From the Cover: Multigeneration analysis reveals the inheritance,specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis

The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) system has emerged as a powerful tool for targeted gene editing in many organisms, including plants. However, all of the reported studies in plants focused on either transient systems or the first generation after the CRISPR/Cas system was stably transformed into plants. In this study we examined several plant generations with seven genes at 12 different target sites to determine the patterns, efficiency, specificity, and heritability of CRISPR/Cas-induced gene mutations or corrections in Arabidopsis. The proportion of plants bearing any mutations (chimeric, heterozygous, biallelic, or homozygous) was 71.2% at T1, 58.3% at T2, and 79.4% at T3 generations. CRISPR/Cas-induced mutations were predominantly 1 bp insertion and short deletions. Gene modifications detected in T1 plants occurred mostly in somatic cells, and consequently there were no T1 plants that were homozygous for a gene modification event. In contrast, ∼22% of T2 plants were found to be homozygous for a modified gene. All homozygotes were stable to the next generation, without any new modifications at the target sites. There was no indication of any off-target mutations by examining the target sites and sequences highly homologous to the target sites and by in-depth whole-genome sequencing. Together our results show that the CRISPR/Cas system is a useful tool for generating versatile and heritable modifications specifically at target genes in plants.Genome engineering tools are important for plant functional genomics research and plant biotechnology. The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) system has been successfully used for efficient genome editing in human cell lines, zebrafish, and mouse (1–3) and recently applied to gene modification in plants (4–10). In this system a short RNA molecule guides the associated endonuclease Cas9 to generate double strand breaks (DSBs) in the target genomic DNA, which lead to sequence mutations as a result of error-prone nonhomologous end-joining (NHEJ) DNA damage repair or to gene correction or replacement as a result of homology-dependent recombination (HR) (11). It was shown that engineered CRISPR/Cas caused mutations in target genes or corrections in transgenes in transient expression assays in plant protoplasts and tobacco leaves (10). Importantly, stable expression of the CRISPR/Cas in transgenic Arabidopsis, tobacco, and rice plants led to mutations (mostly indels) in target genes and correction of a transgene (4–9). However, it was not known whether the gene mutations and corrections occurred in somatic cells only or whether some of the mutations and corrections happened in germ-line cells and thus may be heritable. Additionally, it is unclear how specific the CRISPR/Cas is in plants. Previous studies in human cell lines indicated a high frequency of off-target effect of CRISPR/Cas-induced mutagenesis (12, 13) but a lower off-target effect in mice and zebrafish (14, 15). Here we show that the CRISPR/Cas-induced transgene correction or mutations in endogenous plant genes and transgenes detected in Arabidopsis T1 plants occurred mostly in somatic cells. However, some of the gene modifications were transmitted through the germ line and were heritable in Arabidopsis T2 and T3 plants following the classic Mendelian model. Mutations caused during DSB repair were predominantly 1 bp insertion and short deletions. Furthermore, our deep sequencing and analysis did not detect any off-targets in multiple CRISPR/Cas transgenic Arabidopsis lines, indicating that the mutagenesis effect of CRISPR/Cas is highly specific in plants.     

