Article
Virology
Emiliya Navrotskaya, Elena Porotikova, Eugeniya Yurchenko, Zsuzsanna Nagyne Galbacs, Eva Varallyay, Svetlana Vinogradova
Summary: The study identified a variety of viruses and viroids in vineyards in Krasnodar Krai using high-throughput sequencing technology. Recombination events were observed in multiple virus genomes, indicating a high genetic diversity. The results highlight the urgent need for long-term strategies to control viral grapevine diseases.
Article
Microbiology
Solomon Maina, Sally L. Norton, Brendan C. Rodoni
Summary: This study compared the use of MiSeq and MinION sequencing technologies for the detection and sequencing of broad bean wilt virus 2 (BBWV2) genome. The results showed high nucleotide identity between the two methods, however, the MinION sequencing had some deletions. This study confirmed the presence of BBWV2 in Australia and proposed the integration of versatile diagnostic genomics tools at the border to safeguard the Australian grains industry.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Jiyeong Choi, Anya Clara Osatuke, Griffin Erich, Kristian Stevens, Min Sook Hwang, Maher Al Rwahnih, Marc Fuchs
Summary: Pawpaw trees in New York were found to be infected with tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) based on high-throughput sequencing and testing. The study also revealed high similarity between different isolates of these viruses in pawpaw trees.
Article
Virology
Alfredo Diaz-Lara, Kristian Stevens, Vivian Hayde Aguilar-Molina, Jose Miguel Fernandez-Cortes, Victor Manuel Chabacano Leon, Marcos De Donato, Ashutosh Sharma, Teresa M. Erickson, Maher Al Rwahnih
Summary: This study is the first viral metagenomic analysis of grapevine in Mexico. 48 grapevine plants with virus-like symptoms were sampled and analyzed using high-throughput sequencing (HTS). The results were validated by real-time RT-PCR. Fourteen different viruses were identified, including some that had not been previously reported in Mexico. The impact of these viruses on grapevine production remains unknown.
Article
Infectious Diseases
Vladimir G. Dedkov, Anna S. Dolgova, Marina V. Safonova, Andrei E. Samoilov, Oxana A. Belova, Ivan S. Kholodilov, Alina D. Matsvay, Anna S. Speranskaya, Kamil Khafizov, Galina G. Karganova
Summary: Wad Medani virus (WMV) is a poorly studied arbovirus with unclear medical significance, but recent findings suggest a high potential for variability in WMV strains, leading to the formation of strains with novel properties. These new data can promote better understanding of ecological circulation, relationships within the Orbivirus genus, and the medical significance of the virus.
TICKS AND TICK-BORNE DISEASES
(2021)
Article
Virology
Izabela Fabianska, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, Dietmar Mayer
Summary: High-throughput sequencing (HTS) is effective in detecting both known and unknown viruses in samples, providing support for determining the safety of biological products such as vaccines. Due to the complexity of bioinformatics, standardized and reliable methods are necessary for managing HTS data. The LABRADOR analysis pipeline demonstrates reliable detection of viruses in mixtures of model viruses, vaccines, and clinical samples.
Review
Microbiology
Mark Paul Selda Rivarez, Ana Vucurovic, Natasa Mehle, Maja Ravnikar, Denis Kutnjak
Summary: The pace of tomato virus discovery has increased in the past decade due to the use of high-throughput sequencing (HTS), but further characterization lags behind, especially for economically devastating viruses. There are at least 312 virus, satellite virus, or viroid species associated with tomato, the highest number recorded for any plant, according to databases and literature review.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Chellappan Padmanabhan, Schyler Nunziata, M. Guillermo Leon, Yazmin Rivera, Vessela A. Mavrodieva, Mark K. Nakhla, Avijit Roy
Summary: Citrus leprosis (CiL) is an emerging viral disease of citrus in the Americas caused by Brevipalpus-transmitted viruses. The genetic diversity of viruses associated with CiL makes detection and diagnosis challenging, leading to the use of High-Throughput Sequencing (HTS) protocols. In this study, the HTS assay was used to detect and identify cileviruses infecting different host plants, leading to the discovery of a new strain of CiLV-C2 in hibiscus. These findings are important for citrus industry and further investigation is needed to understand the movement of the new strain from hibiscus to citrus.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Joshua A. Lieberman, Andrew Bryan, James A. Mays, Karen Stephens, Kyoko Kurosawa, Patrick C. Mathias, Dhruba SenGupta, Lori Bourassa, Stephen J. Salipante, Brad T. Cookson
Summary: Broad-range fungal PCR is a powerful tool for identifying pathogens directly from patient specimens, with higher positivity rates and faster turnaround time compared to culture. It is frequently informative for patients at risk of serious fungal disease and complements culture, with a higher sensitivity when combined with culture. Anatomic site may impact assay positivity rates, and formalin-fixed tissue does not negatively affect diagnostic yield.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Plant Sciences
Larissa Carvalho Costa, Benjamin Atha, Xiaojun Hu, Kurt Lamour, Yu Yang, Mary O'Connell, Clint McFarland, Joseph A. Foster, Oscar P. Hurtado-Gonzales
Summary: A method combining high multiplexing PCR and high-throughput sequencing accurately diagnosed multiple fruit tree viruses and viroids, increasing the capacity for large scale diagnostics.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Daichi Morimoto, Naohiro Yoshida, Aya Sasaki, Satoshi Nakagawa, Yoshihiko Sako, Takashi Yoshida
Summary: The bloom-forming toxic cyanobacterium Microcystis aeruginosa interacts with diverse broad- and narrow-host-range viruses. However, the dynamics of the Microcystis population (at the intraspecies level) and viruses with different host ranges remain unknown.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Plant Sciences
Malyaj R. Prajapati, Aakansha Manav, Jitender Singh, Pankaj Kumar, Amit Kumar, Ravindra Kumar, Satya Prakash, Virendra Kumar Baranwal
Summary: A study identified a virus named GarV-E in garlic plants in India, and conducted research on it using high-throughput sequencing. Sequence analysis showed a close relationship of this Indian isolate with GarV-E isolates from China. This study is the first report of GarV-E in Indian garlic.
