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      COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing

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          Abstract

          Background

          Waning immunity occurs in patients who have recovered from COVID-19. However, it remains unclear whether true re-infection occurs.

          Methods

          Whole genome sequencing was performed directly on respiratory specimens collected during two episodes of COVID-19 in a patient. Comparative genome analysis was conducted to differentiate re-infection from persistent viral shedding. Laboratory results, including RT-PCR Ct values and serum SARS-CoV-2 IgG, were analyzed.

          Results

          The second episode of asymptomatic infection occurred 142 days after the first symptomatic episode in an apparently immunocompetent patient. During the second episode, there was serological evidence of elevated C-reactive protein and SARS-CoV-2 IgG seroconversion. Viral genomes from first and second episodes belong to different clades/lineages. Compared to viral genomes in GISAID, the first virus genome has a stop codon at position 64 of orf8 leading to a truncation of 58 amino acids, and was phylogenetically closely related to strains collected in March/April 2020, while the second virus genome was closely related to strains collected in July/August 2020. Another 23 nucleotide and 13 amino acid differences located in 9 different proteins, including positions of B and T cell epitopes, were found between viruses from the first and second episodes.

          Conclusions

          Epidemiological, clinical, serological and genomic analyses confirmed that the patient had re-infection instead of persistent viral shedding from first infection. Our results suggest SARS-CoV-2 may continue to circulate among the human populations despite herd immunity due to natural infection or vaccination. Further studies of patients with re-infection will shed light on protective correlates important for vaccine design.

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          Author and article information

          Journal
          Clin Infect Dis
          Clin. Infect. Dis
          cid
          Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
          Oxford University Press (US )
          1058-4838
          1537-6591
          25 August 2020
          : ciaa1275
          Affiliations
          [1 ] State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology , Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
          [2 ] Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
          [3 ] Department of Medicine, Queen Mary Hospital , Hong Kong Special Administrative Region, China
          [4 ] Department of Accident and Emergency Medicine, Tin Shui Wai Hospital , Hong Kong Special Administrative Region, China
          [5 ] Department of Medicine, North Lantau Hospital , Hong Kong Special Administrative Region, China
          [6 ] Department of Medicine, United Christian Hospital , Hong Kong SAR, China
          [7 ] Department of Pathology, Princess Margaret Hospital , Hong Kong, China
          [8 ] Centre for Health Protection , Department of Health, Hong Kong
          [9 ] School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong , Hong Kong Special Administrative Region, China
          Author notes

          These authors contribute equally.

          Corresponding author: Kwok-Yung Yuen, Email: kyyuen@ 123456hku.hk , Phone number: (852)-22552413, Carol Yu Centre for Infection, State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
          Article
          ciaa1275
          10.1093/cid/ciaa1275
          7499500
          32840608
          7a9d0fa9-1b93-4df2-9200-452a03a4ae6b
          © The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

          This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

          This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.

          History
          : 23 August 2020
          Categories
          Major Article
          AcademicSubjects/MED00290
          Custom metadata
          PAP
          accepted-manuscript

          Infectious disease & Microbiology
          covid-19,sars-cov-2,re-infection,whole genome sequencing,d614g
          Infectious disease & Microbiology
          covid-19, sars-cov-2, re-infection, whole genome sequencing, d614g

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