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.

Study on SARS-CoV-2 strains in Iran reveals potential contribution of co-infection with and recombination between different strains to the emergence of new strains

“…Till now, there have only been a few reports of co-infection with two SARS-CoV-2 strains ( Baang et al, 2021 ; Choi et al, 2020 ; da Silva Francisco Jr et al, 2021 ; Pedro et al, 2021 ). The co-infections in these cases were proposed to demonstrate within host evolution of the virus or independent infections.…”

Distribution of SARS-CoV-2 Lineages in the Czech Republic, Analysis of Data from the First Year of the Pandemic

“…This finding raises the question about the limitations of de novo assembly approach regarding the detection of eventual superinfection events. Recently, there emerged several reports of superinfection with two strains of SARS-CoV-2 [ 24 , 25 , 26 ]. Our sequencing data showed that ~10% of the samples examined (23 of 229 samples) had two SARS-CoV-2 variants present, with a similar frequency (12.8%) observed in an independent Iranian cohort [ 25 ].…”

“…Another limitation is that all samples were anonymous and no follow-up samples or clinical data on the course of COVID-19 were thus available to us. Furthermore, as shown elsewhere [ 24 ], repeated analysis of isolates from several collections (independent, separated isolations from several timepoints) should be investigated in future studies. Authors of the present study are aware of this; however, consider the presented approach being capable to discriminate eventual superinfection to be beneficial.…”

SARS-CoV-2 Persistent Viral Shedding in the Context of Hydroxychloroquine-Azithromycin Treatment

“…Previous case reports and a small series of patients experienced prolonged shedding with SARS-CoV-2 ( Table 4 ) [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ], mostly involving immunocompromised individuals, including patients diagnosed with hematological malignancies in most cases.…”