Genome Sequence of a SARS-CoV-2 VUI 202012/01 Strain Identified from a Patient Returning from London, England, to the Apulia Region of Italy

Loconsole, Daniela; Sallustio, Anna; Accogli, Marisa; Centrone, Francesca; Capozzi, Loredana; Sambro, Laura Del; Parisi, Antonio; Chironna, Maria

doi:10.1128/mra.01487-20

Cited by 13 publications

(10 citation statements)

References 2 publications

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“…Moreover, the increased transmissibility of these strains poses concern about these variants as a possible cause of reinfections as well as postvaccination infections [ 10 ]. In the Apulia region, the VOC 202012/01 was first identified at the end of December 2020 [ 28 ], and its prevalence in Italy in March 2021 has been estimated to be 86.7% [ 29 ]. Further investigation is urgently needed to monitor vaccine effectiveness against these VOC [ 10 ].…”

Section: Discussionmentioning

confidence: 99%

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing

Loconsole

Sallustio

Accogli

et al. 2021

Viruses

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This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two episodes of COVID-19. The first COVID-19 episode was in March 2020, and the second was in January 2021. Both SARS-CoV-2 infections presented with mild symptoms, and seroconversion for SARS-CoV-2 IgG was documented. Genomic analysis showed that the viral genome from the first infection belonged to the lineage B.1.1.74, while that from the second infection to the lineage B.1.177. Epidemiological, clinical, serological, and genomic analyses confirmed that the second episode of SARS-CoV-2 infection in the healthcare worker met the qualifications for “best evidence” for reinfection. Further studies are urgently needed to assess the frequency of such a worrisome occurrence, particularly in the light of the recent diffusion of SARS-CoV-2 variants of concern.

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Section: Discussionmentioning

confidence: 99%

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing

Loconsole

Sallustio

Accogli

et al. 2021

Viruses

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“…To support the accuracy of S gene target failure (SGTF) as a proxy for B.1.1.7 and the estimated frequency of VOC 202012/01 in the Apulia region, 155 SGTF-positive samples were selected to meet the regional requirement for the molecular surveillance and the national requirement to estimate the diffusion of the VOCs in Italy [ 7 ], and subjected to sequencing, which was performed as previously described [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

“…Due to its high prevalence in the UK, SGTF has been used as a proxy to track the circulation of B.1.1.7-lineage VOC [ 13 ]. In the Apulia region (southern Italy), VOC 202012/01 was first identified at the end of December 2020 [ 14 ]. In three flash surveys conducted to estimate the prevalence of VOC 202012/01 in Italy, all of the samples collected in the Apulia region and showing SGTF were confirmed as B.1.1.7-lineage strains by whole-genome sequencing [ 7 , 8 ], suggesting that S gene dropout could be considered a robust proxy for assessing the circulation of the UK variant.…”

Section: Introductionmentioning

confidence: 99%

Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020–March 2021)

Loconsole

Centrone

Morcavallo

et al. 2021

IJERPH

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Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020–March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.

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“…Only the sample collected from the heart transplant recipient was available for molecular characterization. Whole-genome sequencing was performed using the Ion Torrent platform (Thermo Fisher Scientific, Waltham, MA, USA) as previously described [ 17 ].…”

Section: Methodsmentioning

confidence: 99%

Severe COVID-19 by SARS-CoV-2 Lineage B.1.1.7 in Vaccinated Solid-Organ Transplant Recipients: New Preventive Strategies Needed to Protect Immunocompromised Patients

et al. 2021

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Background: Solid-organ transplant (SOT) recipients are at a high risk of severe COVID-19, and are priority for vaccination. Here, we describe three cases of severe COVID-19 caused by SARS-CoV-2 B.1.1.7 lineage in vaccinated SOT recipients. Methods: Three SOT patients were hospitalized in the Policlinico Hospital of Bari (southern Italy) and underwent nasopharyngeal swabs for molecular detection of SARS-CoV-2 genes and spike protein mutations by real-time PCR. One sample was subjected to whole-genome sequencing. Results: One patient was a heart transplant recipient and two were kidney transplant recipients. All were hospitalized with severe COVID-19 between March and May 2021. Two patients were fully vaccinated and one had received only one dose of the BNT162b2 mRNA vaccine. All the patients showed a high viral load at diagnosis, and molecular typing revealed the presence of B.1.1.7 lineage SARS-CoV-2. In all three cases, prolonged viral shedding was reported. Conclusions: The three cases pose concern about the role of the B.1.1.7 lineage in severe COVID-19 and about the efficacy of COVID-19 vaccination in immunocompromised patients. Protecting immunocompromised patients from COVID-19 is a challenge. SOT recipients show a suboptimal response to standard vaccination, and thus, an additive booster or a combined vaccination strategy with mRNA, protein/subunit, and vector-based vaccines may be necessary. This population should continue to practice strict COVID-19 precautions post-vaccination, until new strategies for protection are available.

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Genome Sequence of a SARS-CoV-2 VUI 202012/01 Strain Identified from a Patient Returning from London, England, to the Apulia Region of Italy

Cited by 13 publications

References 2 publications

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing

Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing

Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020–March 2021)

Severe COVID-19 by SARS-CoV-2 Lineage B.1.1.7 in Vaccinated Solid-Organ Transplant Recipients: New Preventive Strategies Needed to Protect Immunocompromised Patients

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