Basic concepts for the realization of adaptive tuned vibration absorbers [15].
\r\n\tWe accept scientific papers which can be presented as original research papers and review papers. The required length of the full chapters is 10-20 pages and the chapters should be original works (not republished).
\r\n\tAs a self-contained collection of scholarly papers, the book will target an audience of practicing researchers, academics, Ph.D. students and other scientists. Since it will be published as an Open Access publication, it will allow unrestricted online access to chapters with no reading or subscription fees.
Tuned vibration absorbers (TVA) and tuned mass dampers (TMD) are used since the beginning of the twentieth century to reduce disturbing vibrations [1]. Basically, this method uses an inertial mass that is elastically coupled to the vibrating host structure [2]. This resonant spring-mass system can be tuned to certain resonance frequencies of the host structure (Figure 1). Then, the device is usually referred to as tuned mass damper (TMD), which is frequently applied to elastic infrastructure objects like towers or bridges. For large objects, several TMDs are distributed among the structure [3].
Generic vibration control set up with a passive TVA.
When the oscillator is tuned to a harmonic disturbance frequency, it is called tuned vibration absorber or vibration neutralizer [4]. Potential applications range from Optical Disc Drives, using an absorber mass of about 40 g [5] to vibrations of ship engines, requiring over 10 tons of oscillating mass [6]. The performance of these devices is mainly limited by the precise tuning to the target frequency. If a certain bandwidth is to be tackled, a high inertial mass has to be used, which usually prevents the application of TVAs in such cases.
In this chapter, several improvements to the traditional passive vibration absorber are introduced that have been made over the last decades, ranging from semi-active or adaptive to active dynamic systems (Figure 2).
Vibration control systems—passive, adaptive, and active.
In the next section, the basics of the different vibration control systems are summarized and examples for realized systems are given. In the last two sections, a system that can be used for adaptive and active vibration control methods is presented and the application to an elastic vibrating structure is investigated.
To illustrate the working principle of a passive TVA, the generic example from Figure 1 is studied. The vibrating host structure is represented by a mechanical mobility
The neutralizer is described by its mass
The connection of both systems is represented by:
Obviously, the mobility transfer function has a pair of conjugated complex zeros that match the resonance of the TVA. If the TVA is fully undamped, the mobility of the system at the resonance of the TVA turns to zero, i.e., complete cancellation of vibrations. It can be shown that the performance of the passive TVA is directly proportional to the mass ratio
Accelerance of a 1 kg mass with a TVA tuned to 50 Hz (left); and a 50 Hz mass-spring-system with a TMD (right).
When the relevant frequency range of the host structure contains a resonance, the mobility formulation for
where
Adaptive tuned vibration absorbers have been proposed to overcome this weakness of passive TVAs. By using actuating elements, the resonance frequency of the absorber can be adjusted. In turn, an adaptive TVA can be designed with a smaller inertial mass [10]. In the last decades, numerous concepts have been investigated [11, 12, 13, 14], but the designs can be traced back to some basic principles of adaptation [15] (Table 1).
Basic concepts for the realization of adaptive tuned vibration absorbers [15].
A common approach to alter the resonance frequency of a mechanical oscillator is the adjustment of the mechanical stiffness via the geometry of the spring element; for instance, by moving the inertial mass on a bending beam, which adjusts the effective beam length, as demonstrated for vibration control at ship engines [16]. The most advanced concept is the application of an active dynamic control loop for the adjustment of the resonance frequency. The principle can be briefly explained with a TVA represented by a simple mechanical oscillator (Figure 4), which can be excited by an integrated actuation force
Feedback control to adjust the resonance frequency.
where d is the damping coefficient and k is the stiffness of the oscillator. The feedback loop is closed by using the acceleration
is applied, Eq. (5) can be reformulated to:
Thus, by feeding back forces proportional to the acceleration of the mass, the effective mass of the system can be altered. Similarly, by using an integral controller, a velocity feedback loop can be realized to adjust the damping of the system. In order to enhance the vibration absorption effect, active removal of system damping can be considered [8]. Also, a further integration can be implemented in order to obtain the position of the mass. By feeding back this signal, the stiffness of the absorber can be adjusted [17].
The frequency range that can be covered by the adaptation mechanism is a key performance parameter for an adaptive TVA. As studied in [15], the active control system is limited by the stability margins of the control loop. These margins are mainly defined by the inherent phase lag of many signal processing components, but also by the geometrical arrangement of the sensor and the actuator.
By applying an electrical shunt circuit to the piezoelectric element, the stiffness can be varied without using a sensor component [18]. By using active circuits to realize negative capacitances, a broad adaptation frequency range can be realized. However, the active circuits have to be designed with respect to the high voltages that occur at the piezoelectric elements, which still remain a challenge [19].
Most versatile are active vibration control systems using dynamic actuation [20]. In this case, the force is generated by an inertial mass, which is excited by an active element. To enable a broad band actuation, the inertial mass is usually mounted with soft springs to the host structure, which causes a resonance in the system. Thus, the resulting force exciting the host structure exhibits a dynamic behavior, and the inertial mass actuator can be treated as a constant force generator only when being driven well above the resonance frequency. The frequency response of an inertial mass actuator with a mass m, resonance frequency
A simple example of an inertial mass actuator with a resonance frequency of 10 Hz is shown in Figure 5.
Basic model of an inertial mass actuator and its frequency response function.
Inertial mass actuators have been used for active vibration control in cars [21], trains [22], or building floors [23]. For very large structure like wind turbines actuation for the first dominating mode with a large force is required. Then, the concepts of the TMD and the inertial mass actuator converge to the active tuned mass damper [24]. Recent developments also treat non-linearities in the host structures by extending the theoretical considerations for tuning of the system and the control law [26].
If the host structure is a non-linearly oscillating system, extended considerations are necessary in the design of those systems.
Mostly, electrodynamic actuation is preferred, because it enables a straightforward system design for a low resonance frequency.
Still, some work is dedicated to the integration of piezoelectric actuation. Since piezoelectric actuators possess very high resonance frequencies, proper designs have to be found that make such stiff actuators applicable for an oscillator with a low resonance frequency. However, the advantage of using piezoelectric actuation is the capability of the piezoelectric actuators to function as structural elements and partly carry the inertial mass, enabling compact systems with less movable parts.
Piezoelectric TVA systems can also be used in a hybrid mode. While being tuned to one resonance frequency, they can be actively driven at higher frequencies and work as inertial mass actuators [25].
When the inertial mass actuator is driven well above its resonance frequency, it represents an ideal force generator. Thus, arbitrary active vibration control methods are applicable. Two basic concepts should be briefly repeated (Figure 6).
