Objective To investigate the relationship between dynamic changes of plasma D-dimer and survival rate of the esophageal carcinoma patients pre-and post-operation.Methods 30 cases of normal control group,160 cases of esophageal cancer group( including operation cases n =112),with the gold standard method for the determination of plasma D-dimer.Results There was a link between the level of D-dimer,TNM staging,lymph node metastasis and tumor size in esophageal carcinoma patients.Compared with the preoperation,the plasma D-dimer is significantly elevated 2 years later( t =7.35,P ＞ 0.05 ).Conclusion Before or after the operation,dynamic changes of plasma D-dimer had a relationship with short-term survival rate.

Objective:To understand the genome characteristics of group A rotavirus (RVA) strains among hospitalized children under 5 years of age with acute diarrhea in Fuzhou sentinel hospital in 2020.Methods:The ELISA method was used for screening RVA-positive stool samples of hospitalized children under 5 years of age, then 11 gene segments of RVA-positive samples were sequenced and typed after amplification by RT-PCR, and their homology and phylogenetic analysis were performed by Molecular Evolutionary Genetics Analysis (MEGA).Results:Twenty RVA whole genome sequences were successfully obtained, including 4 kinds of G/P gene combinations-G9P[8] (55%), G3P[8] (25%), G8P[8] (15%) and G2P[4] (5%). DS-1-like reassortant strains accounted for 40% of the whole genomes. Strains of the same type have high sequence homology, are closely related to the virus strains that currently circulating in the world. There are mutations at multiple important antigenic sites on VP7, VP4 and NSP4 fragments. The variation of amino acid substitutions of VP7, VP4 and NSP4 fragments is complicated, and there are many amino acid substitutions in the antigenic regions.Conclusions:G3P[8] and G8P[8] DS-1-like reassortants were detected for the first time in Fuzhou, amino acid substitutions were observed in the antigenic regions of the VP7, VP4 and NSP4 gene. Due to the emergence of uncommon DS-1-like reassortant strains and multiple important antigenic regions substitutions, it is necessary to continuously monitoring genome characteristics of RVA strains to provide scientific evidence for the pandemic prevention and vaccine immunization strategies.

Objective:To investigate the prevalence and genotypes of parechovirus A (PeV-A) in hospitalized children with acute gastroenteritis under 5 years of age in Fuzhou, China.Methods:We performed a real-time RT-PCR to screen for PeV-A from stool samples and amplify VP3/VP1 junction region by nested RT-PCR to identify PeV-A type.Results:The result showed that 28 of 316 (8.86%) children with acute gastroenteritis were positive for PeV-A, two cases were co-infected with calicivirus, none with rotavirus, adenovirus or astrovirus. Totally 21 cases were PeV-A1, 1 case was PeV-A3 and 2 cases were PeV-A6 among 24 cases who were positive for PeV-A; PeV-A1 was the most prevalent strain with the proportion of 87.5%. The infection with PeV-A mainly occurred in children under 1 year of age and was prevalent between August and October.Conclusions:PeV-A1 was a main pathogen in PeV-A in hospitalized children with acute gastroenteritis in Fuzhou, and the children under 1 year of age were the main target population of PeV-A1.

