Comparative Evaluation of 19 Reverse Transcription Loop-Mediated Isothermal Amplification Assays for Detection of SARS-CoV-2

Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a global pandemics. To facilitate the detection of SARS-CoV-2 infection, various RT-LAMP assays using 19 sets of primers had been developed, but never been compared. We performed comparative evaluation of the 19 sets of primers using 4 RNA standards and 29 clinical samples from COVID-19 patients. Six of 15 sets of primers were firstly identified to have faster amplification when tested with four RNA standards, and were further subjected to parallel comparison with the remaining four primer sets using 29 clinical samples. Among these 10 primer sets, Set-4 had the highest positive detection rate of SARS-CoV-2 (82.8%), followed by Set-10, Set-11, Set-13 and Set-14 (75.9%), and Set-14 showed the fastest amplification speed (< 8.5 minutes), followed by Set-17 (< 12.5 minutes). Based on the overall detection performance, Set-4, Set-10, Set-11, Set-13, Set-14 and Set-17 that target Nsp3, S, S, E, N and N gene regions of SARS-CoV-2, respectively, are determined to be better than the other primer sets. Two RT-LAMP assays with the Set-14 primers in combination with any one of four other primer sets (Set-4, Set-10, Set-11, and Set-13) are recommended to be used in the COVID-19 surveillance.

Temporal dynamics of human respiratory and gut microbiomes during the course of COVID-19 in adults

SARS-CoV-2 infects multiple organs including the respiratory tract and gut. Whether regional microbiomes are disturbed significantly to affect the disease progression of COVID-19 is largely unknown. To address this question, we performed cross-sectional and longitudinal analyses of throat and anal swabs from 35 COVID-19 adults and 15 controls by 16S rRNA gene sequencing. The results allowed a partitioning of patients into 3-4 categories (I-IV) with distinct microbial community types in both sites. Lower-diversity community types often appeared in the early phase of COVID-19, and synchronous fast restoration of both the respiratory and gut microbiomes from early dysbiosis towards late near-normal was observed in 6/8 mild COVID-19 adult patients despite they had a relatively slow clinical recovery. The synchronous shift of the community types was associated with significantly positive bacterial interactions between the respiratory tract and gut, possibly along the airway-gut axis. These findings reveal previously unknown interactions between respiratory and gut microbiomes, and suggest that modulations of regional microbiota might help to improve the recovery from COVID-19 in adult patients.

Construction of an HIV-1 Tat-dependent MazF expression vector / 中华实验和临床病毒学杂志

Objective@#To construct a Tat-dependent MazF expression vector pcDNA3.1-GFP-HA-MazF-U3TAR.@*Methods@#HIV-1 U3TAR and MazF gene were amplified from pCR2.1-U3TAR and pET28a-MazF, respectively. Two gene fragments were linked together to form U3TAR-MazF by an overlapping PCR, and then cloned into pMD18T. An N-terminal HA tag was added to MazF to form U3TAR-MazF-HA. After double enzyme digestion using EcoR I and Hind Ⅲ, U3TAR-MazF-HA was reversely inserted into pcDNA 3.1 to form pcDNA3.1-HA-MazF-U3TAR. Then, a fluorescent reporter gene GFP was inserted into the downstream of U3TAR to form pcDNA3.1-GFP-HA-MazF-U3TAR.@*Results@#The co-transfection experiments with pcDNA3.1-tat-flag showed that pcDNA3.1-GFP-HA-MazF-U3TAR is Tat dependent. MazF was expressed only under the presence of Tat. In addition, compared with the cells transfected with pcDNA3.1-GFP-HA-MazF-U3TAR, less green fluorescent signal was observed in the cells co-transfected with pcDNA3.1-GFP-HA-MazF-U3TAR and pcDNA3.1-tat-flag, indicating that expressed MazF down-regulated the expression of GFP.@*Conclusions@#The expression vector pcDNA3.1-GFP-HA-MazF-U3TAR will provide an important tool for the development of MazF-based AIDS gene therapy strategies.

Study on the relationship of serum pulmonary surfactant protein and vascular endothelial growth factor related indexes to lung cancer / 国际检验医学杂志

Objective To study the relationship of serum pulmonary surfactant protein and vascular endothelial growth factor re‐lated indexes to lung cancer .Methods Totally 56 patients with lung cancer in our hospital from September 2014 to December 2015 were selected as the observation group ,56 healthy personnel at the same period were selected as the control group ,then the serum pulmonary surfactant protein and vascular endothelial growth factor related indexes of control group and observation group ,obser‐vation group with different stages and pathological classifications were compared ,and the relationship between serum pulmonary surfactant protein and vascular endothelial growth factor related indexes and lung cancer were satisfacted with Logistic analysis .Re‐sults The serum pulmonary surfactant protein and vascular endothelial growth factor related indexes of observation group were all higher than those of control group ,and the serum pulmonary surfactant protein and vascular endothelial grow th factor related inde‐xes of observation group with higher stages were all higher than those of patients with lower stages ,and the levels of patients with adenocarcinoma were all higher than those of patients with squamous cell carcinoma ,and the serum pulmonary surfactant protein and vascular endothelial growth factor related indexes all had close relationship to the lung cancer (all P<0 .05) .Conclusion The serum pulmonary surfactant protein and vascular endothelial growth factor related indexes all have close relationship to the lung cancer ,and those indexes of patients with lung cancer should be paid more attention .

Expression of ERCC1, MSH2 and PARP1 in non-small cell lung cancer and their prognostic value for patients treated with platinum-based chemotherapy / 肿瘤研究与临床

Objective To analyze the expression of excision repair cross-complementation group 1 (ERCC1),MutS protein homolog 2 (MSH2) and poly ADP-ribose polymerase 1 (PARP1) in non-small cell lung cancer (NSCLC) and their prognostic value for patients receiving platinum-based postoperative adjuvant chemotherapy.Methods Immunohistochemistry was applied to detect the expression of ERCC1,MSH2 and PARP1 in 111 cases of NSCLC paraffin embedded surgical specimens.Through OG-Rank survival analysis,the prognostic value of the ERCC1,MSH2,PARP1 and the related clinic pathological factors were evaluated.Cox regression analysis was used to determine whether ERCC1,MSH2 and PARP1 were independent prognostic factors or not.Results Among the 111 NSCLC patients,the positive expression rates of ERCC1,MSH2 and RARP1 were 33.3 ％(37/111),36.9 ％(41/111) and 55.9 ％(62/111),respectively.Besides,a total of 72 patients who received platinum-based chemotherapy had complete follow-up data.ERCC1 (P＜ 0.001) and PARP1 (P=0.033) were found to be correlated with the survival time while there was no correlation for MSH2 (P =0.298).Patients with both ERCC1 and PARP1 negative had significant longer survival time than those with ERCC1 (P=0.042) or PARP1 (P=0.027) positive alone.Similarly,the survival time of patients with both ERCC1 and PARP1 positive was shorter than those with ERCC1 (P=0.048) or PARP1 (P=0.010) positive alone.Conclusions The NSCLC patients with ERCC1 and (or) PARP1 negative may benefit from platinumbased postoperative adjuvant chemotherapy.The detection of ERCC1 and PARP1 can be used as an important method to assess the prognosis of patients with NSCLC.