tetano
Editor, Senior Moderator
Clin Infect Dis
. 2020 Aug 25;ciaa1275.
doi: 10.1093/cid/ciaa1275. Online ahead of print.
COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing
Kelvin Kai-Wang To[SUP] 1 2 [/SUP], Ivan Fan-Ngai ****[SUP] 3 [/SUP], Jonathan Daniel Ip[SUP] 1 [/SUP], Allen Wing-Ho Chu[SUP] 1 [/SUP], Wan-Mui Chan[SUP] 1 [/SUP], Anthony Raymond Tam[SUP] 3 [/SUP], Carol Ho-Yan Fong[SUP] 1 [/SUP], Shuofeng Yuan[SUP] 1 [/SUP], Hoi-Wah Tsoi[SUP] 1 [/SUP], Anthony Chin-Ki Ng[SUP] 1 [/SUP], Larry Lap-Yip Lee[SUP] 4 [/SUP], Polk Wan[SUP] 5 [/SUP], Eugene Tso[SUP] 6 [/SUP], Wing-Kin To[SUP] 7 [/SUP], Dominic Tsang[SUP] 8 [/SUP], Kwok-**** Chan[SUP] 1 [/SUP], Jian-Dong Huang[SUP] 9 [/SUP], Kin-Hang Kok[SUP] 1 [/SUP], Vincent Chi-Chung Cheng[SUP] 1 2 [/SUP], Kwok-Yung Yuen[SUP] 1 2 [/SUP]
Affiliations
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.
Keywords: COVID-19; D614G; SARS-CoV-2; re-infection; whole genome sequencing.
. 2020 Aug 25;ciaa1275.
doi: 10.1093/cid/ciaa1275. Online ahead of print.
COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing
Kelvin Kai-Wang To[SUP] 1 2 [/SUP], Ivan Fan-Ngai ****[SUP] 3 [/SUP], Jonathan Daniel Ip[SUP] 1 [/SUP], Allen Wing-Ho Chu[SUP] 1 [/SUP], Wan-Mui Chan[SUP] 1 [/SUP], Anthony Raymond Tam[SUP] 3 [/SUP], Carol Ho-Yan Fong[SUP] 1 [/SUP], Shuofeng Yuan[SUP] 1 [/SUP], Hoi-Wah Tsoi[SUP] 1 [/SUP], Anthony Chin-Ki Ng[SUP] 1 [/SUP], Larry Lap-Yip Lee[SUP] 4 [/SUP], Polk Wan[SUP] 5 [/SUP], Eugene Tso[SUP] 6 [/SUP], Wing-Kin To[SUP] 7 [/SUP], Dominic Tsang[SUP] 8 [/SUP], Kwok-**** Chan[SUP] 1 [/SUP], Jian-Dong Huang[SUP] 9 [/SUP], Kin-Hang Kok[SUP] 1 [/SUP], Vincent Chi-Chung Cheng[SUP] 1 2 [/SUP], Kwok-Yung Yuen[SUP] 1 2 [/SUP]
Affiliations
- PMID: 32840608
- DOI: 10.1093/cid/ciaa1275
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.
Keywords: COVID-19; D614G; SARS-CoV-2; re-infection; whole genome sequencing.