Feedback and feedforward control of an inertial mass actuator.
The feedback control system (Figure 6, left) is often applied to implement skyhook damping or other concepts which aim at influencing the characteristics of the host structure. Further details on control methods like velocity feedback or positive position feedback can be found in [27].
Feedforward control is usually implemented with adaptive digital filters [28]. The main field of application for active control of vibrations is narrowband or harmonic disturbance forces exciting the host structure. To compensate those, a reference signal with the same frequency is generated and filtered in order to match the phase angle and amplitude for an optimal suppression of the disturbance.
To illustrate the characteristics of the introduced vibration control systems, the basic example (Figure 1) is used once more [7]. As disturbance, a harmonic excitation force of 1 N with slowly sweeping frequency between 40 and 60 Hz is considered. As a performance indicator, the RMS of the acceleration of the host structure is used. A passive TVA, an adaptive TVA, and an active system with an inertial mass actuator driven by an adaptive FXLMS algorithm are compared. The mechanical parameters of the different devices are summarized in (Table 2).
System | Passive | Adaptive | Active |
---|---|---|---|
Resonance frequency [Hz] | 50 | 50 (+/ 5Hz adaptation range) | 10 |
Mass [kg] | 0.5 | 0.1 | 0.1 |
Damping coefficient [−] | 0.01 | 0.01 | 0.03 |
Parameters of the compared vibration control systems (from [7]).
The result summarizing numerical simulations of all three configurations is presented in Figure 7. Obviously, the active system shows the best performance using just a moderate additional mass, however at the expense of a complex system set up using digital signal processing and a dynamic actuation, which can cause issues when scaling the system for vibration control of very large structures. The adaptive and the passive vibration absorber cause similar vibration reduction; however, the passive system uses a five times higher mass than the adaptive (Figure 7).
RMS acceleration of a vibrating host structure with different vibration control systems.
Summarizing, the solution for an optimal vibration control system depends to the given vibration problem and the respective requirements and restrictions like allowed amount of added mass, possibility for energy supply, or the characteristics of the disturbance (Table 3).
System | Passive | Adaptive | Active |
---|---|---|---|
Vibration reduction | Medium | Medium | High |
System complexity | Low | Medium | High |
Energy supply | None | During adaptation (depending to the concept) | Continuously |
Added mass | High | Low | Low |
Bandwidth | Low | Medium | High |
Comparison of passive, adaptive and active control systems.
This motivated the development of a vibration control system that can be used to realize passive, adaptive, and active vibration control systems, which will be introduced in the next section. This might be especially useful for prototyping purposes when an evaluation of different system concepts is needed. Furthermore, the system can be used to implement hybrid systems that combine passive, adaptive and active control.
The vibration control device introduced here utilizes piezoelectric actuators due to their ability to carry high static mechanical loads while providing static and dynamic actuation forces. This should enable a multifunctional system. The design follows the well-known mechanical oscillator consisting of a bending beam as spring element and a tip mass. In parallel to the bending beam, two piezoelectric stack actuators are connecting the base and the tip mass (Figure 6).
In phase static actuation or static preloads by the screws apply tensile forces to the bending beam, which alters the stiffness and enables adaptation of the resonance frequency. Alternatively, out-of-phase dynamic operation of the piezoelectric actuators generates bending movements of the beam, which causes transverse dynamic forces at the base of the absorber. More details on the design can be found in [29, 30].
The adaptation by static preloading can be described by the differential equation for the axially loaded Euler-Bernoulli beam:
Here, additional beam stiffness is generated by the tensile force
Thus, for the mechanical preloading the force is evaluated by:
Hereby, the displacement of the screw
The product of the electro-mechanical constant
To solve the aforementioned differential Eq. (9), an adequate trial function is chosen and the boundary conditions are defined. From this, follows the system of equations to be solved to gain the constants of the trial function [30].
Also, the effective transverse stiffness of the beam
Mechanical model of the vibration control device.
Considering a tip mass at position
As mentioned above, the piezo actuators can be used in dynamic operation (out of phase) to generate transverse forces. This enables the system to work as an inertial mass actuator at frequencies above its first natural frequency. To estimate the characteristics of the force
In order to include the geometry of the mass, the distance from the end of the beam to the center of gravity of the mass is defined by
The free stroke at this point due to the actuator force
In a similar manner, the stiffness
Hence, considering a tip mass
According to the sketch (Figure 9) a prototype was built that is shown in Figure 10.
Design of the vibration control device.
Implemented prototype of the adaptive vibration absorber/inertial mass actuator.
A thin beam is clamped between two steel blocks, which represents the mounting of the inertial mass actuator. The width of the beam is large compared to its length to prevent torsion. The whole pattern of the mounting is suited for a connection to a shaker, a heavy breadboard or the test structure addressed subsequently. On the other side of the beam, the inertial mass is attached. Two simple steel blocks are used to realize the clamping of the beam, which can be changed easily for experiments. For assembling the piezoelectric actuators the beam is equipped with slotted holes. Monolithic multilayer actuators by CeramTec with a base area of
Quantity | Symbol | Value | Unit |
---|---|---|---|
Beam | |||
Length | l | 41.5 | mm |
Width | b | 60 | mm |
Thickness | d | 0.5 | mm |
Young’s modulus | E | 2.2∙1011 | N/m−2 |
Mass | |||
Mass | m | 1.078 | kg |
Actuator | |||
Stiffness | kA | 42∙106 | Nm−1 |
Max. block force | FB,max. | 2000 | N |
Parameters of the actuator systems.
To analyze the dynamic characteristics of the inertial mass actuator, tests were performed. The whole actuator was mounted to a rigid, heavy base plate which can be treated as an infinitely small mechanical admittance in the considered frequency range (Figure 11). The tip mass was instrumented with an accelerometer and excited by an impulse hammer in order to gain the resonance frequencies by evaluating the respective frequency response functions depending on both conditions—mechanical and electrical preload.
Test set up for the dynamic analysis of the adaptive vibration absorber.
Exemplarily the frequency responses for electrical tuning are depicted in Figure 12. Obviously, the effect of preloading is significant and has to be taken into account. The analytical model which is introduced in the preceding section is validated by the experimental results. Some differences between experimental and analytical frequency responses can be observed for very low DC voltages, where the absorber does not exhibit perfect characteristics of a single-degree-of-freedom oscillator. This could be caused by a poor mechanical coupling between the piezo stacks and the structure when nearly no pre-load is applied. For very high pre-loads around 140 V, the model predicts higher tuning effects than measured in the experiment (Figure 12). In this case, the analytical model might not perfectly predict the contact characteristics of the ball joints, which can be non-linear for high mechanical loads.