Objective:To improve the efficiency and success rate of human adenovirus 3 (HAdV-3) whole genome sequencing, a high-throughput sequencing method for the whole genome of HAdV-3 based on multiplex PCR was established.Methods:Multiplex PCR primers suitable for the whole genome amplification of HAdV-3 were designed. The whole genome sequence of HAdV-3 was amplified by multiplex PCR, and the specificity of the amplification product was preliminarily verified by agarose gel electrophoresis. High-throughput sequencing of the multiplex PCR products was performed using Illumina second-generation sequencing. After obtaining the sequence, software such as CLC and IGV were used to analyze the effective data amount, average sequencing depth, and whole genome coverage obtained by high-throughput sequencing, then the sequencing quality was evaluated. Based on the whole genome sequencing result, a phylogenetic tree was constructed to confirm the virus type and analyze homology of the sequences, and then the accuracy of this method was evaluated.Results:A total of 70 (35 pairs) multiplex PCR amplification primers for the whole genome of HAdV-3 were designed, with amplicon size of approximately 1 200 bp. And the expected whole genome coverage could reach 99.8% (with a total genome length of approximately 35 240 bp). Agarose gel electrophoresis analysis showed that the size of the multiplex PCR products was consistent with expectations, and the amplification specificity was high. The high-throughput sequencing result showed that the whole genome sequences obtained by this method were complete and intact, and the genome coverage was consistent with expectations. Sequence quality analysis showed that the high-throughput sequencing method based on multiplex PCR could obtain more effective data and greater sequencing depth, resulting in more uniform whole genome coverage. Phylogenetic analysis showed that the evolutionary typing result of viral DNA sequenced after multiplex PCR amplification were consistent with those of viral DNA sequenced directly and had high homology, indicating that the multiplex PCR method had high amplification fidelity and the results obtained in combination with high-throughput sequencing were accurate.Conclusions:A high-throughput sequencing method for the whole genome of HAdV-3 based on multiplex PCR was established in this study successfully. This method could improve the efficiency and success rate of HAdV-3 whole genome sequencing, aiming to provide better technical support and reference for HAdV-3 pathogen surveillance and epidemic source-tracing based on whole genome sequencing.

Objective:A genome-wide molecular characterization of FJ21351116, a strain of G3P[8]-E2 2021 collected in Fujian, China, was performed.Methods:Whole genome sequencing of FJ21351116 was performed using a high-sensitivity group A rotavirus whole genome sequencing method. Genomic characteriza-tion of the virus was assessed by nucleic acid sequence analysis using MEGA 11.0, Geneious 9.0.2 and DNASTAR software. Neutralization epitopes of VP7 and VP4 (VP8*) were analyzed using BioEdit v. 7.0.9.0 and PyMOL v. 2.5.2.Results:In this study, FJ21351116 was shown to be a G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 genotype, and the result of phylogenetic tree showed that the VP7, VP4, VP3, and NSP2-NSP5 genes of the FJ21351116 strain were related to the equine-like DS-1-like G3P[8] genes that have been detected in Japan in recent years. VP6, VP1, VP2, and NSP1 genes are closely related to G2P[4] in most countries, especially in Singapore, suggesting that this strain was formed by genetic reassortment during the evolution of equine-like G3P[8] and G2P[4]. Evolutionary relationships between the VP7/VP4 genes of FJ21351116 and Rotarix and RotaTeq vaccines suggest that the multiple mutations in both VP7 and VP4 (VP8*) neutralizing antigenic epitopes and vaccine amino acid sites. It is hypothesized that the Rotarix and RotaTeq vaccines may be less effective against equine DS-1-like G3P[8] RVA, and the sequence differences with Rotarix are higher than those with RotaTeq.Conclusions:In this study, we found a rare case of DS-1-like G3P [8] RVA strain in China. Currently, horse-like DS-1-like G3P [8] RVA is relatively rare in China and may be poorly protected by vaccine strains, emphasizing the importance of continuous monitoring of RVA strains and the development of efficient and full-coverage RVA vaccines.