Article
Biotechnology & Applied Microbiology
Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Eleni E. Adam, Andreas Scorilas
Summary: Survivin, a member of the inhibitor of apoptosis protein family, is upregulated in malignant tumors and exists in multiple alternative splicing variants. A novel targeted DNA-seq assay identified fourteen new survivin alternative splice variants, shedding light on their expression profiles and potential biological functions. Further studies will be crucial in understanding how survivin isoforms regulate cell proliferation and apoptosis in cancer, offering new diagnostic and therapeutic opportunities.
Article
Biochemistry & Molecular Biology
Leland B. Hyman, Clare R. Christopher, Philip A. Romero
Summary: Experimental methods focusing on individual properties of single cells have highlighted the significance of cell-to-cell variability in biological processes. SNAPD, a technology for single-cell nucleic acid profiling in droplets, provides a rapid, high-throughput approach for analyzing transcriptional markers in cell populations, allowing for cell classification and quantification in heterogeneous samples.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Virology
Tomoyuki Nabeshima, Junya Abe
Summary: Vitis coignetiae samples from northern Japan were found to be infected with multiple RNA viruses, with three newly identified virus species assigned to different genera based on sequence identity and phylogenetic analysis.
Article
Microbiology
Alina Matsvay, Marina Dyachkova, Ivan Mikhaylov, Daniil Kiselev, Anna Say, Valentina Burskaia, Ilya Artyushin, Kamil Khafizov, German Shipulin
Summary: The first complete genome sequence of a tern atadenovirus (TeAdV-1) is characterized in this study. TeAdV-1 shows unique gene structure and short inverted terminal repeats compared to known representatives of the Atadenovirus genus. Phylogenetic analysis confirms its taxonomic affiliation and suggests TeAdV-1 as a separate species.
Article
Virology
Anna Gladkikh, Vladimir Dedkov, Alena Sharova, Ekaterina Klyuchnikova, Valeriya Sbarzaglia, Olga Kanaeva, Tatyana Arbuzova, Nadezhda Tsyganova, Anna Popova, Edward Ramsay, Areg Totolian
Summary: This article describes the regional features of the COVID-19 pandemic in the Northwestern federal district of Russia in 2021. The study highlights the impact of vaccination on reducing severe cases and mortality rate, and analyzes the relationship between epidemiological indicators and locally circulating genetic variants.
