期刊
JOURNAL OF CLINICAL MICROBIOLOGY
卷 59, 期 1, 页码 -出版社
AMER SOC MICROBIOLOGY
DOI: 10.1128/JCM.02142-20
关键词
SARS-CoV-2; COVID-19; metagenomic sequencing; diagnostics; respiratory viruses
类别
资金
- Pediatric Research Alliance Center for Childhood Infections and Vaccines
- NIH [P51 OD011132, S10 OD026799, K08 AI13948]
- Center for AIDS Research [P30 AI050409]
- Children's Healthcare of Atlanta
Our study found that current broad-spectrum molecular testing algorithms can identify most respiratory viral infections among SARS-CoV-2 PUIs when available and implemented consistently.
Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUls. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUls (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUls (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A En = 3], human metapneumovirus [n = 2], and human coronavirus OC43 = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUls, lower cycle threshold (C-T) values correlated with greater SARS-CoV-2 read recovery by mNGS (R-2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.
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