Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster
Abstract
:1. Introduction
2. Materials and Methods
2.1. Number of Individuals and RT-PCR Test
2.2. Viral Whole-Genome-Sequencing
2.3. Serological Tests
3. Results
3.1. Case Study
3.2. Description of the Transmission Chain
3.3. Viral Sequencing Interpretation
3.4. Viral Sequencing Contextualisation
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ID | Transmission Event | Transmission Level | Viral Sequence | |||||
---|---|---|---|---|---|---|---|---|
Factory | Family1 | Family2 | Clade | Other Non-Clade Basal Mutations (%) | ||||
P1 | X | X | 0 | 20B | A3660G (93%) | T11194C (55%) | ||
P35 | 0 | 20B | ||||||
P36 | 1 (P35) | 20B | ||||||
P37 | 2 (P36) | 20B | G4432T (99%) | |||||
P2 * | X | X | 0 | 20A | G24077T | |||
P12 | X | 1 (P2) | 20A | G24077T (100%) | ||||
P13 | X | X | 1 (P2) | 20A | G24077T (100%) | |||
P14 | X | X | 1 (P2) | 20A | G24077T (100%) | |||
P15 | X | X | 1 (P2) | 20A | G24077T (100%) | T14418C (54%) | G26634T (100%) | |
P16 | X | X | 1 (P2) | 20A | G24077T (100%) | C2062T (70%) | C6279A (65%) | |
P17 | X | 1 (P2) | 20A | G24077T (86%) | ||||
P21 | X | 1 (P2) | 20A | G24077T (100%) | ||||
P22 | X | 1 (P2) or 2 (P13/P14) | 20A | G24077T (100%) | ||||
P23 | X | 1 (P2) or 2 (P13/P14) | 20A | G24077T (100%) | ||||
P24 | X | 1 (P2) | 20A | G24077T (100%) | C4456T (82%) | |||
P25 | X | 1 (P2) | 20A | G24077T (98%) | ||||
P26 | X | 1 (P2) | 20A | G24077T (100%) | ||||
P28 | X | 2 (P15) | 20A | G24077T (100%) | G26634T (73%) | |||
P29 | X | 2 (P4/P20) | 20A | G24077T (100%) | ||||
P31 | 2 (P21) | 20A | G24077T (100%) | |||||
P32 | 3 (P31) | 20A | G24077T (100%) | |||||
P33 | 2 or 3 (P22) | 20A | G24077T (100%) | |||||
P34 | 3 or 4 (P33) | 20A | G24077T (100%) |
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Pedro, N.; Fernandes, V.; Cavadas, B.; Guimarães, J.T.; 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. https://doi.org/10.3390/v13061116
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(6):1116. https://doi.org/10.3390/v13061116
Chicago/Turabian StylePedro, Nicole, Veronica Fernandes, Bruno Cavadas, João Tiago Guimarães, Henrique Barros, Margarida Tavares, and Luisa Pereira. 2021. "Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster" Viruses 13, no. 6: 1116. https://doi.org/10.3390/v13061116