Detection of African genotype in Hyalomma tick pools during Crimean Congo hemorrhagic fever outbreak, Rajasthan, India, 2019

Sahay, Rima R.; Dhandore, Suhas; Yadav, Pragya D; Chauhan, Arun; Bhatt, Lenin; Garg, Veena; Gupta, Nivedita; Nyayanit, Dimpal A; Shete, Anita M.; Singh, Ruchi; Patil, Savita; Sharma, Himanshu; Meena, Deepa; Gupta, Jyoti; Gawande, Pranita; Kalele, Kaumudi; Jain, Rajlaxmi; Mali, Deepak; Malhotra, Bharati; Nag, Vijayalakshmi; Khatri, Prabhat Kiran; Kaur, Harmanmeet; Vijay, Neetu; Singh, Sujeet Kumar; Gopalakrishnan, Maya

doi:10.1016/j.virusres.2020.198046

Cited by 10 publications

(5 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, we have identified re-assortment of CCHFV strain from the human sample and tick-pool circulating in Gujarat state in year 2019. The presence of re-assortment of Asian-West African strains within the Hyalomma tick pools from Rajasthan state, India and now in human from Gujarat state emphasize the movement of ticks through animal trade and tick bites to human spreading the infection in both the states [5]. We observed that the distribution of the amino acid mutations was not linked to any specific geographical location or increased virulence.…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 58%

“…In India, CCHF cases were confirmed during the period, 2011 to 2019 from Gujarat state and in 2014, 2015 and 2019 from Rajasthan state [3,4,5]. The clinical presentation starts with fever, myalgia, diarrhoea and vomiting during the prodromal phase, progresses to ecchymoses, petechial rash, bleeding from mucosal/punctured sites, coagulation disorders, fatal hemorrhagic manifestations including disseminated intravascular coagulation and death [6,7,8,9].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019

et al. 2021

Self Cite

View full text Add to dashboard Cite

Background Thirty-four CCHF cases (17 fatal; 17 survived) were confirmed from Gujarat state, India during the year 2019. We aimed to find out the viral load, antibody kinetics, cytokine profile and phylogenetic analysis between fatal and non- fatal cases. Methods Thirty four cases were included in this study. Blood and urine samples were collected from all the cases on the day of admission to hospital. Non-fatal cases were followed weekly for understanding the profile of viral kinetics, anti-CCHFV IgM and IgG antibodies. We also quantified the cytokines in both fatal and non-fatal cases. For epidemiological correlation, livestock were screened for anti CCHF IgG antibodies and the tick pool specimens were tested by real time RT-PCR. Virus isolation was attempted on tickpools and human specimens and phylogenetic analysis performed on human and ticks complete genome sequences. Results CCHF cases were detected throughout year in 2019 with the peak in August. Out of 34 cases, eight secondary CCHF cases were reported. Cases were predominantly detected in males and in 19–45 years age group (55.88%). The persistence of viremia was observed till 76th POD in one case whereas anti-CCHFV IgM and IgG was detected amongst these cases from the 2nd and 20th POD (post onset date) respectively. Positivity observed amongst livestock and tick pools were was 21.57% and 7.4% respectively. The cytokine analysis revealed a significant increase in the level of serum IL-6, IL-10 and IFN-γ during the acute phase of the infection, but interestingly IL-10 lowered to normal upon clearance of the virus in the clinically recovered case. Fatal cases had high viral RNA copy numbers. Bleeding from one or two mucosal sites was significantly associated with fatality (OR-16.47;p-0.0034 at 95% CI). We could do CCHF virus isolation from two cases. Phylogenetic analysis revealed circulation of re-assortment of Asian-West African genotypes in humans and ticks. Conclusions The persistence of CCHF viral RNA was detected till 76th POD in one of the survivors. The circulation of a re-assortment Asian-West African genotype in a CCHF case is also reported first time from India.

show abstract

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 58%

Section: Introductionmentioning

confidence: 99%

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…To verify whether such an approach is capable of finding yet unknown reassortment events, we assembled all available sequences of CCHFV and analysed them with PDDM and PDCP (Figures 3 and 4). As a result, the novel reassortant virus MCL-19-T-1812 was uncovered, which had not been detected before (Sahay et al, 2020). In other words, the proposed approach makes it possible to find reassortant viruses based on the automated analysis steps.…”

