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Clin Lab Med ; 42(2): 203-222, 2022 06.
Article in English | MEDLINE | ID: covidwho-2130437


Though rapid antigen tests have historically problematic performance characteristics for the diagnosis of respiratory viral infections such as influenza, they have attained an unprecedented level of use in the context of the COVID-19 pandemic. Ease of use and scalability of rapid antigen tests has facilitated a democratization and scale of testing beyond anything reasonably achievable by traditional laboratory-based testing. In this chapter, we discuss the performance characteristics of rapid antigen testing for SARS-CoV-2 detection and their application to non-traditional uses beyond clinical diagnostic testing.

COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Immunologic Tests , Pandemics
EBioMedicine ; 67: 103355, 2021 May.
Article in English | MEDLINE | ID: covidwho-1385438


BACKGROUND: There is increasing concern that persistent infection of SARS-CoV-2 within immunocompromised hosts could serve as a reservoir for mutation accumulation and subsequent emergence of novel strains with the potential to evade immune responses. METHODS: We describe three patients with acute lymphoblastic leukemia who were persistently positive for SARS-CoV-2 by real-time polymerase chain reaction. Viral viability from longitudinally-collected specimens was assessed. Whole-genome sequencing and serological studies were performed to measure viral evolution and evidence of immune escape. FINDINGS: We found compelling evidence of ongoing replication and infectivity for up to 162 days from initial positive by subgenomic RNA, single-stranded RNA, and viral culture analysis. Our results reveal a broad spectrum of infectivity, host immune responses, and accumulation of mutations, some with the potential for immune escape. INTERPRETATION: Our results highlight the potential need to reassess infection control precautions in the management and care of immunocompromised patients. Routine surveillance of mutations and evaluation of their potential impact on viral transmission and immune escape should be considered.

COVID-19/immunology , Immune Evasion , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/virology , SARS-CoV-2/genetics , COVID-19/virology , Child, Preschool , Evolution, Molecular , Female , Genome, Viral , High-Throughput Nucleotide Sequencing , Humans , Immunity, Humoral , Male , Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology , SARS-CoV-2/classification , SARS-CoV-2/immunology , Sequence Analysis, RNA , Whole Genome Sequencing , Young Adult
J Clin Microbiol ; 59(2)2021 01 21.
Article in English | MEDLINE | ID: covidwho-1044803


Testing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been burdened by the scarcity of testing materials and personal protective equipment for health care workers. The simple and painless process of saliva collection allows for widespread testing, but enthusiasm is hampered by variable performance compared to that of nasopharyngeal swab (NPS) samples. We prospectively collected paired NPS and saliva samples from a total of 300 unique adult and pediatric patients. SARS-CoV-2 RNA was detected in 32.2% (97/300) of the individuals using the TaqPath COVID-19 Combo kit (Thermo Fisher). Performance of saliva and NPS was compared against the total number of positives regardless of specimen type. The overall concordances for saliva and NPS were 91.0% (273/300) and 94.7% (284/300), respectively. The values for positive percent agreement (PPA) for saliva and NPS were 81.4% (79/97) and 89.7% (87/97), respectively. Saliva yielded detection of 10 positive cases that were negative by NPS. For symptomatic and asymptomatic pediatric patients not previously diagnosed with COVID-19, the performances of saliva and NPS were comparable (PPA, 82.4% versus 85.3%). The overall values for PPA for adults were 83.3% and 90.7% for saliva and NPS, respectively, with saliva yielding detection of 4 fewer cases than NPS. However, saliva performance for symptomatic adults was identical to NPS performance (PPA of 93.8%). With lower cost and self-collection capabilities, saliva can be an appropriate sample choice alternative to NPS for detection of SARS-CoV-2 in children and adults.

COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Saliva/virology , Specimen Handling/methods , Adolescent , Adult , COVID-19/pathology , COVID-19/virology , COVID-19 Nucleic Acid Testing , Child , Child, Preschool , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Prospective Studies , SARS-CoV-2/genetics , Sensitivity and Specificity , Viral Load , Young Adult