Objective:To optimize and evaluate the pretreatment method for high-throughput sequencing of fecal and tissue samples to improve the sensitivity of high-throughput sequencing in the study of virome.Methods:For fecal samples, five virus-positive samples that have been detoxified from feces were selected, mixed as the simulated samples, and filters made of different materials were used, different processing times were set for nucleases, and different kits were used to extract nucleic acid. For tissue samples, two virus-positive samples that have been detected in animal tissues, filter and nuclease treatment were used, and different extraction method were used to extract nucleic acid. TaqMan real-time PCR was used to quantitatively evaluate the impact of each treatment on the virus and the advantages and disadvantages were compared. We used the SYBR Green real-time PCR quantitative method to evaluate the removal effect of the above method on bacteria 16S rRNA and host 12S rRNA genome.Results:For fecal samples, the 0.22 μm PES filter showed a better filtering effect, and the PVDF material filter reduces the sample volume; 2 h nuclease digestion was better than 1 h digestion to remove bacteria, and the virus loss was less; the use of RPMK kits can effectively reduce bacteria, but the effect of extracting some viruses was poor, and the MVSK kit has a better effect of extracting viral nucleic acid. For tissue samples, 0.22 μm PES filter filtration, nuclease digestion for 1 h and VNAEK II kit extraction of nucleic acid were the best, Trizol LS combined with the RPMK method was better for gDNA removal, but the virus loss was larger. The virus loss of the whole process of the pretreatment method of feces and tissue samples was (1.7-3.0) Ct and (1.6-2.5) Ct, respectively.Conclusions:The optimal method for fecal samples was to filter with a PES filter, then digest with nuclease for 2 hours, and then extract nucleic acids using the MVSK kit; the optimal method for tissue samples was to filter with a PES filter, then perform 1 h nuclease digestion, and then use VNAEK II kit to extract nucleic acids.

Objective:To understand the prevalence of human parechovirus (HPeV) in neonates of Hunan Provincial People’s Hospital, and analyze genetic evolutionary characteristics.Methods:From June to September 2021, fecal samples of inpatient neonates were collected in Hunan Provincial People′s Hospital. TaqMan real-time qPCR and RT-PCR were used for HPeV screening and genotyping. High-throughput sequencing and PCR were used to obtain whole genomes. Phylogenetic analysis was performed after sequencing.Results:A total of 123 fecal samples of neonates were collected, of which 22 were HPeV positive, with 17.89% positive rate. All the strains belonged to the HPeV-1 genotype. One full-length genomic sequence of 7 269 bp were obtained, and provisionally named Hunan/HPeV/2021, which has the highest nucleotide identity with known HPeV-1 genotype, with 86.6%-91.9% nucleotide identity. The nucleotide and amino acid identity of open reading frame (ORF) with known similar sequences were 90.3%-92.6% and 97.3%-98.3%, respectively. The phylogenetic analysis showed that Hunan/HPeV/2021 belongs to the HPeV-1 genotype, which is clustered into the same clade as the popular HPeV-1 strains in China.Conclusions:HPeV has a high prevalence in inpatient neonates of Hunan Provincial People’s Hospital and belong to the HPeV-1 genotype.