niman Posted August 25, 2020 Report Share Posted August 25, 2020 Hong Kong patient (33M) has been infected by two distinct lineages (deposited at GISAID). The first infection, HKU-200823-001 (clade V collected March 26, 2020) with a 58 aa truncation in orf8, was easily distinguished from HKU-200823-002, clade G (infected during travel to UK/Spain with collection date August 17, 2020) Link to comment Share on other sites More sharing options...
niman Posted August 25, 2020 Author Report Share Posted August 25, 2020 Virus detail Virus name: hCoV-19/Hong Kong/HKU-200823-001/2020 Accession ID: EPI_ISL_516798 Type: betacoronavirus Lineage (GISAID Clade): B.2 (V) Passage details/history: Original Sample information Collection date: 2020-03-26 Location: Asia / Hong Kong Host: Human Link to comment Share on other sites More sharing options...
niman Posted August 25, 2020 Author Report Share Posted August 25, 2020 Virus detail Virus name: hCoV-19/Hong Kong/HKU-200823-002/2020 Accession ID: EPI_ISL_516799 Type: betacoronavirus Lineage (GISAID Clade): B.1.79 (G) Passage details/history: Original Sample information Collection date: 2020-08-17 Location: Asia / Hong Kong Host: Human Additional location information: travel from Spain via the United Kingdom Link to comment Share on other sites More sharing options...
niman Posted August 25, 2020 Author Report Share Posted August 25, 2020 ACCEPTED MANUSCRIPT COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing Kelvin Kai-Wang To, Ivan Fan-Ngai Hung, Jonathan Daniel Ip, Allen Wing-Ho Chu, Wan-Mui Chan, Anthony Raymond Tam, Carol Ho-Yan Fong, Shuofeng Yuan, Hoi-Wah Tsoi, Anthony Chin-Ki Ng ... Show more Author Notes Clinical Infectious Diseases, ciaa1275, https://doi.org/10.1093/cid/ciaa1275 Published: 25 August 2020 Article history PDF Split View Cite Permissions Icon Permissions Share 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. https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa1275/5897019 Link to comment Share on other sites More sharing options...
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