Molecular ecology of microalgal viruses

A great amount of virus particles exist in natural waters. Each virion is considered to have its own ecological role, affecting the maintenance and fluctuation of aquatic ecosystems. We have been studying viruses infectious to micro-plankton, especially those infecting phytoplankton. Red tides are caused by drastic increase in abundance of plankton. We succeeded in elucidating that viral infection is one of the most important factors determining the dynamics and termination of algal blooms by means of field survey and molecular experiments. In addition, we demonstrated that the interrelationship between viruses and their hosts are highly complicated, and might be determined by the molecular-structural difference of viral capsids among distinct virus ecotypes. Furthermore, in the process of our investigation on various aquatic algal viruses, their importance as genetic sources has also been suggested. In order to deeply understand the mechanism of aquatic ecosystem, more intensive studies as for aquatic viruses are urgently required.     

Molecular characterization of adeno-associated viruses infecting children

Although adeno-associated virus (AAV) infection is common in humans, the biology of natural infection is poorly understood. Since it is likely that many primary AAV infections occur during childhood, we set out to characterize the frequency and complexity of circulating AAV isolates in fresh and archived frozen human pediatric tissues. Total cellular DNA was isolated from 175 tissue samples including freshly collected tonsils (n = 101) and archived frozen samples representing spleen (n = 21), lung (n = 16), muscle (n = 15), liver (n = 19), and heart (n = 3). Samples were screened for the presence of AAV and adenovirus sequences by PCR using degenerate primers. AAV DNA was detected in 7 of 101 (7%) tonsil samples and two of 74 other tissues (one spleen and one lung). Adenovirus sequences were identified in 19 of 101 tonsils (19%), but not in any other tissues. Complete capsid gene sequences were recovered from all nine AAV-positive tissues. Sequence analyses showed that eight of the capsid sequences were AAV2-like (approximately 98% amino acid identity), while the single spleen isolate was intermediate between serotypes 2 and 3. Comparison to the available AAV2 crystal structure revealed that the majority of the amino acid substitutions mapped to surface-exposed hypervariable domains. To further characterize the AAV capsid structure in these samples, we used a novel linear rolling-circle amplification method to amplify episomal AAV DNA and isolate infectious molecular clones from several human tissues. Serotype 2-like viruses were generated from these DNA clones and interestingly, failed to bind to a heparin sulfate column. Inspection of the capsid sequence from these two clones (and the other six AAV2-like isolates) revealed that they lacked arginine residues at positions 585 and 588 of the capsid protein, which are thought to be essential for interaction with the heparin sulfate proteoglycan coreceptor. These data provide a framework with which to explore wild-type AAV persistence in vivo and provide additional tools to further define the biodistribution and form of AAV in human tissues.     

Molecular biology of Hendra and Nipah viruses

The structure and genetic organization of Hendra and Nipah viruses places them in the subfamily Paramyxovirinae. However, low homology with other subfamily members and several novel biological and molecular features such as genome length and F(0 )cleavage site suggest classification in a new genus within the Paramyxovirinae.     

Approaches of the diagnosis of hepatitis viruses

Hepatitis virus infection occurs in close to a billion people worldwide at some point in their lifetimes. Hepatitis B and C viruses together account for infections in half a billion people and are considered the most carcinogenic of any known biological agent. The diagnostic approaches to detect hepatitis viruses are discussed.     

Molecular and biologic characteristics of attenuated rubella viruses

AIM: To study stability/variability of rubella virus vaccine strain "Orlov-B" during its adaptation to other tissue substrate. MATERIALS AND METHODS: Vaccine strains of rubella virus Wistar 27/3 and "Orlov-B" as well as wild type strains "Orlov-D" and "Lebedev" were used. Rhesus monkeys were used as laboratory animals. Standard virological, molecular and statistical methods were applied. RESULTS: Obtained as a result of adaptation to other tissue substrate - diploid human cell line M-22 - strain "Orlov-D" demonstrated stability on RCT40 sign in in vitro experiments. Comparative genotyping of "Orlov-B" and "Orlov-D" strains on gene E1 showed identity of nucleotide sequences of both variants. Genetic stability of virus on the gene coding the most immunogenic protein E1 was confirmed in vivo: the stable high immunogenic and protective activity of both "Orlov-B" and "Orlov- D" strains was demonstrated in experiments on rhesus macaques. CONCLUSION: New data on stability of attenuated rubella virus vaccine strains have practical significance for the development of new vaccines.     