Frequency response functions of the adaptive vibration absorber for different DC voltages (electrical tuning) - simulation results (left) and experimental results (right).
The comparison of the measured and the calculated resonance frequencies is shown in Figure 13 for both cases (mechanical and electrical tuning). By mechanical preloading a larger frequency shift compared to electrical preloading is realized. This can be explained by the limited blocking force of the piezo actuators. However, a good match between the experimental values for the resonance frequencies and the calculated results is observed for both cases.
Variation of resonance frequency by mechanical (left) and electrical preloading (right).
The performance of both tuning concepts is comparable to adaptive absorbers, which use motors for the variation of the spring geometry investigated in preliminary work [15].
For the evaluation active force generated by the device, the piezoelectric actuators were driven with a swept sine signal by the analyzer. A simple analogue circuit realizes an out of phase driving signal for one of the actuators in order to excite the bending mode of the actuator system to produce transverse forces, and the acceleration of the tip mass was measured (Figure 14). Since the mounting can be assumed to be rigid, the block force can be directly derived from the acceleration and the mass.
Test set up for the measurement of the dynamic block force of the actuator.
For this test, different preloads from
Calculation (left) and measurement (right) of the dynamic block force of the actuator.
In the frequency range above the first resonance and
To evaluate the performance in an active vibration control system, the actuator was mounted to a lightweight truss structure (Figure 16). The actuator was instrumented with accelerometers at its base and at the inertial mass.
Test set up for the active control experiment (left) and detail of the actuator instrumentation (right).
In the first step, the adaptive absorber was tuned by mechanical pre-load to a structural mode, which resulted in a vibration absorption effect at
Tuning of the adaptive absorber to the first elastic mode of the truss.
In the next step, the active control system was set up and tuned. Two control loops were implemented successively and connected (Figure 18). First, an active velocity feedback loop
Block diagram of the control system.
The cut-off frequency
Control results for the truss structure.
Here,
Since the actuator is not symmetric, a bending moment is exciting at its base additional to the transverse force. This results in lowering of a higher resonance frequency from
Adaptive and active vibration control systems can outperform passive systems in terms of additional mass and vibration reduction. However, the different systems cause an increase of system complexity and need for additional power supply. Thus, alternative feasible approaches should be evaluated to find the optimal solution for a given vibration problem. To enable experimental prototyping, a design for a TVA has been introduced, that can be used for passive, adaptive, and active vibration control. It has also been shown that an advantage of such an integrated system can be applied to hybrid systems that work as passive absorbers in the lower frequency range and a can excite active forces at higher frequencies.
Epstein–Barr virus (EBV), a ubiquitous human herpesvirus discovered in 1964 is classified as a group I carcinogen by the International Agency for Research on Cancer (IARC), since the latent infection by EBV has been estimated to be responsible for 200,000 cancer cases worldwide [1], including Burkitt lymphoma, Hodgkin lymphoma, NK/T cell lymphoma (NKTCL), nasopharyngeal carcinoma (NPC), and a subset of gastric carcinomas. It has been shown that viruses can contribute to the biology of multistep oncogenesis and are implicated in many of the hallmarks of cancer [2]. Notably, the discovery of links between viral infection and cancer types has provided actionable opportunities, such as the use of human papilloma virus (HPV) vaccines as a preventive measure, to reduce the global impact of cancer. However, until now, approved vaccines for EBV have not been available.
\nEBV has a double stranded DNA genome comprised of approximately 172 kilobases. The expression products cover at least 86 proteins and 46 functional small-untranslated RNAs [3, 4, 5]. EBV has two distinct life cycles: latency and lytic replication. During latency, viral genomes only express a limited number of latent proteins (EBV-determined nuclear antigen 1 (EBNA1), 2, 3A, 3B, and 3C and EBNA leader protein (EBNA-LP); latent membrane protein 1 (LMP1) and LMP2 (which encodes two isoforms, LMP2A and LMP2B)), noncoding EBV-encoded RNAs (EBER1 and EBER2), and viral miRNAs (BHRF1-miRNA and BART-miRNA). EBV latency is categorized as three latency types (latency I–III). EBV genomes in type-I latency are known to express EBNA1 and EBER. EBV genomes in type-II latency are known to express more genes such as EBNA-LP, LMP1, LMP2A, and LMP2B. EBV genomes in type-III latency are known to express most restricted latent genes including EBNA2, EBNA3A, EBNA3B, and EBNA3C. Lytic genes encode viral transcription factors (e.g., BZLF1), a viral DNA polymerase (BALF5) and associated factors, and viral glycoproteins (e.g., gp350/220 and gp110) and structural proteins (capsid and tegument proteins).
\nSouthern blot of restriction fragment length polymorphisms was first used to detect EBV strain variation, and Sanger sequencing of certain specific viral genes (e.g., EBNA1 and LMP1) was later developed to detect sequence diversity. Now, on the basis of high-throughput sequencing, genome-wide analysis is becoming possible.
\nPrior to 2013, EBV whole genome sequences available from GenBank were limited to less than 10 strains (B95-8, EBV-WT, GD1, AG876, GD2, HKNPC1, Akata, and Mutu). The prototypic type 1 EBV strain B95-8 was the first complete genome sequenced from an individual with infectious mononucleosis using a conventional strategy (i.e., subcloning followed by Sanger sequencing) [6]. Subsequently, a more representative type 1 EBV reference genome, human herpesvirus 4 complete wild type genome, was constructed by using B95-8 as the backbone with an 11-kb deletion segment provided by the Raji sequences (named EBV-WT) [7]. AG876 was the unique complete type 2 EBV sequence from a Ghanaian case of Burkitt lymphoma [8]. Akata and Mutu were sequenced from Burkitt lymphoma cell lines from a Japanese patient and a Kenyan patient, respectively [9]. GD1 [10], GD2 [11] and HKNPC1 [12] were isolated from NPC patients.
\nSince 2014, a new technology named Hybrid Capture (Figure 1), has marked a new era of EBV genome sequencing. Using the method of target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, de novo assembly, and joining of contigs can yield complete EBV genomes. The development of high-throughput sequencing technologies enabled sequencing of EBV genomes derived from a wide variety of clinical samples, such as tumor biopsy samples [13]. The number of available EBV sequences is increasing exponentially and up to now, more than 500 EBV genomes have been sequenced from a variety of human malignancies, including NPC, lymphoma, gastric cancer, and lung cancer, as well as from healthy carriers [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]. Progress has made it possible that the population-based case–control studies of EBV strain variation in EBV-related cancer patients as compared with the healthy population and a comprehensive survey of EBV integration in a variety of human malignancies can be effectively conducted [20, 25, 26, 27]. These developments have revealed that various EBV strains are differentially distributed throughout the world, and that the behavior of cancer-derived EBV strains is different from that of the prototype EBV strain of noncancerous origin.
