Summary

Vaccines against SARS-CoV-2 are very effective, but some mutations could reduce protection. Here we report a case of SARS-CoV-2 infection with a P.1.1 variant lacking the Y501 mutation in a vaccinated individual in Italy. Carefully monitoring breakthrough infections is important for assessing viral spreading of potential vaccine-resistant variants.

Dear EditorWe read with interest the recently published manuscript of Dimeglio et al., exploring the SARS-CoV-2 immune response and vaccination of healthcare workers post-infection1Dimeglio C Herin F Miedougé M Da-Silva I Porcheron M Martin-Blondel G Soulat JM Izopet J. One year later: SARS-CoV-2 immune response and vaccination of healthcare workers post-infection. and here we report a case of SARS-CoV-2 infection with a P.1.1 variant lacking the Y501 mutation in a vaccinated individual in Italy.COVID-19 vaccines are very effective in preventing infections, hospitalizations and deaths. However, several cases of SARS-CoV-2 infections have been reported in vaccinated individuals (called “vaccine breakthrough cases”) inoculated with one or both doses of vaccine2Hacisuleyman E Hale C Saito Y Blachere NE Bergh M Conlon EG Schaefer-Babajew DJ DaSilva J Muecksch F Gaebler C Lifton R Nussenzweig MC Hatziioannou T Bieniasz PD Darnell RB. Vaccine Breakthrough Infections with SARS-CoV-2 Variants.. This indicates that a small percentage of fully vaccinated subjects can be infected when exposed to the virus. Recently, in the UK, South Africa, Brazil and most recently in India3Rambaut A Loman N Pybus O et al.Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations., 4Tegally H. Wilkinson E. Giovanetti M. et al.Detection of a SARS-CoV-2 variant of concern in South Africa., 5Faria NR Mellan TA Whittaker C et al.Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus. SARS-CoV-2 variants of concern (VOC) have been identified. These new variants harbor mutations in the spike protein, and particularly in the receptor binding domain (RBD). These VOC are important because they show that a number of viral mutations are emerging with a potential impact on infectivity, immune escape and vaccine effectiveness.

In the University Campus Biomedico Hospital (UCMB – Rome, Italy), vaccination of health care workers began on December, 2020 soon after followed by active monitoring of potential breakthrough cases. For this reason, all health care workers, regardless of their symptomatic status, were tested weekly by molecular assay on nasopharyngeal swabs.

Here, we report the first case of SARS-CoV-2 P.1.1 infection lacking N501 mutation in a fully vaccinated (Pfizer) 22-year-old female nurse, working in the COVID-Center of the UCBM.