Degenerate target sites mediate rapid primed CRISPR adaptation

Prokaryotes encode adaptive immune systems, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR associated), to provide resistance against mobile invaders, such as viruses and plasmids. Host immunity is based on incorporation of invader DNA sequences in a memory locus (CRISPR), the formation of guide RNAs from this locus, and the degradation of cognate invader DNA (protospacer). Invaders can escape type I-E CRISPR-Cas immunity in Escherichia coli K12 by making point mutations in the seed region of the protospacer or its adjacent motif (PAM), but hosts quickly restore immunity by integrating new spacers in a positive-feedback process termed “priming.” Here, by using a randomized protospacer and PAM library and high-throughput plasmid loss assays, we provide a systematic analysis of the constraints of both direct interference and subsequent priming in E. coli. We have defined a high-resolution genetic map of direct interference by Cascade and Cas3, which includes five positions of the protospacer at 6-nt intervals that readily tolerate mutations. Importantly, we show that priming is an extremely robust process capable of using degenerate target regions, with up to 13 mutations throughout the PAM and protospacer region. Priming is influenced by the number of mismatches, their position, and is nucleotide dependent. Our findings imply that even outdated spacers containing many mismatches can induce a rapid primed CRISPR response against diversified or related invaders, giving microbes an advantage in the coevolutionary arms race with their invaders.Bacteria and Archaea are regularly exposed to bacteriophages and other mobile genetic elements, such as plasmids. To control the competing effects of horizontal gene transfer, a spectrum of resistance strategies have evolved in prokaryotes (1). One of the most widespread and well-characterized are the CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated) systems, which provide bacterial “adaptive immunity” (1–8). Simply, CRISPR-Cas functions in three major steps. First, in a process termed “adaptation,” short sequences are derived from the invading element and incorporated into a CRISPR array (9). CRISPR arrays are composed of short repeats that are separated by the foreign-derived sequences, termed “spacers.” Second, CRISPRs are transcribed into a pre-CRISPR RNA (pre-crRNA), which is then processed into short crRNAs, which encompass portions of the repeats and most—or all—of the spacer. Finally, as part of a Cas ribonucleoprotein complex, the crRNAs guide a sequence-specific targeting of complementary nucleic acids (for recent reviews, see refs. 1–7).CRISPR-Cas systems are divided into three major types (I–III) and further categorized into subtypes (e.g., I-A to I-F) (10). The mechanisms of both crRNA generation and interference differ between the types and there are even significant differences between closely related subtypes. However, Cas1 and Cas2 are the only two Cas proteins completely conserved across all CRISPR-Cas systems and they are crucial for adaptation in Escherichia coli (10–12). The acquisition of new spacers is the most poorly understood stage in CRISPR-Cas immunity, mainly hindered by the paucity of robust laboratory assays to monitor this process (reviewed in ref. 9). Streptococcus thermophilus is highly proficient at spacer acquisition and provided much of the early insight into adaptation, showing that new spacers are typically acquired at one end of the CRISPR array from either phages (13–15) or plasmids (16). Recently, spacer acquisition has been detected in a variety of other systems (11, 12, 17–20). Adjacent to the expanding end of the array is the leader region, which harbors the promoter for pre-crRNA expression and sequences important for spacer acquisition (12, 21). Recent studies in E. coli in the type I-E system have shown that spacer acquisition can occur from phages and plasmids either when the Cas1 and Cas2 proteins are overexpressed or if the native cas genes are up-regulated, because of deletion of hns (11, 12, 20–22). The DNA targets (termed “protospacers”) of newly acquired spacers are consistently flanked by protospacer-adjacent motifs (PAMs), with the E. coli type I-E consensus 5′-protospacer-CTT-3′. PAMs were originally identified computationally (23) and were shown to play a role in interference in an early study (14). The importance of PAMs in the recognition and selection of precursor-spacers (prespacers) during adaptation was demonstrated unequivocally using assays that were independent of interference (12, 21). The simple overexpression of Cas1 and Cas2, in the absence of other cas genes, demonstrated these are the only Cas proteins essential for adaptation and are likely to recognize PAMs (12).Adaptation consists of two related stages, termed “naïve” and “primed” (9). Naïve adaptation occurs when a bacterium harboring a CRISPR-Cas system is infected by a new foreign element that it has not previously encountered. Although the acquisition of a new spacer can result in effective protection from the element, point mutations within the protospacer or PAM allow the element to escape CRISPR-Cas targeting (14, 24, 25). This aspect had been viewed as a weakness of CRISPR-Cas interference, but recent studies show that a positive feedback loop—called priming—occurs, which enables one or more new spacers to be acquired (11, 20, 22). Specifically, single mutations within either the PAM or the seed region of the protospacer, although inactive for interference, promote the rapid acquisition of new spacers from the same target (11). Priming is proposed to allow an effective response against viral or plasmid escapees through the incorporation of new spacers. Unlike naïve adaptation, priming is more complex, and in type I-E systems requires Cas1, Cas2, crRNA, the targeting complex termed Cascade [CRISPR-associated complex for antiviral defence, composed of Cse1, Cse2, Cas7, Cas5, and Cas6e (26–28)] and the Cas3 nuclease/helicase (11). Interestingly, the vast majority of spacers acquired through priming are derived from the same DNA strand as the original priming spacer (11, 20, 22). In addition, priming in E. coli was abolished by two mutations in the protospacer and PAM regions (11).In this study, we generated a mutagenic variant library of a protospacer and PAM region and used both individual high-throughput plasmid-loss assays and next-generation sequencing to determine the limits of both direct interference and indirect interference through priming. Our results demonstrate that direct interference tolerates mutations mostly at very specific positions in the protospacer, whereas priming tolerates extensive mutation of the PAM and protospacer regions. The results have wide evolutionary consequences for primed acquisition and could explain the retention of multiple “older” spacers in CRISPR arrays.     

