Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.

Analysis the antibiotic resistance of 253 ureaplasma urealyticum to 8 antibacterial agents in vitro / 中国基层医药

Objective To analyze the antibiotic resistance of ureaplasma urealyticum(UU) in vitro in Yangjiang,and instruct the clinical treatment for the ureaplasma urealyticum infection.Methods 538 secretion samples of urethra and cervix were collected and cultured ureaplasma urealyticum in vitro,the drug sensitive test of UU from 253 patients was conducted and detected their drug resistance.Results The 253 positives cases were found in 538 samples.The drug sensitive test results were:the highest sensitivity rates were clarithromycin(731%) and roxithromycin(679%).The resistance rates of rest drugs were azithromycin(771%),josamycin(708%),minocycline(664%),ciprofloxacin(538%),sparfloxacin(435%),doxycycline(423%),the total resistance rate was 489%.Conclusion To treat the ureaplasma urealyticum infection,the first choices are clarithromycin and roxithromycin.