPN
Nakamura Y, Katano H, Nakajima N, et al. SARS-CoV-2 is localized in cardiomyocytes: a postmortem biopsy case. Int J Infect Dis. 2021;111:43-46.
Van Cleemput J, van Snippenberg W, Lambrechts L, et al. Organ-specific genome diversity of replication-competent SARS-CoV-2. Nat Commun. 2021;12:6612.
Harvey WT, Carabelli AM, Jackson B, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19:409-424.