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Alenquer M, Milheiro Silva T, Akpogheneta O, Ferreira F, Vale-Costa S, Medina-Lopes M, Batista F, Garcia AM, Barreto VM, Paulino C, Costa J, Sobral J, Diniz-da-Costa M, Ladeiro S, Corte-Real R, Delgado Alves J, Leite RB, Demengeot J, Rocha Brito MJ, Amorim MJ. Saliva molecular testing bypassing RNA extraction is suitable for monitoring and diagnosing SARS-CoV-2 infection in children. PLoS One 2022; 17:e0268388. [PMID: 35704567 PMCID: PMC9200166 DOI: 10.1371/journal.pone.0268388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/28/2022] [Indexed: 01/08/2023] Open
Abstract
Background Adults are being vaccinated against SARS-CoV-2 worldwide, but the longitudinal protection of these vaccines is uncertain, given the ongoing appearance of SARS-CoV-2 variants. Children remain largely unvaccinated and are susceptible to infection, with studies reporting that they actively transmit the virus even when asymptomatic, thus affecting the community. Methods We investigated if saliva is an effective sample for detecting SARS-CoV-2 RNA and antibodies in children, and associated viral RNA levels to infectivity. For that, we used a saliva-based SARS-CoV-2 RT-qPCR test, preceded or not by RNA extraction, in 85 children aged 10 years and under, admitted to the hospital regardless of COVID-19 symptomatology. Amongst these, 29 (63.0%) presented at least one COVID-19 symptom, 46 (54.1%) were positive for SARS-CoV-2 infection, 28 (32.9%) were under the age of 1, and the mean (SD) age was 3.8 (3.4) years. Saliva samples were collected up to 48 h after a nasopharyngeal swab-RT-qPCR test. Results In children aged 10 years and under, the sensitivity, specificity, and accuracy of saliva-RT-qPCR tests compared to NP swab-RT-qPCR were, respectively, 84.8% (71.8%–92.4%), 100% (91.0%–100%), and 91.8% (84.0%–96.6%) with RNA extraction, and 81.8% (68.0%–90.5%), 100% (91.0%–100%), and 90.4% (82.1%–95.0%) without RNA extraction. Rescue of infectious particles from saliva was limited to CT values below 26. In addition, we found significant IgM positive responses to SARS-CoV-2 in children positive for SARS-CoV-2 by NP swab and negative by saliva compared to other groups, indicating late infection onset (>7–10 days). Conclusions Saliva is a suitable sample type for diagnosing children aged 10 years and under, including infants aged <1 year, even bypassing RNA extraction methods. Importantly, the detected viral RNA levels were significantly above the infectivity threshold in several samples. Further investigation is required to correlate SARS-CoV-2 RNA levels to viral transmission.
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Affiliation(s)
- Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tiago Milheiro Silva
- Pediatric Infectious Disease Unit, Hospital Dona Estefânia, Centro Hospitalar Universitário Lisboa Central, Lisboa, Portugal
| | - Onome Akpogheneta
- Lymphocyte Physiology Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Sílvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Mónica Medina-Lopes
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Frederico Batista
- Department of Medicine 4, Hospital Prof Doutor Fernando Fonseca, Amadora, Portugal
| | - Ana Margarida Garcia
- Pediatric Infectious Disease Unit, Hospital Dona Estefânia, Centro Hospitalar Universitário Lisboa Central, Lisboa, Portugal
| | - Vasco M. Barreto
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Cathy Paulino
- Genomics Unit, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João Costa
- Genomics Unit, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João Sobral
- Genomics Unit, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Susana Ladeiro
- Genomics Unit, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Rita Corte-Real
- Molecular Biology Laboratory, Department of Clinical Pathology, Centro Hospitalar Universitário Lisboa Central, Lisboa, Portugal
| | - José Delgado Alves
- Department of Medicine 4, Hospital Prof Doutor Fernando Fonseca, Amadora, Portugal
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ricardo B. Leite
- Genomics Unit, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Jocelyne Demengeot
- Lymphocyte Physiology Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria João Rocha Brito
- Pediatric Infectious Disease Unit, Hospital Dona Estefânia, Centro Hospitalar Universitário Lisboa Central, Lisboa, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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Alenquer M, Ferreira F, Lousa D, Valério M, Medina-Lopes M, Bergman ML, Gonçalves J, Demengeot J, Leite RB, Lilue J, Ning Z, Penha-Gonçalves C, Soares H, Soares CM, Amorim MJ. Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies. PLoS Pathog 2021; 17:e1009772. [PMID: 34352039 PMCID: PMC8341613 DOI: 10.1371/journal.ppat.1009772] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding SARS-CoV-2 evolution and host immunity is critical to control COVID-19 pandemics. At the core is an arms-race between SARS-CoV-2 antibody and angiotensin-converting enzyme 2 (ACE2) recognition, a function of the viral protein spike. Mutations in spike impacting antibody and/or ACE2 binding are appearing worldwide, imposing the need to monitor SARS-CoV2 evolution and dynamics in the population. Determining signatures in SARS-CoV-2 that render the virus resistant to neutralizing antibodies is critical. We engineered 25 spike-pseudotyped lentiviruses containing individual and combined mutations in the spike protein, including all defining mutations in the variants of concern, to identify the effect of single and synergic amino acid substitutions in promoting immune escape. We confirmed that E484K evades antibody neutralization elicited by infection or vaccination, a capacity augmented when complemented by K417N and N501Y mutations. In silico analysis provided an explanation for E484K immune evasion. E484 frequently engages in interactions with antibodies but not with ACE2. Importantly, we identified a novel amino acid of concern, S494, which shares a similar pattern. Using the already circulating mutation S494P, we found that it reduces antibody neutralization of convalescent and post-immunization sera, particularly when combined with E484K and with mutations able to increase binding to ACE2, such as N501Y. Our analysis of synergic mutations provides a signature for hotspots for immune evasion and for targets of therapies, vaccines and diagnostics.
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Affiliation(s)
- Marta Alenquer
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Filipe Ferreira
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Mariana Valério
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Mónica Medina-Lopes
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | | | - Juliana Gonçalves
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa; Lisboa, Portugal
| | - Jocelyne Demengeot
- Lymphocyte Physiology Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Ricardo B. Leite
- Genomics Unit, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Jingtao Lilue
- Bioinformatics Unit, Instituto Gulbenkian de Ciência; Oeiras, Portugal
| | - Zemin Ning
- The Wellcome Trust Sanger Institute; Hinxton, United Kingdom
| | | | - Helena Soares
- CEDOC NOVA, Centro de Estudos de Doenças Crónicas, Nova Medical School, Universidade Nova de Lisboa; Lisboa, Portugal
| | - Cláudio M. Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa; Oeiras, Portugal
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência; Oeiras, Portugal
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