<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bajpai, Manali</style></author><author><style face="normal" font="default" size="100%">Khilari, Ajinkya</style></author><author><style face="normal" font="default" size="100%">Likhitkar, Bhagyashree</style></author><author><style face="normal" font="default" size="100%">Musale, Pankaj</style></author><author><style face="normal" font="default" size="100%">Jadhav, Santoshkumar</style></author><author><style face="normal" font="default" size="100%">Dhanikachalam, Velu</style></author><author><style face="normal" font="default" size="100%">Kakramkar, Payal</style></author><author><style face="normal" font="default" size="100%">Bhave, Kaustubh</style></author><author><style face="normal" font="default" size="100%">Swaminathan, Marimuthu</style></author><author><style face="normal" font="default" size="100%">Joshi, Sachin</style></author><author><style face="normal" font="default" size="100%">Shanmugam, Dhanasekaran</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Detection and variant characterization of lumpy skin disease virus from dairy cattle in India</style></title><secondary-title><style face="normal" font="default" size="100%">Virus Evolution</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">genotyping by sequencing</style></keyword><keyword><style  face="normal" font="default" size="100%">lumpy skin disease</style></keyword><keyword><style  face="normal" font="default" size="100%">multiplexed nested PCR</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxford Nanopore technology</style></keyword><keyword><style  face="normal" font="default" size="100%">virus surveillance</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2025</style></year><pub-dates><date><style  face="normal" font="default" size="100%">DEC</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">veaf090</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;
	The spread of a severe and often fatal form of lumpy skin disease (LSD) in cattle and water buffaloes has caused widespread mortality and morbidity of these animals in India. To track and understand the genetic changes occurring in the virus and to enable routine surveillance of the virus, multiplexed polymerase chain reaction (PCR) and sequencing methods were developed and validated in this study. Multiplexed nested PCR for LSD virus (LSDV) detection was optimized using skin lesion swabs and nasal samples collected from symptomatic and asymptomatic animals. For genotyping, overlapping PCRs to amplify the entire LSDV genome were developed and tested on field samples collected from the Maharashtra and Odisha states of India. Analysis of LSDV genomes from 41 field samples collected in 2022 and 2023 revealed the presence of highly conserved novel mutations. Phylogenetic analysis shows that a distinct genotype of LSDV has spread across India, which warrants genomic surveillance of the virus in the coming years to track the evolution and transmission of the virus. The non-invasive sample collection, detection, and genotyping methods described in this study can facilitate large-scale surveillance of LSDV in dairy animals.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;
	Foreign&lt;/p&gt;
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	4.5&lt;/p&gt;
</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Musale, Pankaj</style></author><author><style face="normal" font="default" size="100%">Khilari, Ajinkya</style></author><author><style face="normal" font="default" size="100%">Gade, Rohini</style></author><author><style face="normal" font="default" size="100%">Dhanikachalam, Velu</style></author><author><style face="normal" font="default" size="100%">Jadhav, Santoshkumar</style></author><author><style face="normal" font="default" size="100%">Bajpai, Manali</style></author><author><style face="normal" font="default" size="100%">Turakani, Bhagya</style></author><author><style face="normal" font="default" size="100%">Joshi, Akshay</style></author><author><style face="normal" font="default" size="100%">Prajapati, Amar</style></author><author><style face="normal" font="default" size="100%">Srivastava, Anand</style></author><author><style face="normal" font="default" size="100%">Swaminathan, Marimuthu</style></author><author><style face="normal" font="default" size="100%">Joshi, Sachin</style></author><author><style face="normal" font="default" size="100%">Shanmugam, Dhanasekaran</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Identification of genetic variations linked to buparvaquone resistance in Theileria annulata infecting dairy cattle in India</style></title><secondary-title><style face="normal" font="default" size="100%">Plos One</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2025</style></year><pub-dates><date><style  face="normal" font="default" size="100%">JUL</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">e0326243</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;
