Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel

Smith, Darci R.; Singh, Christopher N.; Green, Jennetta; Lueder, Matthew R.; Arnold, Catherine; Voegtly, Logan J.; Long, Kyle A.; Rice, Gregory K.; Luquette, Andrea E.; Miner, Haven L.; Glang, Lindsay; Bennett, Andrew J.; Miller, Ruth; Malagón, Francisco; Cer, Regina Z.; Bishop‐Lilly, Kimberly A.

doi:10.3389/fmed.2021.836658

Cited by 5 publications

(3 citation statements)

References 32 publications

(29 reference statements)

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“…Studies conducted in adults suggested that infections with the Delta variant were associated with more severe disease and higher viral loads than infections with previous variants (25,(39)(40)(41)(42)(43)(44)(45). On the other hand, subsequent reports using national US trends or EHR data not linked to specific variants showed that disease severity in children during the Delta wave was comparable to that described with the circulation of previous variants (19,22).…”

Section: Discussionmentioning

confidence: 94%

Differences in SARS-CoV-2 Clinical Manifestations and Disease Severity in Children and Adolescents by Infecting Variant

Quintero¹,

Eisner²,

Sayegh³

et al. 2022

Emerg. Infect. Dis.

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rapidly spread worldwide, causing a global pandemic with major social and economic disruption. Although the effects of COVID-19 have been greater in adults, children also are infected with SARS-CoV-2, and COVID-19 can lead to severe outcomes in pediatric patients (1-3). Nevertheless, the spectrum of clinical manifestations in children is broad and ranges from asymptomatic to mild upper respiratory infection to pneumonia or the more severe multisystem inflammatory syndrome in children (MIS-C), which typically occurs 2 to 6 weeks after acute SARS-CoV-2 infection (4-7).Since the COVID-19 pandemic began, different SARS-CoV-2 variants have circulated worldwide. In the United States, the first variant that replaced the original strain was the Alpha variant (B 1.1.7) that circulated during April-June 2021. The Delta variant (B1.617.2) followed soon after and became predominant during July-mid-December 2021. Since then, different sublineages of Omicron quickly replaced other variants as the predominant variant as of September 2022. These newer variants have demonstrated higher transmissibility and have disproportionally affected unvaccinated persons and other vulnerable populations including children; rates of hospitalization have increased 5-fold to 10-fold in children, depending on the variant and age group (8-13). Epidemiologic studies that rely on SARS-CoV-2 circulation patterns have provided robust information; however, the role of specific SARS-CoV-2 variants on clinical disease severity in children and adolescents with COVID-19 is not fully known.The objective of this study was to assess whether distinct SARS-CoV-2 variants were associated with differences in clinical and laboratory data and cycle threshold (Ct) values (as a surrogate of viral load) in children and adolescents with COVID-19. The Nationwide Children's Hospital (NCH; Columbus, OH, USA) Institutional Review Board approved the study (#STUDY00002002).

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Section: Discussionmentioning

confidence: 94%

Differences in SARS-CoV-2 Clinical Manifestations and Disease Severity in Children and Adolescents by Infecting Variant

Quintero¹,

Eisner²,

Sayegh³

et al. 2022

Emerg. Infect. Dis.

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“…The visualization of CPE is particularly sensitive in staining revealed techniques ( 20 , 36 ). Further, both techniques are time-consuming and required to perform in a BSL-3 laboratory, limiting their use ( 37 ).…”

Section: Discussionmentioning

confidence: 99%

Comparison among plaque assay, tissue culture infectious dose (TCID ) and real-time RT-PCR for SARS-CoV-2 variants quantification