In early-January 2021, the nurse received the first vaccine dose followed by the second shot three weeks after. Two weeks after second dose of vaccine, a first Quantitative IgG anti-spike chemiluminescent assay tested positive with 2362 BAU/mL. Quantitative IgG anti-spike assay was repeated after 45 and 90 days confirming positive results with 1029 BAU/mL and 432 BAU/mL, respectively. Three months after the second dose the patient started presenting mild symptoms (headache and fever), compatible with a viral infection. At this time, a rapid SARS-CoV-2 N protein Chemiluminescent assay was performed on nasopharyngeal swab, revealing a positive result (>5000 pg/mL). The same swab was then tested for the detection of SARS-CoV-2 RNA by multiplex real-time PCR Allplex™ SARS-CoV-2 assay (Seegene Inc, Seoul, Korea). Cycle threshold values (Cts) of N, E and RdRp/S targets were 17, 18, and 18 respectively. Whole genome sequencing was then conducted on the same swab by Myseq II Illumina. Consensus sequences were generated by de novo assembling using Genome Detective (https://www.genomedetective.com/)6Cleemput S Dumon W Fonseca V Abdool Karim W Giovanetti M Alcantara LC Deforche K de Oliveira T Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.. A total of 1,323,357 mapped reads were obtained, resulting in a sequencing mean depth >1,000X and a coverage of >99.8%. Sequences were aligned using MAFFT7Nakamura T. Yamada K.D. Tomii K. Katoh K. Parallelization of MAFFT for large-scale multiple sequence alignments. and submitted to IQ-TREE 2 for maximum likelihood (ML) phylogenetic analysis8Minh B.Q. Schmidt H.A. Chernomor O. Schrempf D. Woodhams M.D. von Haeseler A. Lanfear R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era..Lineages assessment, conducted using Phylogenetic Assignment of Named Global Outbreak Lineages tool (available at https://github.com/hCoV-2019/pangolin), revealed the new strain belonged to the P.1.1 lineage. Phylogenetic inference by combining our new isolate (EPI_ISL_2488760) with a representative dataset available on GISAID (https://www.gisaid.org/) up to May 31th, 2021 demonstrated that the newly obtained genome belongs to P.1.1 lineage and clustered significantly with SARS-CoV-2 P.1.1 strains isolated in Italy between March and May 2021 (Figure 1a, b) (Bootstrap=0.80, SH-aLTR=0.80). Further, we analyzed the mutational profile of the newly generated strain to determine its lineage-defining mutations. The identified lineage harbored all the P.1.1 lineage specific mutations (Figure 1c), with the exception of the N501Y, a specific mutation that seems to be linked with an increased transmissibility9Davies NG Abbott S Barnard RC Jarvis CI Kucharski AJ Munday JD Pearson CAB Russell TW Tully DC Washburne AD Wenseleers T Gimma A Waites W Wong KLM van Zandvoort K Silverman JD CMMID COVID-19 Working Group COVID-19 Genomics UK (COG-UK) Consortium Diaz-Ordaz K Keogh R Eggo RM Funk S Jit M Atkins KE Edmunds WJ Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.. We also identified another Spike mutation, namely S640F, which currently is growing in many samples worldwide (Figure 1c).

Figure 1Genomic detection of the SARS-CoV-2 P.1 variant of concern in a vaccine breakthrough case in Italy. a) Maximum likelihood (ML) phylogenetic tree including the newly isolate obtained in this study plus n=1631 SARS-CoV-2 strains belonging to the P.1 lineage collected up to May 28th, 2021. b) Representation of the zoom of the Italian P.1 clade. Branch support (Bootstrap = 0.80, SH-aLTR = 0.80) is shown at key node. c) Variant map of the P.1 lineage-defining-mutations was mapped against the SARS-CoV-2 genome structure. Lineage-defining mutation are highlighted in red.

As observed through the course of the pandemic, these mutations highlight the ability of SARS-CoV-2 to generate new viral strains. In particular, these newly identified mutations likely represent a new SARS-CoV-2 variant probably able to escape vaccine protection, although to a certain extent, as indicated by the lack of severe symptoms. The lack of the N501Y may be linked to high transmissibility and immune evasion as indicated also for the new path followed by the delta new variant (B1.617.2). Probably, the vaccine immune pressure could select less prevalent strains leading to their emergence.

At present, it is not clear how widely this variant is currently present in Italy and worldwide. Nonetheless, our case report, clearly indicate the importance of genetic sequencing and analysis to promptly identify and characterize variants as soon as possible both in vaccinated individuals and in the general population.

Ethical Statement

This research was approved by the University of Campus Biomedico Ethics Review Committee (Approval number 8.1(21).21 OSS).

Funding

MG is supported by Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - FAPERJ.

Author contributions

Conception and design: SA, MG, ER, DZ, MC. Samples collection: MF, LDF, MF, RV, FA Clinical data collection: DD, GAM Laboratory evaluation: SA, ER, Performed the experiments: MF, LDF, MF, RV, FA, MG VF Analyzed the data: SA, MC, ER, MG, FP Writing: SA, MG, ER, MC

Declaration of Competing Interest

The authors declare no competing interests.

Acknowledgments

We thank personnel from Health Surveillance System from the University of Campus Biomedico that helped with samples, sources and epidemiological data collection. We also would like to thank all the authors who have kindly deposited and shared genome data on GISAID. A table with genome sequence acknowledgments can be found in Supplementary Table 1.

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DOI: https://doi.org/10.1016/j.jinf.2021.06.026

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© 2021 Published by Elsevier Ltd on behalf of The British Infection Association.

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