HIV in serum of Nepalese patient with Fever of Unknown Origin - SRA

SRX25789386: HIV in serum of Nepalese patient with Fever of Unknown Origin
1 ILLUMINA (NextSeq 500) run: 5M spots, 1.5G bases, 630.3Mb downloads

Design: The serum sample collected from the FUO case was subjected for total nucleic acid extraction using the Invitrogen Pure Link TM Viral RNA/DNA mini kit [Thermo Fisher Scientific] following the instruction manual and eluted in 50 L RNAse-free water. The nucleic acid was randomly amplified using a random-primer protocol. The reverse transcription with randomized primer was carried in round A and PCR amplification was carried in round B. Sample specific Round A PCR used 31 bases random primer sequence (TACCGTAGAGCTGCTANNNNNNNNNNNNNNN) and round B PCR used a 16 specific leading primer sequence of round A(TACCGTAGAGCTGCTA). Promega M-MLVReverse Transcriptase (Fisher scientific) was used for reverse transcription. A library was constructed using the Illumina DNA Prep kit.

Submitted by: Washington University in St. Louis

Study: HIV Nepal Fever of Unknown Origin Raw sequence reads

PRJNA1148996 • SRP527804 • All experiments • All runs

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A patient with fever of unknown origin presented to the referral infectious disease hospital of Nepal. Metagenomic sequencing of patient serum recovered a near complete HIV-1 genome. This virus was distinct from the previous 444 HIV-1 genomes from Nepal in Genbank and showed shared 92.51% nucleotide identity with HIV 1 subtype C isolate of India (AF067158.1).

Sample: HIV in serum of Nepalese patient with Fever of Unknown Origin

SAMN43226821 • SRS22420834 • All experiments • All runs

Organism: Human immunodeficiency virus 1

Library:

Name: N936_I12181_39217_Nepal_Manandhar_FUO_N0000841_F04_UDP0126_AGGAGGTATC_TGCCAACTGG_S53

Instrument: NextSeq 500

Strategy: WGS

Source: METAGENOMIC

Selection: RANDOM PCR

Layout: PAIRED

Runs: 1 run, 5M spots, 1.5G bases, 630.3Mb

Run	# of Spots	# of Bases	Size	Published
SRR30329167	5,019,323	1.5G	630.3Mb	2024-08-23

ID:: 34822295

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