	Buparvaquone (BPQ) is used for the treatment of bovine theileriosis, a tickborne disease caused by parasites of the Theileria genus. Studies on T. annulata have linked the mechanism of BPQ resistance predominantly to genetic variations in the parasite cytochrome b (cytb) gene. In addition, cryptic mechanisms of resistance involving the parasite peptidyl-prolyl isomerase (pin1) and dihydroorotate dehydrogenase (dhodh) genes require assessment. In India, where bovine theileriosis is endemic, and BPQ is widely used for treatment, it is necessary to establish the prevalence of genetic variations linked to BPQ resistance. In this study, multiplexed PCR amplification and nanopore sequencing method was used for genotyping the complete gene loci of the three target genes. Analysis of 454 T. annulata field samples collected from seven different states of India revealed the presence of previously reported BPQ resistance associated variations S129G, A146T and P253S in cytb gene and A53P in pin1 gene. The A146T and I203V variations in cytb were found to be prevalent and mostly co-occurring, and their role in BPQ resistance needs further evaluation. This study has revealed the presence of previously reported BPQ resistance-linked mutations in cytb and pin1 genes in T. annulata infecting dairy cattle in India and establishes an Oxford nanopore sequencing method suitable for large-scale surveillance of genetic variation in Theileria parasites from field samples.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;
	Foreign&lt;/p&gt;
</style></custom3><custom4><style face="normal" font="default" size="100%">&lt;p&gt;
	3.2&lt;/p&gt;
</style></custom4></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Khilari, Ajinkya</style></author><author><style face="normal" font="default" size="100%">Sharma, Shweta</style></author><author><style face="normal" font="default" size="100%">Bajpai, Manali</style></author><author><style face="normal" font="default" size="100%">Viswan, K. Anju</style></author><author><style face="normal" font="default" size="100%">Chaturvedi, Rini</style></author><author><style face="normal" font="default" size="100%">Mirdha, Bijay R.</style></author><author><style face="normal" font="default" size="100%">Rahi, Manju</style></author><author><style face="normal" font="default" size="100%">Sharma, Amit</style></author><author><style face="normal" font="default" size="100%">Shanmugam, Dhanasekaran</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Targeted genomic surveillance unveils genetic variations linked to regional malaria drug resistance dynamics in India</style></title><secondary-title><style face="normal" font="default" size="100%">Open Forum Infectious Diseases</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">drug resistance</style></keyword><keyword><style  face="normal" font="default" size="100%">malaria</style></keyword><keyword><style  face="normal" font="default" size="100%">Oxford nanopore</style></keyword><keyword><style  face="normal" font="default" size="100%">P. falciparum</style></keyword><keyword><style  face="normal" font="default" size="100%">pfMDR15</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2026</style></year><pub-dates><date><style  face="normal" font="default" size="100%">MAR</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">13</style></volume><pages><style face="normal" font="default" size="100%">ofag106</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;
	Background India has made substantial progress in reducing Plasmodium falciparum malaria cases and has set a target to eliminate malaria by 2030. Although artemisinin-based combination therapy (ACT) treatment remains effective, tracking regional differences in genetic variants associated with antimalarial resistance is required for effective drug policy implementation.Methods We analyzed 238 P. falciparum clinical samples from 6 Indian states by sequencing 15 parasite genes associated with reduced drug effectiveness. The method involved nanopore sequencing of target gene amplicons derived from dried blood spots using a highly-sensitive PfMDR15 surveillance panel.Results India's historical policy of artesunate-sulfadoxine-pyrimethamine in central India and artemether-lumefantrine in the Northeast has shaped contrasting resistance profiles. In the Northeast, chloroquine resistance persisted at high frequency (Pfcrt K76T and CVIET haplotype; Pfaat1 S258L), alongside quintuple and sextuple Pfdhfr-Pfdhps haplotypes conferring complete sulfadoxine-pyrimethamine resistance. Central India showed variable chloroquine resistance (parasites largely retained wild-type Pfcrt) and emerging lumefantrine tolerance (Pfmdr1 Y184F, Pfaat1 S258L). Interestingly, Delhi (Central India) parasites resembled profiles from the distant Northeast, which borders South East Asia. The detection of Pfaat1 S258L, previously reported only from Africa and associated with reduced lumefantrine susceptibility, suggests convergent evolution under ACT partner-drug pressure. No WHO-validated Pfk13 artemisinin resistance mutations were detected, supporting continued efficacy of ACT.Conclusions India's resistance landscape is fragmented, with signals of expanding lumefantrine tolerance and importation or evolution of globally relevant mutations. These findings highlight the importance of integrating molecular genomic surveillance into malaria control policy to monitor and protect ACT effectiveness and advance malaria elimination. Monitoring of drug resistance associated mutations in P. falciparum parasites is critical for effective drug treatment. We have demonstrated the use of a scalable genomic surveillance protocol for tracking drug resistance linked mutations in parasite genes from clinical isolates in India. The study suggests extensive regional diversity in antimalarial resistance profiles and provides the first hint of possible emergence of lumefantrine tolerance in India.&lt;/p&gt;
</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><work-type><style face="normal" font="default" size="100%">Article</style></work-type><custom3><style face="normal" font="default" size="100%">&lt;p&gt;
	Foreign&lt;/p&gt;
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	3.5&lt;/p&gt;
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