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Pedro N, Fernandes V, Cavadas B, Guimarães JT, Barros H, Tavares M, Pereira L. Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster. Viruses 2021; 13:1116. [PMID: 34200621 PMCID: PMC8226748 DOI: 10.3390/v13061116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/31/2022] Open
Abstract
Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.
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Affiliation(s)
- Nicole Pedro
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Veronica Fernandes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Bruno Cavadas
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - João Tiago Guimarães
- CHUSJ, Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal; (J.T.G.); (M.T.)
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Henrique Barros
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Margarida Tavares
- CHUSJ, Centro Hospitalar Universitário S. João, 4200-319 Porto, Portugal; (J.T.G.); (M.T.)
- FMUP, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal;
- EPIUnit, Instituto de Saúde Pública, Universidade do Porto, 4050-091 Porto, Portugal
| | - Luisa Pereira
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (N.P.); (V.F.); (B.C.)
- Ipatimup, Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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Farrer RA, Borman AM, Inkster T, Fisher MC, Johnson EM, Cuomo CA. Genomic epidemiology of a Cryptococcus neoformans case cluster in Glasgow, Scotland, 2018. Microb Genom 2021; 7:mgen000537. [PMID: 33620303 PMCID: PMC8190611 DOI: 10.1099/mgen.0.000537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/16/2022] Open
Abstract
In 2018, a cluster of two cases of cryptococcosis occurred at the Queen Elizabeth University Hospital (QEUH) in Glasgow, Scotland (UK). It was postulated that these cases may have been linked to pigeon droppings found on the hospital site, given there have been previous reports of Cryptococcus neoformans associated with pigeon guano. Although some samples of pigeon guano taken from the site yielded culturable yeast from genera related to Cryptococcus, they have since been classified as Naganishia or Papiliotrema spp., and no isolates of C. neoformans were recovered from either the guano or subsequent widespread air sampling. In an attempt to further elucidate any possible shared source of the clinical isolates, we used whole-genome sequencing and phylogenetic analysis to examine the relationship of the two Cryptococcus isolates from the QEUH cases, along with two isolates from sporadic cases treated at a different Glasgow hospital earlier in 2018. Our work demonstrated that these four clinical isolates were not clonally related; while all isolates were from the VNI global lineage and of the same mating type (MATα), the genotypes of the two QEUH isolates were separated by 1885 base changes and belonged to different sub-lineages, recently described as the intercontinental sub-clades VNIa-93 and VNIa-5. In contrast, one of the two sporadic 2018 clinical isolates was determined to belong to the VNIb sub-lineage and the other classified as a VNIV/VNI hybrid. Our work demonstrated that the two 2018 QEUH isolates and the two prior C. neoformans clinical isolates were all genetically distinct. It was not possible to determine whether the QEUH genotypes stemmed from independent sources or from the same source, i.e. pigeons carrying different genotypes, but it should be noted that whilst members of allied genera within the Tremellomycetes were isolated from the hospital environment, there were no environmental isolations of C. neoformans.
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Affiliation(s)
- Rhys A. Farrer
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
| | - Andrew M. Borman
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
- Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
| | - Teresa Inkster
- Department of Microbiology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Matthew C. Fisher
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - Elizabeth M. Johnson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4PY, UK
- Public Health England National Mycology Reference Laboratory, Science Quarter, Southmead Hospital, Bristol BS10 5NB, UK
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Gong X, Xiao W, Cui Y, Wang Y, Kong D, Mao S, Zheng Y, Xiang L, Lu L, Jiang C, Yu X, Zhu Y, Fang Q, Pan H, Wu H. Three infection clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19), Shanghai, China, January to February 2020. Euro Surveill 2020; 25:2000228. [PMID: 32820715 PMCID: PMC7441604 DOI: 10.2807/1560-7917.es.2020.25.33.2000228] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
We report three clusters related with potential pre-symptomatic transmission of coronavirus disease (COVID-19) between January and February 2020 in Shanghai, China. Investigators interviewed suspected COVID-19 cases to collect epidemiological information, including demographic characteristics, illness onset, hospital visits, close contacts, activities' trajectories between 14 days before illness onset and isolation, and exposure histories. Respiratory specimens of suspected cases were collected and tested for SARS-CoV-2 by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assay. The interval between the onset of illness in the primary case and the last contact of the secondary case with the primary case in our report was 1 to 7 days. In Cluster 1 (five cases), illness onset in the five secondary cases was 2 to 5 days after the last contact with the primary case. In Cluster 2 (five cases) and Cluster 3 (four cases), the illness onset in secondary cases occurred prior to or on the same day as the onset in the primary cases. The study provides empirical evidence for transmission of COVID-19 during the incubation period and indicates that pre-symptomatic person-to-person transmission can occur following sufficient exposure to confirmed COVID-19 cases. The potential pre-symptomatic person-to-person transmission puts forward higher requirements for prevention and control measures.
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Affiliation(s)
- Xiaohuan Gong
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- These authors contributed equally to this work
| | - Wenjia Xiao
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- These authors contributed equally to this work
| | - Yan Cui
- These authors contributed equally to this work
- Putuo District Center for Disease Control and Prevention, Shanghai, China
| | - Yuanping Wang
- These authors contributed equally to this work
- Pudong District Center for Disease Control and Prevention, Shanghai, China
| | - Dechuan Kong
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Shenghua Mao
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yaxu Zheng
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Lunhui Xiang
- Baoshan District Center for Disease Control and Prevention, Shanghai, China
| | - Lu Lu
- Huangpu District Center for Disease Control and Prevention, Shanghai, China
| | - Chenyan Jiang
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiao Yu
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yiyi Zhu
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qiwen Fang
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hao Pan
- Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Huanyu Wu
- Department of Infectious Disease Control and Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
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