\nComplete workflow for EBV DNA capture and sequencing.
Hence, the genome-wide characteristics of EBV are essential to assess the diversity of strains isolated from EBV-related malignancies. Meanwhile, understanding the pattern of EBV sequence variation is important for knowing whether there is a disease-related strain-specific or geographic regional variation of EBV strain, and might provide important implications for the development of effective prophylactic and therapeutic vaccine approaches targeting the personalized or geographic-specific EBV antigens in these aggressive diseases.
\nIn this chapter, EBV genomes reviewed are from three common EBV-related cancers in Asia, including NPC, EBV-associated gastric carcinoma (EBVaGC), and NKTCL. The EBV strains include GD1 [10], GD2 [11], HKNPC1 [12], HKNPC2-HKNPC9 [14], EBVaGC1-EBVaGC9 [17], GDGC1-GDGC2 [21], NKTCL-EBV1-NKTCL-EBV8 [23], NKTCL-SC01-NKTCL-SC15 and NKTCL-SG01-NKTCL-SG12 [24] (Table 1).
\nEBV strain | \nOrigin | \nDisease | \nYear | \nRefs | \n
---|---|---|---|---|
GD1 | \nGuangdong, China | \nNPC | \n2005 | \n[10] | \n
GD2 | \nGuangdong, China | \nNPC | \n2011 | \n[11] | \n
HKNPC1 | \nHong Kong, China | \nNPC | \n2012 | \n[12] | \n
HKNPC2-HKNPC9 | \nHong Kong, China | \nNPC | \n2014 | \n[14] | \n
EBVaGC1-EBVaGC9 | \nBeijing, China | \nEBVaGC | \n2016 | \n[17] | \n
GDGC1-GDGC2 | \nGuangdong, China | \nEBVaGC | \n2018 | \n[21] | \n
NKTCL-EBV1-NKTCL-EBV8 | \nBeijing, China | \nNKTCL | \n2019 | \n[23] | \n
NKTCL-SC01-NKTCL-SC15 | \n15 from Southern China, 12 from Singapore | \nNKTCL | \n2019 | \n[24] | \n
NKTCL-SG01-NKTCL-SG12 | \n
EBV genomes reviewed in this chapter
NPC, an EBV-associated epithelial carcinoma, has a unique geographical distribution [28]. A recent World Health Organization (WHO) report estimated that there were around 130,000 new NPC cases worldwide in 2018 [29]. Rare in most of the world, NPC is particularly prevalent in South China and Southeast Asia [30]. In Hong Kong and Guangdong in South China, NPC incidence is as high as 12.8–25.0/100,000 per year [28, 29]. The cause of NPC endemicity remains unknown.
\nMany studies have shown that EBV genome is present in almost all endemic NPC tumors with a unique pattern of virus latent gene expression, suggesting that EBV plays an important role in the tumorigenesis of NPC [31]. Whole genome sequencing is useful for us to understand genomic characterization and divergence. Here, we mainly focus on 11 mostly available full-length genomes of NPC.
\nGD1 (Guangdong strain 1), the first NPC-derived EBV strain with full-length sequences determined using PCR amplification and sub-cloning followed by conventional Sanger sequencing technology, was analyzed from established a lymphoblastoid cell line (LCL) from umbilical cord blood mononuclear cells transformed by saliva virus from a Cantonese NPC patient in 2005 [10]. The entire GD1 sequence is 171,656 bp in length and GD1 belongs to type 1 strain. Many sequence variations in GD1 compared to prototypical strain B95-8 were detected, including 43 deletion sites, 44 insertion sites, and 1413 point mutations. Furthermore, the frequency of some GD1 mutations in Cantonese NPC patients was evaluated, such as a 30-bp deletion in the C terminus of LMP1, and the V-Val subtypes of EBNA1. The results suggested that GD1 is highly representative of the EBV strains isolated from NPC patients in Guangdong, China, an area with the highest incidence of NPC in the world.
\nWith the invention of next-generation sequencing (NGS) systems, it is possible to determine genome-wide sequences and the viral clonality of EBV strains by direct sequencing of EBV genomes in clinical tumors in a time- and cost-effective manner. GD2 with 164,701 bp long was directly sequenced using the Illumina (Solexa) platform, and successfully assembled from an NPC tumor of a patient in Guangdong province, a region in China by the same group who determined GD1 [11]. GD2 was closely related to GD1 by sequence and phylogenetic analyses. The sequence similarities between GD2 and GD1 were 98.76%. GD2 and GD1 shared 505 common single-nucleotide variations (SNVs), including most SNVs in the coding regions (348 [68.91%] SNVs) and seven insertion and deletions (indels). From a comparison with the EBV-WT reference genome, a total of 927 SNVs and 160 indels with genome-wide distribution were found in the GD2 genome. The results revealed that NGS allows the characterization of genome-wide variations of EBV in clinical tumors and provides evidence of monoclonal expansion of EBV in vivo.
\nBecause of the relatively small quantity of viral DNA present in the tumor sample, next-generation sequencing total cellular and viral DNA in a sample is costly and inefficient, and may limit the generation of the high read depth necessary to make high confident base calls of the viral genome. Using target enrichment technology could increase the relative amount of viral DNA. Kwok et al. reported an approach of PCR enrichment (Amplicon Sequencing) followed by sequencing the amplified products on the Illumina Genome Analyzer IIx platform to determine the genome sequence of an EBV isolate from NPC tumor of a Chinese patient in Hong Kong, designated as HKNPC1 [12]. HKNPC1 is approximately 171,549 bp, and contains 1589 SNVs and 132 indels in comparison to the reference EBV-WT sequence. Non-synonymous SNVs were mainly found in the latent, tegument and glycoprotein genes. The same point mutations were found in glycoprotein (BLLF1 and BALF4) genes of GD1, GD2 and HKNPC1 strains and might affect cell type specific binding. The results showed that whole genome sequencing of EBV in NPC may facilitate discovery of previously unknown variations of pathogenic significance.