Article
Biochemistry & Molecular Biology
Anna Gladkikh, Ekaterina Klyuchnikova, Polina Pavlova, Valeriya Sbarzaglia, Nadezhda Tsyganova, Margarita Popova, Tatiana Arbuzova, Alena Sharova, Edward Ramsay, Andrei Samoilov, Vladimir Dedkov, Areg Totolian
Summary: This study compares three different protocols for SARS-CoV-2 whole genome sequencing library construction and finds that the custom panel method has suitable results and predictable output for the epidemiological surveillance of SARS-CoV-2 variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Roman B. Gorodnichev, Maria A. Kornienko, Maja V. Malakhova, Dmitry A. Bespiatykh, Valentin A. Manuvera, Oksana V. Selezneva, Vladimir A. Veselovsky, Dmitry V. Bagrov, Marina V. Zaychikova, Veronika A. Osnach, Anna V. Shabalina, Oleg V. Goloshchapov, Julia A. Bespyatykh, Anna S. Dolgova, Egor A. Shitikov
Summary: To address the crisis of Klebsiella pneumoniae infections caused by drug-resistant strains, new approaches to antimicrobial therapy, such as using phages or phage derivatives, need to be developed. This study describes the first K. pneumoniae phage from the Zobellviridae family, which was isolated from river water and demonstrates lytic activity against K. pneumoniae strains with the KL20 capsule type. The phage's receptor-binding protein was identified as a polysaccharide depolymerase, showing promise for using depolymerases in antimicrobial therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Boris Y. Karas, Vera E. Sitnikova, Tatiana N. Nosenko, Vladimir G. Dedkov, Natalia A. Arsentieva, Natalia V. Gavrilenko, Ivan S. Moiseev, Areg A. Totolian, Andrey V. Kajava, Mayya V. Uspenskaya
Summary: The development of fast, cheap, and reliable methods for determining seroconversion is crucial. In the context of the COVID-19 pandemic, it is important to study the rate of immune layer formation in different populations and post-vaccination immunity. Attenuated total reflection Fourier transform infrared spectroscopy combined with machine learning was investigated for detecting seroconversion against SARS-CoV-2. The study found clear spectral differences in plasma samples of recovered COVID-19 patients and healthy donors, and achieved high accuracy in identifying specimens using this method.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Virology
Moufid Mhamadi, Idrissa Dieng, Anna S. Dolgova, Cheikh Talibouya Toure, Mignane Ndiaye, Moussa Moise Diagne, Babacar Faye, Anna S. Gladkikh, Vladimir G. Dedkov, Amadou Alpha Sall, Ousmane Faye, Oumar Faye
Summary: In this study, five African Orthobunyavirus viruses from different geographical regions were characterized. The results suggest that the five newly identified strains are Bunyamwera virus strains. Furthermore, two of the five strains were found to be recombinant strains, with fragments from Ngari and Bunyamwera strains. Further investigations are needed to understand the functional impact of these recombinations.
Correction
Virology
Anna Gladkikh, Vladimir Dedkov, Alena Sharova, Ekaterina Klyuchnikova, Valeriya Sbarzaglia, Olga Kanaeva, Tatyana Arbuzova, Nadezhda Tsyganova, Anna Popova, Edward Ramsay, Areg Totolian
Article
Chemistry, Analytical
Anastasiia Kirichenko, Ekaterina Bryushkova, Vladimir Dedkov, Anna Dolgova
Summary: The aim of this study was to develop a highly specific and easily standardized system for the detection of Nipah virus RNA. A Dz_NiV biosensor was designed based on a split catalytic core, and it was shown that only in the presence of synthetic target Nipah virus RNA, active 10-23 DNAzymes would assemble. This assembly was accompanied by stable fluorescence signals from cleaved fluorescent substrates, and a detection limit of 10 nM was achieved for the synthetic target RNA. The biosensor, constructed via a simple and easily modifiable process, may be used for the detection of other RNA viruses.
Article
Infectious Diseases
Aminata Badji, Mignane Ndiaye, Alioune Gaye, Idrissa Dieng, El Hadji Ndiaye, Anna S. Dolgova, Moufid Mhamadi, Babacar Diouf, Ibrahima Dia, Vladimir G. Dedkov, Oumar Faye, Mawlouth Diallo
Summary: This study investigated the diversity of tick species, tick infestation rates in livestock, and livestock infections with Crimean-Congo haemorrhagic fever virus (CCHFV) in different localities of Senegal. The results showed a high prevalence of tick infestation and the presence of CCHFV in tick samples. It confirms the active circulation of CCHFV in ticks and highlights the need for effective measures to control tick infestation in livestock and prevent future infections in humans.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Article
Virology
Areg A. Totolian, Viacheslav S. Smirnov, Alexei A. Krasnov, Edward S. Ramsay, Vladimir G. Dedkov, Anna Y. Popova
Summary: This study analyzed the relationship between the types of SARS-CoV-2 vaccines used in different countries and the COVID-19 incidence proportion. The results showed that the reported cases were strongly correlated with testing coverage and the proportions of vaccine types used. Countries that predominantly used vector and whole-virion vaccines had a significantly lower incidence proportion compared to countries that predominantly used mRNA vaccines.
Article
Agriculture, Dairy & Animal Science
Kristina Andreevna Kalinina, Vladimir Vladimirovich Besprozvannykh, Yulia Viktorovna Tatonova, Mikhail Yurievich Shchelkanov
Summary: The study on Echinochasmus pseudobeleocephalus n. sp. revealed that despite its morphological similarities to the European species Echinochasmus beleocephalus, the Far Eastern trematodes examined do not belong to the European species based on molecular data analysis. The analysis of phylogenetic relationships within the family Echinochasmidae supported the status of E. pseudobeleocephalus n. sp. as an independent species.
