背景:SARS-CoV-2大流行迅速上升,全球传播,以及2022年omicron变体的多样化。鉴于这种变体在全球范围内的压倒性优势及其多样化的血统,迫切需要确保诊断测定能够检测广泛循环的omicron亚谱系。
方法:从威斯康星州(n=94)收集的SARS-CoV-2PCR确认感染的剩余临床VTM样本(n=733),纽约(n=267),和南卡罗来纳州(n=372)在整个2022年进行了测序,机密,并使用m2000实时SARS-CoV-2,AlinitymSARS-CoV-2,IDNOWCOVID-19v2.0,BinaxNOWCOVID-19Ag卡进行了测试,和PanbioCOVID-19快速测试装置测定。
结果:获得了n=641/733(87.4%)样品的序列和谱系分类,其中包括δ(n=6)和2022年所有主要SARS-CoV-2omicron变体的代表(BA.1,BA.2,BA.3,BA.4,BA.5,BE,BF,BQ.1和XBB)。通过分子测定RealTime(n=624)测试了各种omicron谱系的面板,平均m(n=80),和IDNOWv2.0(n=88),结果显示所有样品的100%检测。BinaxNOW和Panbio的敏感性为494/533(92.7%)和416/469(88.7%),分别对于>4log10拷贝/测试的标本,与冷冻标本的预期性能一致。此外,BinaxNOW在1-4天的临床样本中证明了SARS-CoV-2的检测,在>4log10拷贝/测试的BA.1感染患者中,症状发作后长达18天。
结论:该数据突出了2022年SARS-CoV-2omicron变体的增加和多样化,并证明了5种测试检测方法中的每一种都可以检测到全球循环的omicron变体的广度。
The SARS-CoV-2 pandemic saw the rapid rise, global spread, and diversification of the omicron variant in 2022. Given the overwhelming dominance of this variant globally and its diverse lineages, there is an urgent need to ensure that diagnostic assays are capable of detecting widely circulating omicron sub-lineages.
Remnant clinical VTM samples from SARS-CoV-2 PCR confirmed infections (n = 733) collected in Wisconsin (n = 94), New York (n = 267), and South Carolina (n = 372) throughout 2022 were sequenced, classified, and tested with m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, ID NOW COVID-19 v2.0,
BinaxNOW COVID-19 Ag Card, and Panbio COVID-19 Rapid Test Device assays.
Sequences and lineage classifications were obtained for n = 641/733 (87.4%) samples and included delta (n = 6) and representatives from all major SARS-CoV-2 omicron variants circulating in 2022 (BA.1, BA.2, BA.3, BA.4, BA.5, BE, BF, BQ.1, and XBB). Panels of diverse omicron lineages were tested by molecular assays RealTime (n = 624), Alinity m (n = 80), and ID NOW v2.0 (n = 88) with results showing 100% detection for all samples.
BinaxNOW and Panbio had sensitivities of 494/533 (92.7%) and 416/469 (88.7%), respectively for specimens with >4 log10 copies/test, consistent with expected performance for frozen specimens. Furthermore,
BinaxNOW demonstrated SARS-CoV-2 detection in clinical samples 1-4 days, and up to 18 days post-symptom onset in BA.1 infected patients with >4 log10 copies/test.
This data highlights the rise and diversification of SARS-CoV-2 omicron variants over the course of 2022 and demonstrate that each of the 5 tested assays can detect the breadth of omicron variants circulating globally.