侵染天南星科植物病毒的分子鉴定及其生态学研究

通过病毒粒子部分提纯和形态学观察,发现侵染我国南方天南星科植物的病毒主要有线状和球状两种形态．经病毒基因组序列分析确定线状病毒为芋花叶病毒(DsMV);经血清学反应和序列分析确定球状病毒为黄瓜花叶病毒(CMV)．CMV CP基因序列同源性分析的结果表明,侵染天南星科的CMV是相对独立的种内变异类型,归属于亚组L同时,CMV存在对天南星科植物的适应性变异．对采自我国海南、湖南、浙江、上海等地的126个天南星科植物样品进行RNA核酸斑点杂交检测,获得病毒检测结果。海南省样品DsMV的检出率为73．3％,CMV的检出率为46．7％;湖南省样品DsMV的检出率为100％,CMV的检出率为38.5％;浙江省样品DsMV的检出率为93．0％,CMV的检出率为7．0％;上海市样品DsMV的检出率为100％,尚没有检测到CMV,首次证实了自然条件下CMV作为天南星科植物主要病毒的存在,在我国南方地区,该病毒对天南星科植物的自然侵染受到气候、季节和寄主等生态因子的影响。DsMV则在天南星科植物上普遍存在。     

Molecular filtration for recovery of waterborne viruses of fish

The effectiveness of tangential flow filtration (TFF) for the recovery of infectious hematopoietic necrosis virus (IHNV) and infectious pancreatic necrosis virus (IPNV) from large volumes of water was evaluated. In laboratory studies, virus recovery from IHNV-seeded water following concentration by TFF was approximately 13%. However, the addition of 0.1 and 1% fetal bovine serum to deionized water stabilized the virus, increasing virus recoveries to 95%. The addition of 0.03 and 0.3% beef extract resulted in IHNV recoveries of 80 and 61%, respectively. Similar results were obtained with IPNV-seeded water. Field studies using the TFF procedure were conducted with water from areas where IHNV is endemic. IHNV was detected in effluent from an adult steelhead trout (Salmo gairdneri) holding pond at an estimated concentration of 1 PFU/5 ml of water. It was also detected at levels of 1 PFU/50 ml in water from a 2-m-diameter circular tank containing IHNV-infected steelhead trout fry. IHNV isolated in samples taken from the Metolius River was detected by TFF at estimated levels of 1 PFU/3 liters.     

Miniature RT-PCR system for diagnosis of RNA-based viruses

This paper presents an innovative portable chip-based RT-PCR system for amplification of specific nucleic acid and detection of RNA-based viruses. The miniature RT-PCR chip is fabricated using MEMS (Micro-electro-mechanical-system) techniques, and comprises a micro temperature control module and a PDMS (polydimethylsiloxane)-based microfluidic control module. The heating and sensing elements of temperature control module are both made of platinum and are located within the reaction chambers in order to generate a rapid and uniform thermal cycling. The microfluidic control module is capable of automating testing process with minimum human intervention. In this paper, the proposed miniature RT-PCR system is used to amplify and detect two RNA-based viruses, namely dengue virus type-2 and enterovirus 71 (EV 71). The experimental data confirm the ability of the system to perform a two-step RT-PCR process. The developed miniature system provides a crucial tool for the diagnosis of RNA-based viruses.     

Molecular evolution of the tick-borne encephalitis and Powassan viruses

Issues associated with newly emerging viruses, their genetic diversity, and viral evolution in modern environments are currently attracting growing attention. In this study, a phylogenetic analysis was performed and the evolution rate was evaluated for such pathogenic flaviviruses endemic to Russia as tick-borne encephalitis virus (TBEV) and Powassan virus (PV). The analysis involved 47 nucleotide sequences of the TBEV genome region encoding protein E and 17 sequences of the PV NS5-encoding region. The nucleotide substitution rate was estimated as 1.4 × 10⁻⁴ and 5.4 × 10⁻⁵ substitutions per site per year for the E protein-encoding region of the TBEV genome and for the NS5 genome region of PV, respectively. The ratio of non-synonymous to synonymous nucleotide substitutions (dN/dS) in viral sequences was calculated as 0.049 for TBEV and 0.098 for PV. The highest dN/dS values of 0.201–0.220 were found in the subcluster of Russian and Canadian PV strains, and the lowest value of 0.024 was observed in the cluster of Russian and Chinese strains of the Far Eastern TBEV genotype. Evaluation of time intervals between the events of viral evolution showed that the European subtype of TBEV diverged from the common TBEV ancestor approximately 2750 years ago, while the Siberian and Far Eastern subtypes emerged approximately 2250 years ago. The PV was introduced into its natural foci of the Russian Primorskii krai only approximately 70 years ago; these strains were very close to Canadian PV strains. The pattern of PV evolution in North America was similar to the evolution of the Siberian and Far Eastern TBEV subtypes in Asia. The moments of divergence between major genetic groups of TBEV and PV coincide with historical periods of climate warming and cooling, suggesting that climate change was a key factor in the evolution of flaviviruses in past millennia.