CRISPR-Cas9-Mediated Cytosine Base Editing Screen for the Functional Assessment of CALR Intron Variants in Japanese Encephalitis Virus Replication.

The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes viral encephalitis in humans, pigs and other mammals across Asia and the Western Pacific. Genetic screening tools such as CRISPR screening, DNA sequencing and RNA interference have greatly improved our understanding of JEV replication and its potential antiviral approaches. However, information on exon and intron mutations associated with JEV replication is still scanty. CRISPR-Cas9-mediated cytosine base editing can efficiently generate C: G-to-T: A conversion in the genome of living cells. One intriguing application of base editing is to screen pivotal variants for gene function that is yet to be achieved in pigs. Here, we illustrate that CRISPR-Cas9-mediated cytosine base editor, known as AncBE4max, can be used for the functional analysis of calreticulin (CALR) variants. We conducted a CRISPR-Cas9-mediated cytosine base editing screen using 457 single guide RNAs (sgRNAs) against all exons and introns of CALR to identify loss-of-function variants involved in JEV replication. We unexpectedly uncovered that two enriched sgRNAs targeted the same site in intron-2 of the CALR gene. We found that mutating four consecutive G bases in the intron-2 of the CALR gene to four A bases significantly inhibited JEV replication. Thus, we established a CRISPR-Cas9-mediated cytosine-base-editing point mutation screening technique in pigs. Our results suggest that CRISPR-mediated base editing is a powerful tool for identifying the antiviral functions of variants in the coding and noncoding regions of the CALR gene.

The epidemiology and disease burden of children hospitalized for viral infections within the family Flaviviridae in China: A national cross-sectional study.

BACKGROUND: Viruses of the family Flaviviridae, including Japanese encephalitis virus (JEV), dengue virus (DENV), yellow fever virus (YFV) and hepatitis C virus (HCV), are widely distributed worldwide. JEV, DENV and YFV belong to the genus Flavivirus, whereas HCV belongs to the genus Hepacivirus. Children's symptoms are usually severe. As a result, rates of hospitalization due to infection with these viruses are high. The epidemiology and disease burden of hospitalized children have rarely been described in detail to date. The objective of this study was to report the general epidemiological characteristics, clinical phenotype, length of stay (LOS), burden of disease, and potential risk factors for hospitalized children infected with JEV, DENV, YFV, or HCV in Chinese pediatric hospitals. METHODOLOGY: A cross-sectional study of epidemiology and disease burden of children hospitalized for Flaviviridae virus infections between December 2015 and December 2020 in China was performed. Face sheets of discharge medical records (FSMRs) were collected from 27 tertiary children's hospitals in the Futang Research Center of Pediatric Development and aggregated into FUTang Update medical REcords (FUTURE). Information on sociodemographic variables, clinical phenotype, and LOS as well as economic burden was included in FSMRs and compared using appropriate statistical tests. FINDINGS: The study described 490 children aged 0-15 years hospitalized for infections with Flaviviridae viruses. Japanese encephalitis (JE) cases are the highest, accounting for 92.65% of the total hospitalization cases caused by Flaviviridae virus infection. The incidence of JE peaked from July to October with a profile of a high proportion of severe cases (68.06%) and low mortality (0.44%). Rural children had a significantly higher incidence than urban children (91.63%). Most hospitalized dengue cases were reported in 2019 when dengue outbreaks occurred in many provinces of China, although only 14 dengue cases were collected during the study period. Yellow fever (YF) is still an imported disease in China. The hospitalizations for children with hepatitis C (HC) were not high, and mild chronic HC was the main clinical phenotype of patients. Among the four viral infections, JE had the highest disease burden (LOS and expenditure) for hospitalized children. CONCLUSION: First, the present study reveals that JE remains the most serious disease due to Flaviviridae virus infection and threatens children's health in China. Many pediatric patients have severe illnesses, but their mortality rate is lower, suggesting that existing treatment is effective. Both JEV vaccination and infection control of rural children should represent a focus of study. Second, although the dual risks of indigenous epidemics and imports of DENV still exist, the prevalence of DENV in children is generally manageable. Third, YFV currently shows no evidence of an epidemic in China. Finally, the proportion of children with chronic hepatitis C (CHC) is relatively large among hospitalized children diagnosed with HCV. Thus, early and effective intervention should be offered to children infected with HCV to ease the burden of CHC on public health.

Comparative evaluation of bioassay and ELISA for detection of Japanese encephalitis virus in field collected mosquitos.

Comparative evaluation of enzyme-linked immunosorbent assay (ELISA) and bioassay (virus isolation in Toxorhynchites splendens larvae and identification by immunofluorescence test using virus specific monoclonal antibody) was carried out in order to define a suitable strategy for monitoring Japanese encephalitis virus infection in field mosquitos. A total of 8,850 adult female mosquitos in 177 pools (Culex tritaeniorhynchus 91, Cx. vishnui 59 and Cx. fuscocephala 27) collected from an endemic area of Tamil Nadu were examined by both the techniques. In ELISA, 9 pools which had optical densities (OD) equal to the mean of normal infected pools plus > or = 4 standard deviations (SD) mean considered positive and all of them were virus positive by the bioassay also. Sixty-five pools had OD = Mean + 2-3 SD and 103 pools had OD = Mean + < 2 SD of normal pools. From these groups, 12 (18.5%) and 8 (7.8%) pools respectively were found to be virus positive by the bioassay. In total 29 (16%) pools were positive by the bioassay as against 9 (5%) by ELISA. This study demonstrated that the bioassay is sensitive for estimation of true positives and ELISA is a rapid screening system. A protocol has now been developed for surveillance in which field pools are first screened by ELISA and only those with OD = Mean + > or 2 SD are assayed in Toxorhynchites. By excluding a large majority of pools with low OD (Mean + < 2 SD), which are likely to yield to only a small percentage of true positives, the cost, time and labor involved are greatly reduced.(ABSTRACT TRUNCATED AT 250 WORDS)