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Data from: Neurologic manifestations in an infant with COVID-19

Cite this dataset

Mishra, Nischay et al. (2020). Data from: Neurologic manifestations in an infant with COVID-19 [Dataset]. Dryad.


Currently, there are over 1.9 million confirmed cases of Coronavirus disease 2019 (COVID-19) globally with over 590,000 cases in the United States.1 The number of COVID-19 positive children in the United States is unknown. A report summarizing 72,314 COVID-19 cases from the Chinese Center for Disease Control and Prevention noted 416 COVID-19 positive children under 10.2 An observational study at Wuhan Children's Hospital noted 31 COVID-19 positive children under 1 year with the youngest confirmed case in a 1 day old.3 Cases were largely characterized by upper respiratory tract infection or pneumonia, fever, cough and pharyngeal erythema.3 Concomitant neurologic problems have been reported amongst COVID-19 positive adult patients.


  • Sequencing on the Illumina NextSeq 550 platform (Illumina, San Diego, CA, USA) resulted in 159,204,153 (150 bp) single end reads. The reads were adapter trimmed and filtered based on the average quality scores, presence of indeterminate nucleotides and homopolymeric regions. Host background levels were determined by mapping filtered reads against human reference database using Bowtie2 mapper (v 2.2.9 (1)). The host-subtracted reads were de-novo assembled using MIRA (4.0 (2)) assembler. Contigs and unique singletons aligned against GenBank nucleotide database using Megablast tool from NCBI. Sequences with poor or no homology from Megablast were screened with BLASTX against the viral GenBank protein database. The filtered reads were mapped to the coronavirus and rhinovirus strains identified from blast.

1) Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

2) Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol 99:45–56

Usage notes

We are providing Zipped FASTq file for each of the following sample after human host-substraction and quality check.


Original ID CII ID Species Sample Type Barcode
IPS-553 COVID-AS Human Anal swab G5
IPS-554 COVID-BS Human nasopharyngeal swab G7
IPS-556 COVID-SERUM Human Serum G11
IPS-557 COVID-PLASMA Human Plasma H1


Bill & Melinda Gates Foundation, Award: INV-006216