Article
Infectious Diseases
Anna S. Gladkikh, Thang M. Cao, Ekaterina O. Klyuchnikova, Manh H. Dao, Alena A. Sharova, Vasilina D. Melnichenko, Margarita R. Popova, Tatiana V. Arbuzova, Valeriya A. Sbarzaglia, Nadezhda A. Tsyganova, Edward Ramsay, Vladimir G. Dedkov
Summary: This study investigates the epidemiology and genetic diversity of COVID-19 in Southern Vietnam, revealing the main circulating variants and their distribution. The effectiveness of restrictive measures in Vietnam helped keep the incidence at a low level, but the relaxation of these measures and the spread of the Delta lineage contributed to a logarithmic increase in cases.
BMC INFECTIOUS DISEASES
(2023)
Article
Infectious Diseases
Harold Salant, Yaarit Nachum-Biala, Doni Zivotofsky, Tsachi Even Tzur, Gad Baneth
Summary: This study describes the presentation, clinical signs, parasitemia levels, laboratory findings and treatment of dogs infected with B. negevi. Treatment with imidocarb dipropionate was helpful for recovery from clinical disease but did not facilitate parasite elimination, and it is therefore recommended to treat canine B. negevi infection with the combination of atovaquone and azithromycin.
TICKS AND TICK-BORNE DISEASES
(2024)
Article
Infectious Diseases
Gervillien Arnold Malonga, Almoustapha Issiaka Maiga, Dimitry Moudiongui Mboungou Malanda, Mahamadou Saliou, Juth ece Private Malanda-Kiminou, Oumar Dolo, Anicet Luc Magloire Boumba, Alhassane Ba, Robert Murphy, Jean Felix Peko, Anne-Genevieve Marcelin, Vincent Calvez, Stephane Marot
Summary: A serological survey in sub-urban areas of the capital cities of Congo and Mali reveals human contact with Crimean-Congo hemorrhagic fever virus (CCHFV) associated with previously described CCHFV risk factors.
TICKS AND TICK-BORNE DISEASES
(2024)
Article
Infectious Diseases
Aleksander Wymazal, Sabina Nowak, Robert W. Myslajek, Anna Bajer, Renata Welc-Faleciak, Maciej Szewczyk, Iga Kwiatkowska, Kinga M. Stepniak, Michal Figura, Agnieszka Kloch
Summary: The wolf population in Central and Eastern Europe has been increasing, but their frequent contacts with humans make them a potential zoonotic reservoir. This study found a high prevalence of tick-borne pathogens in free-ranging wolves from Poland.
TICKS AND TICK-BORNE DISEASES
(2024)
Article
Infectious Diseases
Nannet D. Fabri, Hans Heesterbeek, Joris P. G. M. Cromsigt, Frauke Ecke, Hein Sprong, Lonneke Nijhuis, Tim R. Hofmeester, Nienke Hartemink
Summary: In many parts of the northern hemisphere, different species of deer, small mammals, and birds coexist and their composition can strongly influence the outbreak potential of tick-borne pathogens. This study investigates how the abundance and composition of vertebrate communities affect the basic reproduction number R0 of tick-borne pathogens, and shows that species composition plays a substantial role in the outbreak potential of tick-borne diseases.
TICKS AND TICK-BORNE DISEASES
(2024)
Article
Infectious Diseases
Lynn M. Osikowicz, Maria R. Rizzo, Andrias Hojgaard, Sarah E. Maes, Rebecca J. Eisen
Summary: This article describes the prevalence and diversity of Lyme disease in the United States. By using different detection methods, the authors found various species of spirochetes present in specific tick species, revealing the potential transmission of pathogens among ticks.
TICKS AND TICK-BORNE DISEASES
(2024)
Review
Infectious Diseases
El-Sayed El-Alfy, Ibrahim Abbas, Somaya Saleh, Rana Elseadawy, Ragab M. Fereig, Mohamed Abdo Rizk, Xuenan Xuan
Summary: Published data on tick-borne pathogens in camels worldwide have been collected, providing an overview of their global prevalence and species diversity. Evidence of natural infection of camels with certain tick-borne pathogens is limited, particularly because most of the camels were considered healthy at the time of sampling. More research is needed to understand the role of camels in maintaining and transmitting these pathogens.
TICKS AND TICK-BORNE DISEASES
(2024)
Article
Infectious Diseases
Saana Sipari, Mikko Kiljunen, Minna Nylund, Eva R. Kallio
Summary: This study introduces a stable isotope analysis method to directly identify tick breeding hosts by sampling field collected larvae. The results show that stable isotope signatures can reflect the diet of the breeding host of the mother tick.
TICKS AND TICK-BORNE DISEASES
(2024)
