Phylogenetic and immunological investigations of complete TSA56 ORF of Orientia tsutsugamushi present in acute encephalitis syndrome cases from eastern Uttar Pradesh, India

Deciphering the genotypic diversity and epidemiology of scrub typhus genotypes in India: A systematic review and meta-analysis

BACKGROUND

Scrub typhus is a significant cause of Acute Febrile Illness in India and presents a range of clinical manifestations influenced by the genotypes of the causative agent, Orientia tsutsugamushi. Understanding the distribution of these genotypes is crucial for public health planning, diagnostic accuracy, and vaccine development.

METHODS

In this systematic review, we analyzed 18 studies from an initial pool of 2013 records identified through database searches following PRISMA guidelines. The relevance of the findings to the genotype prevalence of Scrub typhus in India was taken into consideration throughout the selection process. Various genotyping methods, predominantly Polymerase Chain Reaction (PCR), were used in these studies to identify genotypes such as Karp, Gilliam, Kato, and others.

RESULTS

The review revealed diverse prevalence rates of Scrub typhus genotypes across different Indian states. The Karp genotype is the most prevalent in India, with a pooled prevalence of 47 %, followed by the Kato genotype at 40 % and the Gilliam genotype at 28 %. The Karp genotype showed significant variability, with prevalence rates ranging from 100 % in Andhra Pradesh (2018) to 6.16 % in Uttar Pradesh (2016-2017). The Kato genotype's presence varied significantly, with high prevalence in certain states like Karnataka and absence in others like Andhra Pradesh. The Gilliam genotype also displayed a unique distribution pattern, dominating in Uttar Pradesh with a prevalence of 93.8 % in some years. Other genotypes like Boryong, IHS-II, Neimeng, Kuroki, TA763, and Kawasaki also showed varied prevalence across states. There was significant heterogeneity in the prevalence rates of different genotypes among studies, as indicated by I2 statistics.

CONCLUSION

The diversity in Scrub typhus genotypes across India underscores the disease's complex epidemiology, presenting diagnostic challenges and opportunities for targeted public health interventions. For efficient disease management and control plans in India, it is imperative to understand the changing genetic landscape of scrub typhus through ongoing study and surveillance.

Molecular and serological evidence of chikungunya virus infection with high case fatality among pediatric population with acute encephalitis syndrome: first report from Eastern Uttar Pradesh, India

Acute encephalitis syndrome (AES) outbreaks in children of Eastern Uttar Pradesh (E-UP) region of India have been a longstanding public health issue, with a significant case fatality rate of 20-25%. Since past decade, a rise in chikungunya (CHIK) cases has been occurring, which is a reported etiology of AES. However, the burden of chikungunya virus (CHIKV) among pediatric AES (pAES) is unknown from E-UP. We included 238 hospitalized pAES cases. The presence of IgM antibodies for CHIKV, and Dengue virus (DENV) was tested, and RT-PCR was performed for CHIKV and DENV in serologically confirmed CHIKV and DENV pAES cases. Positive samples were sequenced using Sangers sequencing. Further, to check for co-infection, IgM antibodies for other AES etiologies including Japanese encephalitis virus (JEV), Leptospira and Orientia tsutsugamushi (OT) in serum were also investigated. IgM ELISA demonstrated 5.04% (12) positivity for CHIKV. Among CHIKV IgM positive, 3 (25%, 3/12) pAES patients died. CHIKV genome was detected in 3 pAES specimens. Among which, 2 CHIKV cases were also positive for OT DNA. Partially sequenced CHIKV were genotyped as ECSA. The overall finding indicates evidence of CHIKV infection with high case fatality among pAES patients from E-UP. This study advocates constant serological and molecular surveillance of CHIKV in AES endemic regions of India.

Integration of IgM ELISA and 56 kDa gene PCR in management of pediatric acute encephalitis syndrome associated with scrub typhus

OBJECTIVES

To identify the potential target genes for detection of Orientia tsutsugamushi (OT) in pediatric acute encephalitis syndrome (pAES).

METHODS

DNA was extracted from whole blood of 100 pAES cases having tested positive (n = 41) and negative (n = 59) for scrub typhus (ST) by IgM ELISA. These samples were subjected to standard PCR for 56 kDa, 47 kDa, 16 s rRNA, groEL, traD genes and the newly identified 27 kDa gene.

RESULTS

Among the selected gene targets, 56 kDa demonstrated its superiority for OT detection over the other tested genes. The presence of OT was confirmed via PCR targeting 56 kDa gene in 17 out of the 41 (41.4 %) IgM-positive ST AES cases and 38 out of the 59 (64.4 %) ST IgM negative cases. None of the other gene targets were amplified.

CONCLUSION

Integration of serological diagnosis with molecular diagnostics targeting the 56 kDa gene for routine testing of AES patients would facilitate detection of OT in AES endemic regions.

CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus

Orientia tsutsugamushi is responsible for causing scrub typhus (ST) and is the leading cause of acute encephalitis syndrome (AES) in AES patients. A rapid and sensitive method to detect scrub typhus on-site is essential for the timely deployment of control measures. In the current study, we developed a rapid, sensitive, and instrument-free lateral flow assay (LFA) detection method based on CRISPR/Cas12a technology for diagnosing ST (named LoCIST). The method is completed in three steps: first, harnessing the ability of recombinase polymerase for isothermal amplification of the target gene; second, CRISPR/Cas12a-based recognition of the target; and third, end-point detection by LFA. The detection limit of LoCIST was found to be one gene copy of ST genomic DNA per reaction, and the process was complete within an hour. In 81 clinical samples, the assay showed no cross-reactivity with other rickettsial DNA and was 100% consistent with PCR detection of ST. LoCIST demonstrated 97.6% sensitivity and 100% specificity. Overall, the LoCIST offers a novel alternative for the portable, simple, sensitive, and specific detection of ST, and it may help prevent and control AES outbreaks due to ST. In conclusion, LoCIST does not require specialized equipment and poses a potential for future applications as a point-of-care diagnostic.