Section: Discussionmentioning

confidence: 99%

Concatenation of segmented viral genomes for reassortment analysis

Ivanova,

Volchkov,

Deviatkin

2024

Preprint

View full text Add to dashboard Cite

Most reassortment identification methods are based on searching for phylogenetic discrepancies between phylogenetic trees for different segments. Other methods use pairwise genetic distances or compare the position of individual genome components in a tree relative to a reference component of the viral genome. However, such approaches are labour-intensive and hardly scalable.Recent advances in the availability of viral sequencing technologies have led to the sequencing of large numbers of pathogen genomes, making manual processing of this large data difficult. At the same time, recombination analysis methods can process almost any number of sequences simultaneously. Such approaches are not suitable for the simultaneous analysis of multiple segments and are therefore not used to search for reassortment events. However, in the case of sequential concatenation of all segments, the methods of recombination analysis can be used to detect traces of reassortment events.The code is available athttps://github.com/melibrun/Concatenation-of-segmented-viral-genomes-for-reassortment-analysis. The service is implemented as a web applicationhttps://melibrun.shinyapps.io/viralsegmentconcatenator1/. It concatenates segmented viral genomes for reassortment analysis. The tool accepts files in GenBank format as input and generates a set of sequences in fasta format that are sequentially concatenated sequences of viral segments named in accordance with the “strain” field of the GenBank record annotation.In order to use recombination search algorithms in the study of reassortment events, we have developed a method (Virus Segment Concatenator, VSC) to automatically concatenate the sequences of all segments of a virus into a single sequence.The applicability of VSC for automated searches for reassortment events was demonstrated using CCHFV, an H5N5 subtype of influenza virus.

show abstract

“…In India CCHF has been reported from Gujarat since 2011 to 2019. CCHF outbreak was also recorded from three districts Jodhpur, Jaisalmer, and Sirohi of Rajasthan state since August 2019 till November 2019 (Sahay et al, 2020) [24] .…”

Section: Crimean Congo Haemorrhagic Fever (Cchf)mentioning

confidence: 99%

Rodent borne zoonoses: A brief review

Ganjeer¹,

Patyal²,

Shakya³

et al. 2021

Pharma Innovation

View full text Add to dashboard Cite

Rodents are the most abundant and diversified order of living mammals in the world. Since the middle ages they are known to contribute to human diseases, eg. black rats associated with distribution of plague. In modern times also rodents form a threat for public health and a number of pathogens are directly or indirectly transmitted by rodents. Of 2277 extant rodent species, 217 species are reservoirs harboring 66 zoonoses caused by viruses, bacteria, fungi, helminths, and protozoa and play a major role in their transmission and spread in different ways. Among the most important diseases in terms of public health are salmonellosis, plague, leptospirosis, leishmaniasis, toxoplasmosis, rat-bit fever, taeniasis-like Capillaria hepatica, zoonotic babesiosis, Lassa fever, hemorrhagic fever with renal syndrome (HFRS), and the hantavirus cardiopulmonary syndrome (HCPS). In addition, Arenaviruses are responsible for South American Hemorrhagic Fevers (SAHF). Rodents may harbor different complex bacteria, such as Mycobacterium tuberculosis and Mycobacterium microti, Escherichia coli, agents of Tularemia, Tickborne relapsing fever, Bartonellosis, Listeriosis, Lyme disease, Q fever, Ehrlichiosis and others. Recent changes in the global climate and ecosystem composition led to the spread of rodents and rodent-borne pathogens globally. Rodent control in rural environments relies mainly on the use of rodenticides. Other management methods which can be applied are trapping, habitat management (e.g., proofing, sanitation), and biocontrol (e.g., wild or domestic predators, rodent pathogens).

show abstract

Detection of African genotype in Hyalomma tick pools during Crimean Congo hemorrhagic fever outbreak, Rajasthan, India, 2019

Cited by 10 publications

References 9 publications

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019

Concatenation of segmented viral genomes for reassortment analysis

Rodent borne zoonoses: A brief review

Contact Info

Product

Resources

About