Additional file 1 of Search-engine-based surveillance using artificial intelligence for early detection of coronavirus disease outbreak

Additional file 1. Table S1. Correlation coefficients of the query volumes of 32 keywords with the numbers of new cases of coronavirus disease and their query multiples (increases in query volume) from December 30, 2019 to 31 December 2019

Additional file 1: of Antimicrobial resistance and genetic characterization of Shigella spp. in Shanxi Province, China, during 2006–2016

Table S1. Primers for the PCR detection of antimicrobial-resistance determinants used in this study. (PDF 165 kb

Dendrogram displaying the PFGE profiles of the 43 isolates.

<p>The strain number, origin, source, sequence type (ST), and H₂S phenotype are shown for each strain. +, H₂S-producing isolate; −, non-H₂S-producing isolate.</p

Alignment of <i>phsA</i> sequences in 21 <i>S</i>. Choleraesuis.

<p>The deletion of G at position 760 resulted in a frame-shift mutation. The first sequence is H₂S-positive <i>S</i>. Choleraesuis strain SC-B67 (NC_006905.1).</p

Sequence alignment of the <i>phs</i> gene and the protein.

<p>A nonsense mutation at position 208 of the <i>phsA</i> gene results in the replacement of a sense codon (CAG) with a termination codon (UAG) leading to the premature termination of <i>phsA</i>. The first sequence, <i>phsA</i>, is based on <i>S</i>. enterica serotype Typhimurium strain LT2 (GenBank AE006468). *, termination codon; +, H₂S-producing isolate; −, non-H₂S-producing isolate.</p

The methodology of <i>Salmonella</i> detection procedure.

<p>The methodology of <i>Salmonella</i> detection procedure.</p

Electrochemical DNA Biosensor Based on a Tetrahedral Nanostructure Probe for the Detection of Avian Influenza A (H7N9) Virus

A DNA tetrahedral nanostructure-based electrochemical biosensor was developed to detect avian influenza A (H7N9) virus through recognizing a fragment of the hemagglutinin gene sequence. The DNA tetrahedral probe was immobilized onto a gold electrode surface based on self-assembly between three thiolated nucleotide sequences and a longer nucleotide sequence containing complementary DNA to hybridize with the target single-stranded (ss)­DNA. The captured target sequence was hybridized with a biotinylated-ssDNA oligonucleotide as a detection probe, and then avidin-horseradish peroxidase was introduced to produce an amperometric signal through the interaction with 3,3′,5,5′-tetramethylbenzidine substrate. The target ssDNA was obtained by asymmetric polymerase chain reaction (PCR) of the cDNA template, reversely transcribed from the viral lysate of influenza A (H7N9) virus in throat swabs. The results showed that this electrochemical biosensor could specifically recognize the target DNA fragment of influenza A (H7N9) virus from other types of influenza viruses, such as influenza A (H1N1) and (H3N2) viruses, and even from single-base mismatches of oligonucleotides. Its detection limit could reach a magnitude of 100 fM for target nucleotide sequences. Moreover, the cycle number of the asymmetric PCR could be reduced below three with the electrochemical biosensor still distinguishing the target sequence from the negative control. To the best of our knowledge, this is the first report of the detection of target DNA from clinical samples using a tetrahedral DNA probe functionalized electrochemical biosensor. It displays that the DNA tetrahedra has a great potential application as a probe of the electrochemical biosensor to detect avian influenza A (H7N9) virus and other pathogens at the gene level, which will potentially aid the prevention and control of the disease caused by such pathogens

Phylogenetic relationships of all <i>S</i>. Choleraesuis STs from MLST database by eBURST analysis.

<p>All <i>S</i>. Choleraesuis STs were divide into three clonal complexes. The blue solid circle represents the founder clonal complex. The red lines indicate SLVs between STs.</p

Data_Sheet_1_Characterization and Genomic Analysis of SFPH2, a Novel T7virus Infecting Shigella.pdf

Shigellosis, caused by Shigella, is a major global health concern, with nearly 164.7 million cases and over a million deaths occurring annually worldwide. Shigella flexneri is one of the most common subgroups of Shigella with a high incidence of multidrug-resistance. The phage therapy approach is an effective method for controlling multidrug-resistant bacteria. However, only a few Shigella phages have been described to date. In this study, a novel lytic bacteriophage SFPH2 was isolated from a sewage sample obtained from a hospital in Beijing, China, using a multidrug-resistant S. flexneri 2a strain (SF2) isolated from the fecal sample of a dysentery patient. SFPH2 is a member of the Podoviridae virus family with an icosahedral capsid and a short, non-contractile tail. It was found to be stable over a wide range of temperatures (4–50°C) and pH values (pH 3–11). Moreover, SFPH2 could infect two other S. flexneri serotypes (serotypes 2 variant and Y). High-throughput sequencing revealed that SFPH2 has a linear double-stranded DNA genome of 40,387 bp with 50 open reading frames. No tRNA genes were identified in the genome. Comparative analysis of the genome revealed that the SFPH2 belongs to the subfamily Autographivirinae and genus T7virus. The genome shows high similarity with other enterobacterial T7virus bacteriophages such as Citrobacter phage SH4 (95% identity and 89% coverage) and Cronobacter phage Dev2 (94% identity and 92% coverage). A comparison of the fiber proteins showed that minor differences in the amino acid residues might specify different protein binding regions and determine host species. In conclusion, this is the first report of a T7virus that can infect Shigella; SFPH2 has a functional stability under a wide range of temperatures and pH values, showing the potential to be widely applied to control Shigella–associated clinical infections and reduce the transmission rates of S. flexneri serotype 2a and its variants in the environment.</p

Table_1_Inhibition of HBV Expression in HBV Transgenic Mice Using AAV-Delivered CRISPR-SaCas9.DOCX

The chronic production of hepatitis B viral (HBV) antigens could cause inflammation and necrosis, leading to elevation of liver enzymes from necrotic hepatocytes, hepatitis, cirrhosis, hepatocellular carcinoma, and liver failure. However, no current treatment is capable of significantly reducing HBsAg expression in patients. Our previous studies had confirmed the ability of CRISPR-Cas9 in disrupting HBV cccDNA. Here, to inhibit HBV expression efficiently in the mouse model of chronic HBV infection, the miniaturized CRISPR-SaCas9 system compatible with a HBV core region derived guide-RNA had been packaged in recombinant adeno-associated virus (AAV) type 8, which lowered the levels of serum HBsAg, HBeAg, and HBV DNA efficiently in HBV transgenic mice during 58 days continuous observation after vein injection. It further confirms the potential of the CRISPR-Cas9 technique for use in hepatitis B gene therapy.</p