\nThe group of Kwok and colleagues established a complete sequencing workflow comprising target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, de novo assembly, and joining of contigs by Sanger sequencing to yield whole EBV genomes. The sequences of eight NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated HKNPC2 to HKNPC9, were then determined in the same geographic location in order to reveal their sequence diversity [14]. The eight NPC-EBV genome sizes estimated based on the reference EBV-WT sequence ranged from 170,062 bp (HKNPC2) to 171,556 bp (HKNPC3 and -6). A total of 1736 variations were found, including 1601 substitutions, 64 insertions, and 71 deletions, compared to the reference EBV-WT genome. Furthermore, genes encoding latent, early lytic, and tegument proteins and glycoproteins were found to contain nonsynonymous mutations of potential biological significance. Thus, much greater sequence diversity among EBV isolates derived from NPC biopsy specimens is demonstrated on a whole-genome level through a complete sequencing workflow.
\nObtaining whole-genome sequence information for more clinical EBV isolates, with good representation of the EBV repertoire in tumors, could help to address that hypothesis and uncover the pathogenic subtypes of EBV in NPC tumorigenesis. A case–control (62 NPC patients and 142 population carriers) study of NPC in Hong Kong has identified high-risk EBV subtypes with polymorphisms in the EBV-encoded small RNA (EBER) locus [26]. A recent study published in Nature Genetics entitled ‘Genome sequencing analysis identifies high-risk Epstein–Barr virus subtypes for nasopharyngeal carcinoma’ by Xu et al. used large-scale EBV whole-genome sequencing to examine EBV subtypes in an attempt to explain the unique NPC endemicity in South China [25]. Through EBV genomes from 156 NPC cases and 47 controls and two-stage association study, they identified two non-synonymous EBV variants within the BALF2 gene (BamHIA leftward reading frame 2 encoding a single strand DNA binding protein associated with EBV replication) strongly associated with the risk of NPC (odds ratio [OR] = 8.69 for SNP162476_C and OR = 6.14 for SNP163364_T). The cumulative effects of these variants contribute to 83% of the overall risk of NPC in southern China. These studies confirmed the critical role of EBV infection in the pathogenesis of NPC and provided an explanation for the striking epidemiological distribution of this tumor in South China.
\nEBVaGC has been recognized as a distinct subset of gastric carcinoma, accounting for about 10% of total gastric carcinomas [32, 33, 34, 35]. The monoclonal presence of the virus was uniformly distributed in malignant cells of EBV-positive tumors but not observed in the surrounding normal epithelial cells, providing strong evidence to support the role of EBV as an etiologic agent [32, 33]. However, the exact role of EBV in the development and progression of this specific type of gastric carcinoma is not yet clear.
\nProgress has been made in understanding the full spectrum of diversity existent within the EBV genome from EBVaGC clinical tumor samples, since the NGS technology has been developed. Here, 11 EBV strains from primary EBVaGC biopsy samples were included.
\nOur group reported the first genome-wide view of sequence variation of EBV isolated from primary EBVaGC biopsy specimens in 2016 [17]. We used the method of target enrichment of EBV DNA by hybridization, followed by next-generation sequencing. EBV probes were designed according to full-length genome of six available EBV strains, including EBV-WT, B95-8, AG876, GD1, GD2, and HKNPC1. According to the value of coverage of the target region, all DNA sequence generated from GC-EBV strains most resembled GD1. Thus, GD1 was used as the reference EBV genome in our study. De novo assembly was performed for nine sequenced GC-EBV strains. Finally, nine EBVaGC genomes were successfully sequenced, designated EBVaGC1 to EBVaGC9. The genome sizes, estimated based on the reference GD1 sequence, ranged from 171,612 bp (EBVaGC6) to 171,957 bp (EBVaGC1).
\nWhole-genome sequencing of EBV enabled the comparison and thus the determination of EBV variations at the genome level. In our study, 961 variations were observed in the EBVaGC1 to 9 genomes in comparison to the reference GD1, including 919 substitutions, 23 insertions, and 19 deletions. Both latent genes and genes encoding tegument proteins in nine GC-EBV genomes were found to harbor the majority of nonsynonymous mutations, accounting for 58.4% (EBVaGC8) to 84.3% (EBVaGC3) of all nonsynonymous mutations detected for each genome.
\nEBNA1 is essential for maintenance of the EBV episome in latently infected cells and is the only EBV antigen that is consistently expressed in all EBV associated malignancies [36]. Based on the amino acid changes at position 487 in the COOH-terminal region in EBNA1 relative to B95-8 (P-ala), V-val was the most common subtype, accounting for 77.7% of nine GC-EBV strains, followed by P-thrV, accounting for 22.3%. Multiple results showed that V-val is the dominant subtype in Asian regions studies, not only in EBVaGC but also in NPC and healthy donors, while V-val subtype was rarely found in Africa, Europe, and America irrespective of source (lymphoma, NPC, EBVaGC, or healthy donors) [37, 38, 39], indicating that polymorphism of EBNA1 subtypes has geographic differences but is not tumor-specific. Apart from changes in the C-terminus, EBNA1 has variations in the N-terminus. Interestingly, we identified two interstrain recombinants at the EBNA1 locus, which provided a further mechanism for the generation of diversity. EBNA1 N-terminus changes have revealed additional variants that were not simply classified based on the signature amino acid residue 487 in the C-terminus as widely used previously. The N-terminus changes reinforce the need to evaluate the EBV genome more comprehensively in order to characterize the full extent of EBV genetic diversity. A comprehensive investigation into the functional and immunological impact of the naturally occurred EBNA1 sequence variations and interstrain recombinants is required to evaluate their possible significance, which may also be helpful for clarifying the association of EBNA1 subtypes and EBVaGC.
\nIn 2018, NGS was employed to determine the EBV genomes from two EBVaGC specimens, designated as GDGC1 and GDGC2, from Guangdong, China, an endemic area of NPC [21]. Due to the presence of the much more abundant cellular genomic DNA in the DNA preparations, the number of reads belonging to EBV was low, accounting for only 0.02–0.23% of the total reads. However, since the original data were sufficient, the average sequencing depth for genomes GDGC1 and GDGC2 was ~73x and ~24x, respectively, which was sufficient for further analysis. The genome sizes, estimated based on the reference EBV-WT genome sequence, were as follows: GDGC1 (169,611 bp) and GDGC2 (171,299 bp).
\nThe authors reported that a total of 1815 SNPs (146 indels) and 1519 SNPs (106 indels) were found in GDGC1 and GDGC2, respectively, compared with the reference EBV-WT genome. Among these, 1229 SNPs (66 indels) and 1076 SNPs (54 indels) were located in the coding regions for GDGC1 and GDGC2, respectively, while the remaining variations were found in the non-coding regions. Consistent with previous reports [17], there is clear evidence for a higher frequency of SNPs in latent genes, followed by the genes encoding tegument and membrane glycoproteins. In contrast to the frequent mutations that occurred in latent genes, the sequences of promoters and ncRNAs were investigated to be strictly conserved. A few point mutations were found in the sequences of Cp, Qp, Fp and LMP2Ap, and only scattered mutations could be identified in certain ncRNA sequences. Promoters and EBV-generated ncRNAs play important roles in regulating viral processes and in mediating host-virus interactions. Thus, a detailed EBV genome-wide analysis of EBVaGC from Guangdong was performed, which would be helpful for further understanding of the relationship between EBV genomic variation and EBVaGC carcinogenesis.
