Long amplicon HiFi sequencing for mitochondrial DNA genomes

Long-read sequencing technology is a powerful approach with application in various genetic and genomic research. Herein, we developed the pipeline for long amplicon high-fidelity (HiFi) sequencing and then applied it for sequencing mitochondrial DNA (mtDNA) genomes from pools of 79 Tibetan Mastiffs. We amplified the mtDNA genome with long-range PCR using two pairs of primers. Two rounds of circular consensus sequencing (CCS) were conducted and their accuracy was evaluated. The results indicate that the second round of CCS can improve the accuracy of HiFi reads. In addition, the analysis of 79 high-quality mtDNA genomes shows the Tibetan Mastiffs from outside of the Tibetan Plateau experienced hybridization with other dogs. The high quality reads generator (HQGR) software is provided to facilitate data analyses, which is publicly accessible on GitHub (https://github.com/Caizf-script/HQGR). Our long amplicon HiFi sequencing pipeline can also be applied in various target enrichment strategies for small genomes and candidate genes.

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

[Prognosis and related risk factors of acute respiratory distress syndrome in elder patients]

Objective: To study the risk factors associated with the hospital survival rate of elder patients with acute respiratory distress syndrome (ARDS) in Medical/Respiratory Intensive Care Units (MICUs/RICUs) by evaluating the prognosis, and therefore to provide insight into patient treatment strategy. Methods: Twenty MICUs/RICUs of 19 general hospitals in mainland China participated in the multicenter prospective cohort study carried out from Mar 1^st, 2016 to Feb 28^th, 2018. Patients who met the criteria of Berlin ARDS and older than 65 years were recruited. Baseline data, risk factors of ARDS, ventilator setup and prognosis data were collected from all patients. Univariant and multivariant regression analysis were conducted to analyze the factors associated with the prognosis. Results: 170 elder ARDS patients (age≥65 years) met the Berlin ARDS criteria, among whom 8.8% (15/170), 42.9% (73/170) and 48.2% (82/170) patients had mild, moderate and severe ARDS, respectively. The most common predisposing factor for elder ARDS was pneumonia, which was present in 134 patients (78.8%). 37.6% (64/170) patients were treated with noninvasive mechanical ventilation (NIV), but 43.8% (28/64) cases experienced treatment failure. 76.5% (130/170) patients were treated with invasive mechanical ventilation. All patients 80 years or older were given invasive mechanical ventilation. 51.8% (88/170) cases had complications of non-pulmonary organ failure. 61.8% (105/170) patients deceased during hospital stay. Multivariant logistic analysis showed that the independent risk factors for hospital survival rate in elder patients with ARDS were SOFA score (P=0.030, RR=0.725, 95% CI 0.543-0.969), oxygen index after 24 hours of ARDS diagnosis (P=0.030, RR=0.196, 95% CI 0.045-0.853), accumulated fluid balance within 7 days after diagnosis of ARDS (P=0.026, RR=1.000, 95% CI 1.000-1.000) and shock (P=0.034, RR=0.140, 95% CI 0.023-0.863). Conclusion: Among 20 ICUs, the high mortality rate of elder patients with ARDS was correlated with higher 24 hour SOFA score, lower 24 hour oxygen index after ARDS diagnosis, more positive fluid balance within 7 days and concomitant shock. The conservative fluid strategy within 7 days of ARDS diagnosis may benefit the elder ARDS patients.

[A simplified method for detection of genomic subtyps of HBV S-gene]

When the 513 bp amplified fragments of HBV S-gene, known subtypes, were digested with Msp I and BamH I, the following phenomena appeared: adr subtypic 513 bp was fragmentized to 320 bp and 193 bp by Msp I; ayw subtype was digested and fragmentized to 295 bp and 218 bp by BamH I; ayw could also be fragmentized to become 326 bp and 187 bp digested by Msp I. Howerev, adw subtype was not digested by Msp I and BamH I nor adr by BamH I. The experimental patterns in agarose gel electrophoresis were tallied with the expected patterns. Each HBV subtypes gave unique size of digestive fragments which was easy to observe and distinguish on agarose gel. This study provided a new classification scheme for HBV-DNA and could be used for epidemiological investigation of HBV infection.