Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia

Ciuffreda, Laura; Lorenzo-Salazar, José M.; Alcoba-Flórez, Julia; Rodríguez‐Pérez, Hector; Gil-Campesino, Helena; Íñigo-Campos, Antonio; Artola, Diego García-Martínez de; Valenzuela-Fernández, Agustı́n; Hayek-Peraza, Marcelino; Rojo‐Alba, Susana; Álvarez-Argüelles, Marta Elena; Díez-Gil, Oscar; González-Montelongo, Rafaela; Flores, Carlos

doi:10.1016/j.jinf.2021.07.028

Cited by 11 publications

(13 citation statements)

References 9 publications

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“…Genomes included in the dataset were obtained from: ( Choi et al 2020 ; Avanzato et al 2020 ; Reuken et al 2021 ; Tarhini et al 2021 , Kemp et al 2021 Baang et al 2021 ; Stanevich et al 2021 ; Khatamzas et al 2021 ; Borges et al 2021 ; Riddell et al 2022 ; Ciuffreda et al 2021 ; Jensen et al 2021 ; Weigang et al 2021 ). A full description of the dataset is available within the supplementary material of this article.…”

Section: Methodsmentioning

confidence: 99%

Recurrent SARS-CoV-2 mutations in immunodeficient patients

et al. 2022

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Long-term SARS-CoV-2 infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COG-UK dataset. The spike gene receptor binding domain (RBD) and N-terminal domains (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation. There is an apparent selective pressure for mutations which aid cell-cell transmission within the host or persistence which are often different to mutations which aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.

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Section: Methodsmentioning

confidence: 99%

Recurrent SARS-CoV-2 mutations in immunodeficient patients

et al. 2022

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“…In addition, some of the papers focus on spike proteins only. Finally, although we chose to focus on secondary immunodeficiencies due to the larger number of patients with analyzed viral genomes, mutations in primary immunodeficient patients (Bucciol et al, 2021;Ciuffreda et al, 2021;Cabañero-Navalon et al, 2022) are slowly being characterized that could add to the topic of viral evolution in the context of immunodeficiencies at large.…”

Section: Discussionmentioning

confidence: 99%

Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency

Markarian

Galli²,

Patel³

et al. 2022

Front. Microbiol.

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Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.

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“…Samples were selected for sequencing if they showed a cycle threshold (Ct) ≤30 for any of the amplicon targets included in the COVID-19 diagnostic kits. Libraries were prepared following either the Midnight protocol v.4 (Freed et al ., 2020), by means of the Rapid Barcoding kit (SQK-RBK004, Oxford Nanopore Technologies) and sequenced on a MinION and an R9.4 flow cell (Oxford Nanopore Technologies) for 6 hours, or the COVIDSeq Test (Illumina, Inc.) protocol based on the ARTIC V3 amplicons and sequenced on a NextSeq 550 (Illumina) instrument on High Output mode with 36 bp single- or pair-end (after the 7th of September 2021) reads following the procedures described elsewhere (Alcoba-Florez et al ., 2021; Ciuffreda et al ., 2021). Positive and negative amplification controls were included in each run (one for each fraction of 94 samples).…”

Section: Methodsmentioning

confidence: 99%

Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain)

Ciuffreda

González-Montelongo

Alcoba-Flórez

et al. 2022

Preprint

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Several variants of concern (VOCs) explain most of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) epidemic waves in Europe. We aimed to dissect the spread of the SARS-CoV-2 VOCs in the Canary Islands (Spain) between December 2020 and September 2021 at a micro-geographical level. We sequenced the viral genome of 8,224 respiratory samples collected in the archipelago. We observed that Alpha (B.1.1.7) and Delta (B.1.617.2 and sub-lineages) were ubiquitously present in the islands, while Beta (B.1.351) and Gamma (P.1/P.1.1) had a heterogeneous distribution and were responsible for fewer and more controlled outbreaks. This work represents the largest effort for viral genomic surveillance in the Canary Islands so far, helping the public health bodies in decision-making throughout the pandemic.

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Longitudinal study of a SARS-CoV-2 infection in an immunocompromised patient with X-linked agammaglobulinemia

Cited by 11 publications

References 9 publications

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency

Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain)

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