\nThe features of the disease and geographically associated EBV genetic variation as well as the roles that the variation plays in carcinogenesis and evolution remain unclear. A recent study sequenced 95 geographically distinct EBV isolates from EBVaGC biopsies (n = 41) and saliva of healthy donors (n = 54) to detect variants and genes associated with gastric carcinoma from a genome-wide spectrum [20]. BRLF1, BBRF3, and BBLF2/BBLF3 genes had significant associations with gastric carcinoma. LMP1 and BNLF2a genes were strongly geographically associated genes in EBV. The results provided insights into the genetic basis of oncogenic EBV for gastric carcinoma, and the genetic variants associated with gastric carcinoma could serve as biomarkers for oncogenic EBV.
\nExtranodal NKTCL, a rare type of non-Hodgkin lymphoma, is characterized by the presence of EBV in virtually all cases, irrespective of their ethnicity or geographical origin. NKTCL is an aggressive malignancy, predominantly occurs in the nasal, paranasal, and oropharyngeal sites, and is much more prevalent in East Asia and Latin America than in Western countries [40].
\nAlthough the association of this B lymphotropic virus with malignancies of T and NK cell origin was quite unexpected, both the presence of virus sequences in tumor cells and the virus’s oncogenic potency have led to the hypothesis that whether particular EBV strains are preferentially selected in NKTCL. Pathogenesis and genotype analyses of NKTCL have mainly focused on genetic variations in a small fraction of EBV genes before, which is limited to define the spectrum of diversity within the whole genome of EBV. The genome-wide characteristics of EBV are essential to understand the diversity of strains isolated from NKTCL. In 2019, for the first time, 35 NKTCL-derived EBV genomic landscapes at genome-wide level were simultaneously systematically characterized by two groups.
\nOur group directly sequenced EBV-captured DNA from eight primary NKTCL biopsy samples from China using Illumina HiSeq 2500 sequencer platform and presented the eight EBV sequences, designated NKTCL-EBV1-NKTCL-EBV8 [23]. Aiming at knowing the detail of subtype, the obtained DNA sequences were compared with six mostly referenced sequences, including AG876, B95-8, EBV WT, GD1, GD2, and HKNPC1. The GD1 coverage percentages are higher than the rest. The genome sizes, estimated based on the reference GD1 sequence, ranged from 171,590 bp (NKTCL-EBV8) to 172,059 bp (NKTCL-EBV1).
\nWhole-genome sequence alignments revealed extensive nucleotide variation in the eight NKTCL-EBV genomes. In comparison with the most similar GD1 strain, the NKTCL-EBV1 to NKTCL-EBV8 harbored 2072 variations in total, including 1938 substitutions, 58 insertions, and 76 deletions. Among them, 1218 substitutions, 15 insertions, and 26 deletions were located in the coding regions. The number of the nonsynonymous mutations is highest in the gene regions encoding latent proteins in each of the NKTCL-EBV genomes, followed by genes encoding the tegument protein and membrane glycoproteins.
\nEBNA1 and LMP1 are the most frequently studied regions to date. Based on the amino acid changes in certain residues of LMP1 and EBNA1, eight NKTCL-EBVs were sorted to China 1 and V-val subtype, respectively. Of interest, EBNA1 of NKTCL-EBV3 sequence showed clustered away from the other seven NKTCL-EBV strains. Analysis of amino acid sequences of EBNA1 supported that EBNA1 of NKTCL-EBV3 may arise from recombination of GD1 and B95-8. Other two commonly classification systems for LMP-1 gene polymorphisms include a 30-bp deletion in the C terminus and the loss of restriction site Xho I in the N terminus of the gene. LMP1 is a key latent protein with abilities to promote cell proliferation and inhibit cell apoptosis in NKTCL. In our study, the LMP1 strain in NKTCL-EBV1-NKTCL-EBV7, but not NKTCL-EBV8, harbored the 30-bp deletion. The variant of 30-bp deletion of LMP1 has been demonstrated that it is associated with poor prognosis of patients with NKTCL, which might serve as a potential marker to monitor treatment [41]. In addition, eight NKTCL-EBV strains had Xho I restriction site loss at exon 1 of the LMP1 gene.
\nThe other group assembled 27 NKTCL-derived EBV genome sequences retrieved from whole-genome sequencing data using the Hiseq sequencer (Illumina), including 15 EBV-positive NKTCL tumor samples from Southern China and 12 samples from Singapore [24]. The average percentage of EBV sequences in WGS data is 0.45% (0.03–1.06%), and the coverage depth is 222.2X in average (26.7X–612.8X). As ~34 kb of 172 kb of EBV genome are repeat regions, which could not be properly assembled with short-reads sequencing technology, the groups assigned “N” for these regions and subsequently joined the scaffolds, resulting in EBV genomes with ~172 kb in length.
\nThe authors reported that among the 27 NKTCL samples, in average 1152 EBV SNVs for each sample were determined by aligning the viral reads against the reference EBV-WT genome. The most frequent tumor-specific non-synonymous mutations in NKTCL-derived EBV were located at BPLF1 gene (position 49,790–59,239 bp). An average of 44.8 small indels (<50 bp) of EBV were found in each NKTCL sample, and the 30-bp deletion of LMP1 was commonly found in the samples (21/27), with a frequency consistent with the previous study revealed by using Sanger sequencing [42]. Large deletions of EBV (>1 kb) were found in 10 of 27 NKTCL samples, without any sequencing coverage in the deleted regions. The findings provided insights into the understanding of EBV’s role the etiology of NKTCL.
\nA genome-wide association study of 189 patients with extranodal NKTCL, nasal type and 957 controls from Guangdong province, Southern China was performed to identify common genetic variants affecting individual risk of NKTCL [43]. All cases were genotyped with Illumina Human OmniExpress ZhongHua-8 BeadChip, and population controls were scanned by Illumina OmniHumanExpress-24 V1.0 (both Illumina, San Diego, CA, USA). The findings were validated in four independent case–control series. The SNP with the strongest association was rs9277378 (OR 2.65 [95% CI 2.08–3.37]) located with HLA-DPB1, indicating the importance of HLA-DP antigen presentation in the pathogenesis of NKTCL. The pathogenic subtypes of EBV in NKTCL tumorigenesis should be further explored.
