First Identification of Reinfection by a Genetically Different Variant of SARS-CoV-2 in a Homeless Person from the Metropolitan Area of Santiago, Chile

Abstract

The identification and tracking of SARS-CoV-2 infected patients in the general population are essential components of the global strategy to limit the COVID-19 viral spread, specifically for maintaining traceability and suppressing the resurgence of local outbreaks. Public health programs that include continuous RT-qPCR testing for COVID-19 in the general population, viral sequencing, and genomic surveillance for highly contagious forms of the virus have allowed for the identification of SARS-CoV-2 infections and reinfections. This work identified SARS-CoV-2 reinfection in a homeless person, which occurred 58 days after the first COVID-19 diagnosis. Genomic sequencing identified a different Nextstrain classification clade (20A and 20B) and PANGO lineage, with a divergence of 4 single nucleotide variants (SNVs) in S and ORF1ab genes, suggesting reinfection by different viral variants. This study is the first from the great metropolitan area of Santiago, Chile, one of the top ten countries in the world to live during the COVID-19 pandemic. We support the importance of performing intensive genomic surveillance programs in the whole population and high-risk groups, such as homeless people, nearly 20 thousand people in Chile, and have limited access to health care services and poor viral traceability.

Figure 1

Genomic analysis of reinfected homeless patients. (a) Timeline shows the first (June 6th) and second (Aug 3rd) positive diagnosis by RT-qPCR for SARS-CoV-2. Nextstrain viral classification clade is shown for both samples. (b) RT-qPCR data using ORF1ab and RNase P (internal cellular control) probes for the homeless patient from nasopharyngeal swab sampling was obtained on June 6^th (0606-201) and 58 days later, on August 3^rd (0308-063). Cq-values are shown for ORFab (blue point) on the left and RNase P (pink line) on the right. (c) Clade structure of SARS-CoV-2 defined by Nexclade version 1.9.0 in Nextstrain classification: sample 0606-201 in clade 20B and 0308-063 in clade 20A. PANGO lineage classification by pangolin tool (0606-201; B.1 and 0308-063; B.1.1). (d) Genetic diversity plot of both pieces referred to the ancestral SARS-CoV genome. The highest diversity is present at ORF1b, ORF7a, S, and N.