Objective:To investigate the whole genome characteristics and mutation of imported 2019-nCoV and trace potential source at the genomics level, the viral genomes from the specimens of a cluster of COVID-19 cases which were imported from a freighter were directly sequenced and determined by high-throughput sequencing technology and bioinformatics analysis.Methods:Throat swab specimens from the 8 confirmed cases of COVID-19 from the same freighter were collected to perform the whole genome sequencing for 2019-nCoV using the targeted genome amplification, combined with Ion S5 next-generation sequencing (NGS) technology. Varieties of online virus analysis platforms was used to classify the viruses and analyze mutation sites in the whole genome. Phylogenetic analysis software was used to construct a phylogenetic tree for the viruses, combined with the epidemiological data of the case, to speculate about the source of the viruses.Results:Eight complete genome sequences of 2019-nCoV was successfully obtained. The complete genomes of the viruses were 29, 822-29, 865 bp in length, with the average sequencing depth of 11 928×-33 588× and the coverage of 99.73%-99.87%; the result of Pangolin classification showed that all the eight 2019-nCoV genomes belong to VOC/Delta (B.1.617.2) lineage. The result of whole genome mutation analysis showed that compared with the Wuhan reference strain, the median number of nucleotide mutations in the eight 2019-nCoV genome sequences was 35 (31 to 38), and the median number of amino acid mutations was 26 (24-28); the mutation sites were distributed in 8 gene coding regions (ORF1a, ORF1b, S, ORF3a, M, ORF7a, ORF8, N). Further analysis revealed that eight 2019-nCoV genomes contained 23 characteristic mutation sites belonging to the Delta (B.1.617.2·AY.2) variants of 2019-nCoV. Since the mutation sites among the eight 2019-nCoV genomes were not completely overlapped, and the epidemiological survey report showed that the freighter stopped at multiple ports and had personnel alternation, it was speculated that the clustered COVID-19 cases might have different origins. Phylogenetic analysis showed that all the eight 2019-nCoV genomes were on the AY.2 sub-lineage of the B. 1.617.2 lineage. This result was consistent with the result of Pangolin classification and mutation analysis.Conclusions:In this study, 8 whole genome sequences of Delta variants were obtained through NGS technology from the clustered COVID-19 cases which were imported from a freighter. The sequencing method and analysis result in this study could provide reference for the 2019-nCoV mutation analysis and tracing the source of the COVID-19 cases for the prevention and control of the COVID-19 epidemic.

Objective:To confirm the cross-provincial long-distance transmission events of Coronavirus Disease 2019 (COVID-19) by lorry drivers, the origin of infections of the cases and the transmission routes were tracked.Methods:Nasopharyngeal swab specimens from five lorry driver cases of COVID-19, found in Zhangzhou city in March, 2022 when the local outbreaks occurred in adjacent Quanzhou city, Fujian province, were collected to perform 2019 novel coronavirus (2019-nCoV) targeted genome amplification and followed by next-generation sequencing. The sequences were submitted to online 2019-nCoV analysis platforms to classify the type of variant and mutation sites. Phylogenetic tree for the viruses were constructed by phylogenetic analysis software. Combined with the epidemiological investigation, the origin of infections of the cases and the transmission routes were deduced.Results:Five complete genome sequences, with 29 770-29 839 bp in length and 99.53% average genomic coverage, of 2019-nCoV were successfully obtained. The viruses were all Omicron variants and further divided into three different subclades of BA.2. Of the five strains of 2019-nCoV, three were highly similar to the viruses of two distinct lineages co-circulated in Quanzhou city during the period of local outbreak of COVID-19, respectively. Phylogenetic analysis also revealed that the viruses from three infected lorry drivers were highly homologous to that from local outbreaks in Quanzhou city. The viruses from the rest two cases had seven to fourteen nucleotide mutations (corresponding to 5-7 amino acid substitutions) when compared with the viruses in local outbreaks in Quanzhou city, which excluded the involvement of the two cases into the transmission chains of local outbreaks. Combined with the field epidemiological investigations, the result revealed that the origin of infection of 2019-nCoV of the two sporadic lorry driver cases was outside of Fujian province.Conclusions:With the aid of high-throughput sequencing and bioinformatics technology combined with field epidemiological investigations, we speculated in this study that at least three origins of infection of 2019-nCoV in five lorry driver cases and cross-provincial long-distance transmission via two sporadic cases infected outside Fujian province when they returned.