\nPhylogenetic analysis of EBV genomes could demonstrate detailed overall genomic differences in EBV genome within or beyond subtypes of EBV-associated diseases, thus, EBV genomic similarity is likely to better infer the phylogenetic relatedness among EBV genomes.
\nTraditionally, EBV has two distinct subtypes, type 1 and type 2. Type 1 EBV (e.g., B95-8, GD1 and Akata) is the main EBV strain prevalent worldwide, while type 2 EBV (e.g., AG876) is abundant only in parts of Africa and New Guinea. Type 1 and type 2 EBV encode different EBNA2 genes, with only 54% amino acid sequence identity. A recent whole genome sequencing study confirmed that EBNA2 and EBNA3 are the only genes that can distinguish type 1 and type 2 EBV strains [16]. Technologies for genome sequencing were currently developed with tools for genome analysis. High-throughput sequencing technology such as illumine dye sequencing was introduced to successfully sequence viral genomes. As exemplary tools for genome analysis, Molecular Evolutionary Genetics Analysis (MEGA) is used for both conducting statistical analysis of molecular evolution and constructing phylogenetic trees [44].
\nThe NPC genomes from Asian EBV strains, including GD1, GD2, and HKNPC1-HKNPC9, are type 1 viruses and were clustered in a branch distant to the non-Asian strains AG876, B95-8 [14]. Analysis of LMP1 and -2 showed a phylogenetic relationship corresponding to the geographical origin of the viral genomes instead of the type 1 and 2 dichotomy, indicating that LMP1 and -2 genes can serve as geographical markers. GD1 seemed to harbor many mutations that were not present in the other Chinese strains. HKNPC6 and -7 genomes, which were isolated from tumor biopsy specimens of advanced metastatic NPC cases, were distinct from the other NPC-EBV genomes. Future work should investigate the relationship between the distinct lineage of EBV and the clinical stages of NPC.
\nGC-EBV strains, EBVaGC1-EBVaGC9 and GDGC1-GDGC2 involved here, were closely related to all Asian-derived EBV strains, distant to the non-Asian strains, and also showed that the EBV sequences generally clustered in a manner consistent with geographical location [17, 21]. Neighbor-joining trees derived from the sequences of EBNA2 gene showed that all the GC-EBV genomes are type 1 viruses, clustered in a branch with other type 1 EBV strains, distant to the only type 2 EBV strain, AG876. Phylogenetic trees based on the LMP1 gene and whole EBV genomes indicated that the nine EBVaGC strains were closely related to all Asian-derived EBV strains and distant to the non-Asian strains, suggesting that the LMP1 gene can serve as a geographical marker [17]. This is in line with the previous results from the NPC-EBV genomes [14]. In addition, phylogenetic analyses on GDGC1 and GDGC2 derived from specific EBV-encoded gene suggested the presence of at least two parental lineages of EBV, as GDGC1 and GD2 clustered closely, while GDGC2 and GD1 clustered closely [21].
\nIn our recent study, the phylogenetic trees were conducted based on alignment of eight full-length NKTCL-EBVs and previously published 28 strains [23]. Of note, eight NKTCL-EBVs genomes clearly sort into type 1, based on differences in whole genome and especially EBNA2. Eight NKTCL-EBVs were related to other Asian EBV strains, including EBVaGC1–9, HKNPC1–9, GD1, and GD2 obtained from China, and Akata from Japan, whereas none of the specimens was clustered in a branch of non-Asian strains AG876, B95-8, and Mutu. Other group compared the sequences between 27 NKTCL-derived EBV and 164 EBV genome sequences from public database to determine the sequence diversity of EBV [24]. Phylogenetic analysis revealed clear clustering of EBV isolates firstly according to their respective geographic origin; moreover, EBV isolates derived from NKTCL samples tend to cluster closely, apart from clusters by other diseases, supporting the hypothesis of the existence of disease-specific EBV. However, whether the unique EBV has been driving the development of NKTCL or simply adapted to the niche of NKTCL as bystander await further investigations.
\nIn this chapter, phylogenetic analysis was conducted on full-length EBV genomes, including 11 NPC-EBV strains (GD1, GD2, HKNPC1-HKNPC9), 11 GC-EBV strains (EBVaGC1-EBVaGC9, GDGC1-GDGC2), 35 NKTCL-EBV strains (NKTCL-EBV1-NKTCL-EBV8, NKTCL-SC01-NKTCL-SC15, NKTCL-SG01-NKTCL-SG12), B95-8, EBV-WT, Mutu, Akata, and AG876 (Figure 2). The result of phylogenetic tree supports the conclusion that EBV infections are more likely affected by different geographic regions rather than particular EBV-associated malignancies.
\nPhylogenetic trees of EBV genomes. Phylogenetic analyses were conducted using the neighbor-joining (NJ) algorithm implemented in MEGA software (version 6). Bootstrap analysis of 1000 replicates was performed to determine the confidence.
Sequence variations of EBV genes also result in amino acid epitope exchanges, which should have a significant impact on EBV-specific T-cell immunity.
\nAmong the shared non-synonymous SNVs of the Chinese derived GD1, GD2 and HKNPC1 isolates, 34 are associated with known EBV-specific epitopes; 19 and 15 are found in CD8+ and CD4+ epitopes, respectively [12]. HKNPC2-9 genomes harbored nonsynonymous mutations in epitopes specific for both CD4+ and CD8+ T cells [14]. Amino acid changes were found in seven CD8+ epitopes of LMP2, five epitopes of EBNA3A, and three or fewer in other proteins. Thirteen CD4+ epitopes of EBNA1, six in LMP1, six in LMP2, five in EBNA2, and three or fewer in other proteins contained amino acid changes. Some of the nonsynonymous mutations were affecting multiple epitopes.
\nEBVaGC shows EBV type I latency neoplasm, in which EBNA1 is expressed in 100% and LMP2A in about half of EBVaGC cases, respectively [45]. Recent studies show that EBNA1, as well as LMP2A, can be presented to both CD4+ and CD8+ T cells, highlighting its potential importance in the development of therapeutic strategies against EBV-associated malignancies [46, 47]. There is some clear evidence for sequence variation affecting immune recognition of EBNA1 and potential epitope selection for vaccine development [46]. So far, most research on the EBNA1 protein has been focused exclusively on the B95-8 strain alone [46, 47]. Sequence analysis of the gene encoding EBNA1 in EBV isolates from nine EBVaGC specimens has revealed considerable EBNA1 sequence divergence from the B95-8 strain [17]. Importantly, T cell recognition of EBNA1 epitope might be greatly influenced by this sequence polymorphism as adoptive transfer of EBNA1-targeted T cells has a potential use in immunotherapy of EBV associated carcinomas.
