SARS-CoV-2 Omicron Replacement of Delta as Predominant Variant, Puerto Rico

Santiago, Gilberto A.; Volkman, Hannah R.; Flores, Betzabel; Gonzalez, G.; Charriez, Keyla N.; Huertas, Limari Cora; Belleghem, Steven M. Van; Rivera‐Amill, Vanessa; Major, Chelsea G.; Colón, Candimar; Tosado, Rafael; Adams, Laura; Marzan, Melissa; Hernández, Lorena; Cardona, Iris; O’Neill, Eduardo; Paz–Bailey, Gabriela; Papa, Riccardo; Muñoz‐Jordán, Jorge L.

doi:10.3201/eid2904.221700

Cited by 6 publications

(4 citation statements)

References 7 publications

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“…By the fourth week of December 2021, Delta samples only accounted for 19.0 % during this week and then dropped to undetectable levels in the third week of January 2022. These results are consistent with those observed in other university settings, as well as overall patterns recorded both nationally and across the globe [20, 36–38, 67, 68], although studies investigating this particular replacement are limited in number.…”

Section: Discussionsupporting

confidence: 91%

“…Furthermore, given the importance of higher education in society and the need to maintain confidence in the safety of students, studying the dynamics of infectious disease in these institutions has been of special interest [19–27]. There have been multiple previous works which have investigated various aspects of SARS-CoV-2 dynamics in university settings since the pandemic began, ranging from genomic epidemiology to modelling studies and routine surveillance [20–24, 26, 28–35]; however, very few studies have explored the transition from Delta to Omicron variants [36–39], let alone in university populations [40].…”

Section: Introductionmentioning

confidence: 99%

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Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Ciubotariu,

Wilkes,

Kattoor

et al. 2024

Microbial Genomics

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Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the coronavirus disease 2019 (COVID-19) pandemic extends into its fourth year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in higher education settings and will inform public health policy during pandemics. In this study, we generated 793 whole-genome sequences collected over an entire academic year in a university population in Indiana, USA. We clearly captured the rapidity with which Delta variant was wholly replaced by Omicron variant across the West Lafayette campus over the length of two academic semesters in a community with high vaccination rates. This mirrored the emergence of Omicron throughout the state of Indiana and the USA. Further, phylogenetic analyses demonstrated that there was a more diverse set of potential geographic origins for Omicron viruses introduction into campus when compared to Delta. Lastly, statistics indicated that there was a more significant role for international and out-of-state migration in the establishment of Omicron variants at Purdue. This surveillance workflow, coupled with viral genomic sequencing and phylogeographic analyses, provided critical insights into SARS-CoV-2 transmission dynamics and variant arrival.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Ciubotariu,

Wilkes,

Kattoor

et al. 2024

Microbial Genomics

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“…Notably, the Omicron variant emerged as the dominant strain from November 2021, while the Delta variant was scarcely detected. These findings resonate with findings from Puerto Rico, where the BA1 variant emerged replacing Delta as the dominant variant in December 2021, which was followed by increased transmission and a dynamic landscape of Omicron sublineage infections in the population [ 80 ]. Further studies have reported increased transmission and infection attributable to the emergence of the Omicron variant after the replacement of Delta in England, Finland and the United States of America [ 81 , 82 , 83 ].…”

Section: Discussionsupporting

confidence: 85%

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

Shempela,

Chambaro,

Sikalima

et al. 2024

IJMS

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Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.

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“…The classification of primary circulating SARS-CoV-2 variant was based on the time period from their earliest detection in Puerto Rico until the detection of a new major variant: pre-Delta (cases through May 31, 2021), Delta (June 1 to November 30, 2021), and Omicron (after December 1, 2021). 27 For COPA participants with repeated tests, we evaluated BinaxNOW performance for their initial test as well as the repeated test 7-14 days after the initial test. We further stratified this analysis by participant symptom status for the initial and repeated tests.…”

Section: Introductionmentioning

confidence: 99%

Diagnostic Accuracy of the Abbot BinaxNOW COVID-19 Antigen Card Test, Puerto Rico

Madewell,

Major,

Graff

et al. 2023

Preprint

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BackgroundThe COVID-19 pandemic underscored the need for rapid and accurate diagnostic tools. In August 2020, the Abbot BinaxNOW COVID-19 Antigen Card test became available as a timely and affordable alternative for SARS-CoV-2 molecular testing, but its performance may vary due to factors including timing and symptomatology. This study evaluates BinaxNOW diagnostic performance in diverse epidemiological contexts.MethodsUsing RT-PCR as reference, we assessed performance of the BinaxNOW COVID-19 test for SARS-CoV-2 detection in anterior nasal swabs from participants of two studies in Puerto Rico from December 2020 to May 2023. Test performance was assessed by days post symptom onset, collection strategy, vaccination status, symptomatology, repeated testing, and RT-PCR cycle threshold (Ct) values.ResultsBinaxNOW demonstrated an overall sensitivity of 84.1% and specificity of 98.8%. Sensitivity peaked within 1–6 days after symptom onset (93.2%) and was higher for symptomatic (86.3%) than asymptomatic (67.3%) participants. Sensitivity declined over the course of infection, dropping from 96.3% in the initial test to 48.4% in testing performed 7–14 days later. BinaxNOW showed 99.5% sensitivity in participants with low Ct values (≤25) but lower sensitivity (18.2%) for participants with higher Cts (36–40).ConclusionsBinaxNOW demonstrated high sensitivity and specificity, particularly in early-stage infections and symptomatic participants. In situations where test sensitivity is crucial for clinical decision- making, nucleic acid amplification tests are preferred. These findings highlight the importance of considering clinical and epidemiological context when interpreting test results and emphasize the need for ongoing research to adapt testing strategies to emerging SARS-CoV-2 variants.

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SARS-CoV-2 Omicron Replacement of Delta as Predominant Variant, Puerto Rico

Cited by 6 publications

References 7 publications

Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Investigating the rise of Omicron variant through genomic surveillance of SARS-CoV-2 infections in a highly vaccinated university population

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study

Diagnostic Accuracy of the Abbot BinaxNOW COVID-19 Antigen Card Test, Puerto Rico

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