Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

Abstract

A few molecularly proven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases of symptomatic reinfection are currently known worldwide, with a resolved first infection followed by a second infection after a 48 to 142-day intervening period. We report a multiple-component study of a clinically severe and prolonged viral shedding coronavirus disease 2019 (COVID-19) case in a 17-year-old Portuguese female. She had two hospitalizations, a total of 19 RT-PCR tests, mostly positive, and criteria for releasing from home isolation at the end of 97 days. The viral genome was sequenced in seven serial samples and in the diagnostic sample from her infected mother. A human genome-wide array (>900 K) was screened on the seven samples, and in vitro culture was conducted on isolates from three late samples. The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient's mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency. The 900 K profiles confirmed the identity of the patient in the serial samples, and they allowed us to infer that she had polygenic risk scores for hospitalization and severe respiratory disease within the normal distributions for a Portuguese population cohort. The early-on dynamic co-infection may have contributed to the severity of COVID-19 in this otherwise healthy young patient, and to her prolonged SARS-CoV-2 shedding profile.

Keywords: COVID-19 and SARS-CoV-2; co-infection; polygenic risk score; viral shedding; viral whole-genome sequencing.

Figure 1

Timeline of the reported coronavirus disease 2019 (COVID-19) case and main results of the multi-component study conducted on the serial samples. The timeline bar indicates the periods of: symptom onset (yellow); inpatient stays (pink; the black arrow indicates the moment when the patient was transferred to the referral center for Emerging Infectious Diseases at Centro Hospitalar Universitário de São João—CHUSJ); and, home quarantine (blue). It also includes the dates of all the 19 RT-PCR tests performed (green for negative result and red for positive result). The molecular tests were focused either on the virus (RT-PCR crossing point, proportion of clade/lineage affiliation inferred from viral whole-genome sequencing, and in vitro culture) or the host (array containing > 900 K variants and IgG antibody immunoassay reported as sample/calibrator relative light unit index).

Figure 2

Detailed sequence diversity of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolates from the various samples. (A)—Representation of the SARS-CoV-2 genome (genes are indicated) and the variants (only those with 50% frequency in at least one of the eight samples) sequenced in the isolates from the patient serial samples (P1.1 to P1.7) and her mother’s diagnostic sample. Date of sample collections are indicated below the patient samples ID, and the color code reflects the main 20A (in green) or 20B (in pink) SARS-CoV-2 lineage. The gradient bar indicates the frequency of the variants. For easier visualization, the shared variants between 20A and 20B lineages are indicated in doted bars. The boxes highlight either the specific 20A variants (in green) or the 20B-defining variants (in pink; the asterisk calls the attention to the three sequential variants, G28881A-G28882A-G28883C). The red cross indicates missing positions, matching known regions of the SARS-CoV-2 genome that are difficult to sequence. (B)—Phylogenetic tree of the main SARS-CoV-2 clades known so far (19A, 19B, 20A, 20B, and 20C) and the sequences reported here (following the color scheme of A).

Figure 3

Scatter plot of the polygenic risk score (PRS) values and respective density plots for “very severe respiratory confirmed covid” and “hospitalized covid” phenotypes for the Portuguese population cohort (n = 198), and the scatter point value for the patient (in red). The PRS values were calculated based on odd ratios reported online by the COVID-19 host genetics initiative (https://www.covid19hg.org/) [21].