\nNKTCL is associated with type II EBV latency, in which only restricted EBV antigens, namely EBNA1, and LMP1 and 2, are expressed [48]. These EBV encoded proteins might be the targets of immune recognition during its persistent infection, and their nonsynonymous variations in CD4+ and CD8+ T-cell epitopes may affect the efficacy for a cytotoxic T lymphocyte (CTL)-based therapy. Many epitopes were defined and were mapped in EBV antigens and correlated with major histocompatibility complex type in previous studies. In our study, we mainly investigated the amino acid changes in CD4+ and CD8+ T-cell epitopes of EBNA1, LMP1, and LMP2A. Compared with B95-8, amino acids changes were found in 3 CD8+ epitopes of EBNA1, 8 epitopes of LMP1, and 12 epitopes of LMP2A. Eleven CD4+ epitopes of EBNA1, 13 in LMP1, and 9 in LMP2A contained amino acids. Some of the nonsynonymous mutations were affecting multiple epitopes [23]. In another study, alterations of the known T-cell epitopes were examined in EBV sequences derived from NKTCL [24]. Alterations of T-cell epitopes were detected in EBV derived from NKTCL samples. Notably, 21 of these epitopes with significant enrichment in NKTCL samples were restricted to six EBV genes, including EBNA3A (G373D, F325L, I333K, L406P, S412R, H464R, M466R, T585I, and A588P), EBNA3B (A399S, V400L, V417L, K424T, Y662D, and K663E), EBNA3C (P916S), BARF1 (V29A), BCRF1 (V6M), and BNRF1 (G456R, S497G, and A1289T).
\nTherefore, these data have implications for the development of effective prophylactic and therapeutic vaccine approaches targeting the personalized EBV antigens in these aggressive diseases. Adoptive transfer of cytotoxic T cells (CTLs) specific for EBV antigens has proved safe and effective as prophylaxis and treatment for EBV-associated lymphoproliferative disease. Some patients with advanced stage or relapsed EBV-associated malignancies achieved complete remission after treatment with autologous LMP1/2- and EBNA1-specific CTLs or activated by peptides derived from LMP1/2 [49, 50]. Nonetheless, some cases still did not respond to LMP-CTL therapy, and this failure was usually attributed to immune escapes by antigen loss. It is worth noting that all these previous studies used prototype EBV sequence, B95-8, to design full-length LMP epitopes. Therefore, recent work gives an alternative explanation for the lack of tumor response. Whether changes in such epitopes confer immune evasion of the tumor cells may constitute another hypothesis for future testing.
\nViral integration into the host genome has been shown to be a causal mechanism that can lead to the development of cancer [51]. Not surprisingly, known tumor-associated viruses, such as EBV, HBV, HPV16 and HPV18, were among the most frequently detected targets [52]. Notably, the approach of WGS is sensitive to detect viruses. This is particularly true for the common integration verified for HBV, HPV16 and HPV18 in a variety of studies [53, 54, 55]. The known causal role of HPV16 and HPV18 in several tumor entities, which triggered one of the largest measures in cancer prevention, has been the motivation for extensive elucidation of the pathogenetic processes involved. Integration events with high confidence were demonstrated for HBV (liver cancer), HPV16 and HPV18 (in both cervical and head-and neck carcinoma), however, low-confidence integration events were detected for EBV (gastric cancer and malignant lymphoma) [56].
\nComprehensive analyses of WGS datasets may reveal some novel findings on EBV integration. Recently, a comprehensive survey of EBV integration in a variety of human malignancies, including NPC, EBVaGC, and NKTCL was conducted, using EBV genome capture combined with ultra-deep sequencing, which could efficiently detect integrated EBV sequences from background “noise” introduced by nuclear EBV episomes [27]. The EBV integration rates were 25.6% (10/39), 16.0% (4/25), 9.6% (17/177) in the EBVaGC, NKTCL, and NPC tumors, respectively, which were lower than HPV integration in cervical cancer (76.3%) and head and neck squamous cell carcinoma (60.7%), and HBV in hepatocellular carcinoma (92.6%) [54, 57, 58, 59]. They found that EBV integrations into the introns could decrease the expression of the inflammation-related genes, TNFAIP3, PARK2, and CDK15, in NPC tumors [27]. The EBV integration breakpoints were frequently at oriP or terminal repeats, and were surrounded by microhomology sequences, consistent with a mechanism for integration involving viral genome replication and microhomology-mediated recombination, which has an important role in the integration of other tumorigenic viruses, HBV and HPV [54, 59]. Meanwhile, researchers also observed integrations of short EBV fragments into human chromosomes, coincident with episomal EBV genomes in NKTCL, and showed that 31 EBV-host integration sites were detected from eight NKTCL samples, and enriched in the repeat regions of human genome, such as SINE, LINE, and satellite [24].
\nHowever, there are still few studies on EBV integration based on WGS technology. In addition, authors only selected some potential breakpoints to perform PCR and Sanger sequencing for validating. For example, Xu et al. randomly select 12 integrations from 197 breakpoints identified from NPC and other EBV-associated malignancies, and only 10 breakpoints were successfully validated [27]. As integration of EBV sequence into the host genome and the consequent disruption of the important host genes might represent a novel tumorigenesis mechanism in EBV associated malignancies, all the potential EBV integration breakpoints should be validated and biological function of host genes involved should be further conducted.
\nIn conclusion, full-length EBV genomes isolated from primary NPC, EBVaGC, and NKTCL biopsy specimens have been successfully sequenced and the sequence diversity on a whole-genome level has been analyzed, although their pathogenesis remains to be clarified. Phylogenetic analysis has shown that all aforementioned NPC, GC, and NKTCL-EBV strains are type 1 EBV and close to other Asian subtypes, leading to the conclusion that EBV infections are more likely affected by different geographic regions rather than particular EBV-associated malignancies. In addition, sequence variations of EBV genes also result in amino acid epitope exchanges, which should have a significant impact on EBV-specific T-cell immunity. Recent data have provided optimization proposal for selecting EBV genome for treatment from individual patients or at least predominant strains prevalent in geographical regions instead of commonly used B95-8 genome. We acknowledge that further characterizations of the molecular events would provide more information on the exact mechanisms underlying their pathogenic potentials and clinical significance.
\nThis work was supported by grants from National Natural Science Foundation of China (81903155 to Y.L.), and Beijing Municipal Natural Science Foundation (7202023 to Y.L.), and Beijing Hospitals Authority Youth Program (QML20181106 to Y.L.)
\nThe authors declare no conflict of interest.
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