Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants

Abstract

Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between levels of viral RNA and infectious virus for individual variants is unknown. We measured infectious viral titer (using a microfocus-forming assay) and total and subgenomic viral RNA levels (using RT-PCR) in a set of 162 clinical samples containing SARS-CoV-2 Alpha, Delta, and Epsilon variants that were collected in identical swab kits from outpatient test sites and processed soon after collection. We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite this, the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (5.9- and 3.0-fold increase; P < 0.0001, P = 0.014, respectively) or subgenomic E RNA (14.3- and 6.9-fold increase; P < 0.0001, P = 0.004, respectively). In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity for Delta may further explain increased spread, suggesting a need for increased measures to prevent viral transmission.

Pulmonary lesions following inoculation with the SARS-CoV-2 Omicron BA.1 (B.1.1.529) variant in Syrian golden hamsters

“…Previous studies in clinical settings have shown that viral genome of certain SARS-CoV-2 variants is shed at higher levels than for other variants. This increased shedding in part has been suggested to contribute to in the increased spread of these variants [19]. However, .…”

“…Following the identification of SARS-CoV-2 as the cause of coronavirus disease-2019 (COVID- 19), the virus has spread rapidly throughout the world. Since its emergence, viral genomic sequence analysis has allowed tracking of the emergence of SARS-CoV-2 variants.…”

“…Previous studies in clinical settings have shown that viral genome of certain SARS-CoV-2 variants is shed at higher levels than for other variants. This increased shedding in part has been suggested to contribute to in the increased spread of these variants [19]. However, recent analysis of human specimens are indicative for no major differences in shedding between the SARS-CoV-2 variants Delta and Omicron BA.1 [20].…”

Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections

“…These guidelines were initially framed based on contact tracing studies and laboratory studies that looked at culturable active viruses from 2020, which showed less than 5% risk for transmission at the late stage (23)(24)(25). Even though the Delta variant emerged to be more virulent and transmissible during the second wave in India and subsequently in other countries, the viral shedding dynamics of the infectious virus have just started emerging (9,(26)(27)(28)(29). One study that looked at infectious viruses upto15 days showed that infectious viral shedding is longer for the Delta than non-Delta infections (29).…”

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

“…Delta had substantially higher infectivity than Alpha based on the number of infectious units per quantity of viral E-gene RNA (5.9-fold increase; p < 0.0001) or subgenomic E RNA (14.3-fold increase; p < 0.0001) in clinical specimens identified as SARS-CoV-2-positive at the University of Washington Virology Laboratory between March and August 2021 in the United States [262].…”