Cas9-mediated targeting of viral RNA in eukaryotic cells

Clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) systems are prokaryotic RNA-directed endonuclease machineries that act as an adaptive immune system against foreign genetic elements. Using small CRISPR RNAs that provide specificity, Cas proteins recognize and degrade nucleic acids. Our previous work demonstrated that the Cas9 endonuclease from Francisella novicida (FnCas9) is capable of targeting endogenous bacterial RNA. Here, we show that FnCas9 can be directed by an engineered RNA-targeting guide RNA to target and inhibit a human +ssRNA virus, hepatitis C virus, within eukaryotic cells. This work reveals a versatile and portable RNA-targeting system that can effectively function in eukaryotic cells and be programmed as an antiviral defense.Clustered, regularly interspaced, short palindromic repeats–CRISPR associated (CRISPR-Cas) systems act as a prokaryotic adaptive immune system against foreign genetic elements (1–3). These RNA-directed endonuclease machineries use small CRISPR RNAs (crRNAs) that provide sequence specificity and Cas proteins to recognize and degrade nucleic acids (4–7). Our recent work revealed a unique form of prokaryotic gene regulation, whereby Cas9 from Francisella novicida (FnCas9) targets a bacterial mRNA, leading to gene repression (8). Given the ability of specific Cas9 proteins to be reprogrammed to target and cleave DNA in numerous biological systems (7, 9, 10), we hypothesized that FnCas9 could be retargeted to a distinct RNA in eukaryotic cells and lead to its inhibition. To eliminate any confounding interactions of FnCas9 with DNA, we targeted FnCas9 to the +ssRNA virus, hepatitis C virus (HCV), which has no DNA stage in its lifecycle. HCV is an important human pathogen associated with liver fibrosis, cirrhosis, and hepatocellular carcinoma and is the leading cause of liver transplantation (11, 12).     

Nonmuscle myosin heavy chain IIA mediates Epstein–Barr virus infection of nasopharyngeal epithelial cells