Zapata-Cardona¹,

Flórez-Álvarez²,

Gómez-Gallego³

et al. 2022

IJM

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Background and Objectives: SARS-CoV-2 variants of concern (VOC) and interest (VOI) pose a significant threat to pub- lic health because the rapid change in the SARS-CoV-2 genome can alter viral phenotypes such as virulence, transmissi- bility and the ability to evade the host response. Hence, SARS-CoV-2 quantification techniques are essential for timely diagnosis and follow-up. Besides, they are vital to understanding viral pathogenesis, antiviral evaluation, and vaccine de- velopment. Materials and Methods: Five isolates of SARS-CoV-2: D614G strain (B.1), three VOC (Alpha, Gamma and Delta), and one VOI (Mu) were used to compare three techniques for viral quantification, plaque assay, median tissue culture infectiousdose (TCID50) and real-time RT-PCR. Results: Plaque assay showed viral titers between 0.15 ± 0.01×107 and 1.95 ± 0.09×107 PFU/mL while viral titer by TCID50 assay was between 0.71 ± 0.01×106 to 4.94 ± 0.80×106 TCID50 /mL for the five SARS-CoV-2 isolates. The PFU/mL titer obtained by plaque and the calculated from TCID50 assays differed by 0.61 log10, 0.59 log10, 0.59 log10 and 0.96 log10 for Alfa, Gamma, Delta, and Mu variants (p≤0.0007), respectively. No differences were observed for the D614G strain. Real-time PCR assay exhibited titers ranging from 0.39 ± 0.001×108 to 3.38 ± 0.04×108 RNA copies/µL for all variants. The relation between PFU/mL and RNA copies/mL was 1:29800 for D614G strain, 1:11700 for Alpha, 1:8930 for Gamma, 1:12500 for Delta, and 1:2950 for Mu. Conclusion: TCID50 assay was comparable to plaque assay for D614G but not for others SARS-CoV-2 variants. Our data demonstrated a correlation among PFU/mL and E gene RNA copies/µL, units of measure commonly used to quantify the viral load in diagnostic and research fields. The results suggest that the proportion of infectious virions in vitro changes de- pending on the SARS-CoV-2 variant, being Mu, the variant reaching a higher viral titer with fewer viral copies.

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“…From 27 studies from the previous review (Adamson et al 2021, Abu-Raddad et al 2022, Bailly et al 2022, Blanquart et al 2021, Boschi et al 2021, Brunner-Ziegler et al 2022, Costa et al 2022, Emary et al 2021, Eyre et al 2022, Griffin et al 2021, Hsu et al 2021, Ioannou et al 2021, Jacobson et al 2022, Kislaya et al 2022b, Kolobukhina et al 2021, Lumley et al 2021, Luo et al 2021a, McEllistrem et al 2021, Mostafa et al 2021, Muhsen et al 2021, Pajon et al 2021, Pouwels et al 2021, Regev-Yochay et al 2021, Servellita et al 2022, Smith et al 2022, Tande et al 2021, Thompson et al 2021, there was evidence suggesting fully vaccinated cases had higher Ct values than unvaccinated cases (suggesting a lower viral load).…”

Section: Evidence For Pre-delta Variantsmentioning

confidence: 99%

The effect of vaccination on transmission of SARS-CoV-2 (COVID-19): a rapid review

Wiliams¹,

Barrate²,

Winfield³

et al. 2022

Preprint

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This is an update (literature search up to 15 March 2022) of a rapid review examining whether vaccination against SARS-CoV-2 (COVID-19) affects transmission of SARS-CoV-2. Streamlined systematic methodologies were used to accelerate the review process. The update identified 17 additional studies: 6 studies reported on transmission and 11 studies reported viral load. There was high heterogeneity across studies, which varied in design, participant characteristics and SARS-CoV-2 variants reported. Evidence from this update supports previous findings that that transmission of Omicron and Delta variants is lowest in booster-vaccinated people, followed by fully vaccinated people, with the highest rate of transmission in unvaccinated people. Additionally, some studies compared transmission between different variants or sub-variants; risk of transmission appears to be higher with Omicron than Delta, regardless of vaccination status.

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Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel

Cited by 5 publications

References 32 publications

Differences in SARS-CoV-2 Clinical Manifestations and Disease Severity in Children and Adolescents by Infecting Variant

Differences in SARS-CoV-2 Clinical Manifestations and Disease Severity in Children and Adolescents by Infecting Variant

Comparison among plaque assay, tissue culture infectious dose (TCID ) and real-time RT-PCR for SARS-CoV-2 variants quantification

The effect of vaccination on transmission of SARS-CoV-2 (COVID-19): a rapid review

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