EBV causes B lymphomas and undifferentiated nasopharyngeal carcinoma (NPC). Although the mechanisms by which EBV infects B lymphocytes have been extensively studied, investigation of the mechanisms by which EBV infects nasopharyngeal epithelial cells (NPECs) has only recently been enabled by the successful growth of B lymphoma Mo-MLV insertion region 1 homolog (BMI1)-immortalized NPECs in vitro and the discovery that neuropilin 1 expression positively affects EBV glycoprotein B (gB)-mediated infection and tyrosine kinase activations in enhancing EBV infection of BMI1-immortalized NPECs. We have now found that even though EBV infected NPECs grown as a monolayer at extremely low efficiency (<3%), close to 30% of NPECs grown as sphere-like cells (SLCs) were infected by EBV. We also identified nonmuscle myosin heavy chain IIA (NMHC-IIA) as another NPEC protein important for efficient EBV infection. EBV gH/gL specifically interacted with NMHC-IIA both in vitro and in vivo. NMHC-IIA densely aggregated on the surface of NPEC SLCs and colocalized with EBV. EBV infection of NPEC SLCs was significantly reduced by NMHC-IIA siRNA knock-down. NMHC-IIA antisera also efficiently blocked EBV infection. These data indicate that NMHC-IIA is an important factor for EBV NPEC infection.EBV is a nearly ubiquitous human γ-herpesvirus that causes B-cell lymphomas and nasopharyngeal carcinoma (NPC), indicative of tropism for both cell types (1–3). Until recently, the molecular mechanisms of EBV infection of B lymphocytes were better understood than the mechanisms of epithelial cell infection (4). EBV attachment to the B-cell membrane is mediated by interactions between EBV glycoprotein 350 (gp350) and complement receptor type 2 (CR2 or CD21) (5) or CD35 (6). EBV gp42 binding to HLA class II triggers EBV fusion with B cells in the presence of EBV glycoprotein B (gB) and gH/gL (7, 8). For epithelial cells, gH/gL and gB are important for EBV infection (4, 9, 10). Epithelial cells lack HLA class II expression; thus, gp42 cannot trigger EBV and cell fusion. Instead, gp42 inversely suppresses the infection (11), and an antibody against gp350 can enhance infections of CD21/CD35-negative epithelial cells (12). The gH/gL heterodimer is required for virus entry (4) and may be involved in binding (13), as well as fusion of EBV (14–17). However, the crystal structure of EBV gH/gL does not show any known fusion domain (18). It is now thought that gH/gL regulates the fusion function of gB (19). Binding of gH/gL to a subset of αv integrins (e.g., αvβ₅, αvβ₆, or αvβ₈) provides the initial trigger for gB-mediated fusion (16, 20, 21). However, E1D1(gH/gL) antibody or CL59(gH) antibody, with a different epitope, can impair epithelial cell infection (20, 22). Thus, multiple gH/gL domains are critical to EBV infection, and gH/gL may interact with proteins in addition to integrins. Direct interaction of EBV gB amino acids 23–431 with neuropilin 1 (NRP1) and its associated tyrosine kinases is critical for EBV infection of nasopharyngeal epithelial cells (NPECs). NRP1 knock-down or EBV pretreatment with soluble NRP1 suppresses EBV NPEC infection, whereas NRP1 overexpression enhances EBV infection (10). Confocal microscopy and experiments with inhibitors of macropinocytosis indicate that EBV enters NPECs through macropinocytosis and not through clathrin-mediated endocytosis (10).The principal obstacle to identifying factors that may enable more efficient EBV infection of NPECs and better understanding of the role of EBV in NPC is that EBV is remarkably inefficient in infection of primary or B lymphoma Mo-MLV insertion region 1 homolog (BMI1)-immortalized NPECs. As a polycomb complex protein, BMI1 is a proto-oncogene. BMI1 has an important role in regulating proliferation, senescence, and self-renewal of stem cells (23, 24). BMI1 overexpression immortalizes human epithelial cells and mouse embryonic fibroblasts (25, 26). By optimizing the growth of BMI1-immortalized NPEC cultures, we found that BMI1-immortalized NPECs seeded at a 10-fold higher density than used in previous protocols and grew initially as a monolayer. “Spherical cells” then grew above the monolayer. Surprisingly, the spherical cells consistently supported an EBV infection efficiency of ∼20–30%, using an estimated EBV multiplicity of infection (MOI) of 300. Using this more efficient in vitro EBV infection protocol, we identified an interaction between nonmuscle myosin heavy chain IIA (NMHC-IIA) and gH/gL on the cell surface, which was critical for more efficient EBV NPEC infection.     

Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila

The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line–restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25–100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.Experimentally induced mutations in the genomes of model organisms have been the basis of much of our current understanding of biological mechanisms. However, traditional mutagenesis tools have significant drawbacks. Forward genetic approaches such as chemical mutagenesis lack specificity, leading to unwanted mutations at many sites in the genome. Traditional reverse genetic approaches, such as gene targeting by conventional homologous recombination, suffer from low efficiency and therefore are labor intensive. In recent years novel methods have been developed that aim to modify genomes with high precision and high efficiency by introducing double-stand breaks (DSBs) at defined loci (1). DSBs can be repaired by either nonhomologous end joining (NHEJ) or homology-directed repair (HDR). NHEJ is an error-prone process that frequently leads to the generation of small, mutagenic insertions and deletions (indels). HDR repairs DSBs by precisely copying sequence from a donor template, allowing specific changes to be introduced into the genome (2).The type II clustered regular interspersed short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has emerged recently as an extraordinarily powerful method for inducing site-specific DSBs in the genomes of a variety of organisms. The method exploits the RNA-guided endonuclease Cas9, which plays a key role in bacterial adaptive immune systems. Target specificity of Cas9 is encoded by a 20-nt spacer sequence in the crisprRNA, which pairs with the transactivating RNA to direct the endonuclease to the complementary target site in the DNA (3). For genome engineering, crisprRNA and transactivating RNA can be combined in a single chimeric guide RNA (gRNA), resulting in a simple two-component system for the creation of DSBs at defined sites (3). Binding of the Cas9/gRNA complex at a genomic target site is constrained only by the requirement for an adjacent short protospacer-adjacent motif (PAM), which for the commonly used Streptococcus pyogenes Cas9 is NGG (4).Several groups recently demonstrated CRISPR/Cas-mediated editing of the genome of Drosophila melanogaster (5–12), a key model organism for biological research. However, the rate of mutagenesis has varied widely both within and among different studies. Differences in the methods used to introduce Cas9 and gRNAs into the fly likely contribute significantly to different experimental outcomes. Kondo and Ueda (8) expressed both Cas9 and gRNA from transgenes stably integrated into the genome, but all other studies have used microinjection of expression plasmids or of in vitro-transcribed RNA into embryos to deliver one or both CRISPR/Cas components (5–7, 9–11). Much of the currently available evidence suggests that transgenic provision of Cas9 increases rates of germ-line transmission substantially (8, 10, 11). However, the influence of different regulatory sequences within cas9 transgenes on the rate of mutagenesis and on the location where mutations are generated within the organism has not been evaluated. The effect of different promoter sequences on the activities of gRNAs also has not been explored systematically. Therefore it is possible that suboptimal tools are being used currently for many CRISPR/Cas experiments in Drosophila.Previous studies in Drosophila have focused on the use of CRISPR/Cas to create heritable mutations in the germ line. In principle, efficient biallelic targeting within somatic cells of Drosophila would represent a powerful system to dissect the functions of genes within an organismal context. However, the feasibility of such an approach has not been explored so far.Here, we present a versatile CRISPR/Cas toolbox for Drosophila genome engineering consisting of a set of systematically evaluated transgenic Cas9 lines and gRNA-expression plasmids. We describe combinations of Cas9 and gRNA sources that can be used to induce, with high efficiency, loss-of-function mutations in nonessential or essential genes and integration of designer sequences by HDR. Finally, we show that our optimized transgenic tools permit efficient biallelic targeting in a variety of somatic tissues of the fly, allowing the characterization of mutant phenotypes directly in Cas9/gRNA-expressing animals.     

Kaposi's sarcoma-associated herpesvirus LANA recruits the DNA polymerase clamp loader to mediate efficient replication and virus persistence

Kaposi''s sarcoma-associated herpesvirus (KSHV) latently infects tumor cells and persists as a multiple-copy, extrachromosomal, circular episome. To persist, the viral genome must replicate with each cell cycle. The KSHV latency-associated nuclear antigen (LANA) mediates viral DNA replication and persistence, but little is known regarding the underlying mechanisms. We find that LANA recruits replication factor C (RFC), the DNA polymerase clamp [proliferating cell nuclear antigen (PCNA)] loader, to drive DNA replication efficiently. Mutated LANA lacking RFC interaction was deficient for LANA-mediated DNA replication and episome persistence. RFC depletion had a negative impact on LANA’s ability to replicate and maintain viral DNA in cells containing artificial KSHV episomes or in infected cells, leading to loss of virus. LANA substantially increased PCNA loading onto DNA in vitro and recruited RFC and PCNA to KSHV DNA in cells. These findings suggest that PCNA loading is a rate-limiting step in DNA replication that is incompatible with viral survival. LANA enhancement of PCNA loading permits efficient virus replication and persistence, revealing a previously unidentified mechanism for KSHV latency.Kaposi''s sarcoma-associated herpesvirus (KSHV or human herpesvirus 8) has a causative role in Kaposi''s sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman disease (1–4). KSHV infection of tumor cells is predominantly latent. During latent infection, the viral genome persists as a multicopy, circular, extrachromosomal episome (plasmid) (5, 6). To persist, the genome must replicate and segregate to progeny nuclei with each cell division. Latency-associated nuclear antigen (LANA), a 1,162-residue protein, is one of a few KSHV genes expressed in latency. LANA is necessary and sufficient for episome persistence in the absence of other viral genes (7, 8). Both N-terminal LANA (N-LANA) and C-terminal LANA (C-LANA) are essential for function. N-LANA associates with mitotic chromosomes via binding histones H2A/H2B, and C-LANA simultaneously binds KSHV terminal repeat (TR) DNA (7, 9–20). Thus, LANA tethers the viral genome to host chromosomes and distributes viral DNA to daughter nuclei during mitosis. Importantly, LANA, which lacks enzymatic function, also mediates KSHV TR DNA replication (10, 21–23) through recruitment of host cell machinery, but little is known regarding the details of this process.We recently identified an internal 59-aa LANA region critical for efficient DNA replication and persistence (24, 25). Here, we find that LANA recruits replication factor C (RFC), the DNA polymerase clamp [proliferating cell nuclear antigen (PCNA)] loader (26), through this sequence to mediate viral DNA replication and episome persistence.     

Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity

Hepatitis C virus (HCV) has the propensity to cause chronic infection. Continuous immune escape has been proposed as a mechanism of intrahost viral evolution contributing to HCV persistence. Although the pronounced genetic diversity of intrahost HCV populations supports this hypothesis, recent observations of long-term persistence of individual HCV variants, negative selection increase, and complex dynamics of viral subpopulations during infection as well as broad cross-immunoreactivity (CR) among variants are inconsistent with the immune-escape hypothesis. Here, we present a mathematical model of intrahost viral population dynamics under the condition of a complex CR network (CRN) of viral variants and examine the contribution of CR to establishing persistent HCV infection. The model suggests a mechanism of viral adaptation by antigenic cooperation (AC), with immune responses against one variant protecting other variants. AC reduces the capacity of the host’s immune system to neutralize certain viral variants. CRN structure determines specific roles for each viral variant in host adaptation, with variants eliciting broad-CR antibodies facilitating persistence of other variants immunoreacting with these antibodies. The proposed mechanism is supported by empirical observations of intrahost HCV evolution. Interference with AC is a potential strategy for interruption and prevention of chronic HCV infection.Hepatitis C virus (HCV) causes chronic infection in  ～ 70% of infected people, who become at risk for developing severe liver diseases (1). The virus establishes chronic infection by using several molecular mechanisms for averting innate immunity and attenuating effectiveness of adaptive immune responses (2). HCV is one of the most heterogeneous viruses infecting humans and exists in each infected host as a population of genetically related variants (3, 4). Substantial heterogeneity and drastic changes in genetic composition of the intrahost HCV population observed during chronic infections have been interpreted as evidence of a continuous immune escape via random mutations, thereby generating increasing genetic diversity of viral populations in infected individuals (5–7).The observed cross-immunoreactivity (CR) of HCV variants from earlier stages of infection with antibodies (Abs) from later stages and ineffectiveness of Abs to immunoreact with variants from the same stage of infection (7) seemingly support the hypothesis of immune escape as a mechanism of intrahost evolution that contributes to establishment of persistent infections. However, several recent observations are incompatible with this hypothesis. First, the intrahost HIV population diversifies and diverts continuously from acute state to chronic infection until, at the onset of immunodeficiency, it starts losing heterogeneity and eventually stops diverting (8). Surprisingly, a similar temporal pattern of diversity and diversion was observed for intrahost HCV populations (9, 10). Furthermore, for HCV, the consistent increase in negative selection during chronic infection was observed (9–13). The late-stage HCV populations were shown to remain constant and homogeneous under the strong negative selection for years, indicating a high level of intrahost adaptation (9). Certain intrahost HCV variants were observed to persist in infected hosts for up to 16 y (9, 14, 15). These observations suggest that intrahost HCV subpopulations can remain unaffected by the immune system for years over the course of infection.Second, complex dynamics of HCV populations were observed in infected hosts. The density of intrahost subpopulations was found to fluctuate significantly in the course of chronic HCV infection, with some subpopulations persisting at low frequency for years until becoming dominant or reemerging at later stages of infection after being undetectable for a long time (9, 10, 15, 16).Third, the HCV hypervariable region 1 (HVR1) contains neutralizing antigenic epitopes (17, 18). Significant genetic variation of HVR1 during chronic infection was hypothesized to facilitate escape from neutralizing antibodies (17, 18). However, recent genetic and immunological analyses showed that HVR1 antigenic diversity is extensively convergent and effectively limited, with HVR1 variants from different genotypes and subtypes being broadly cross-immunoreactive (19–21).Interactions of intrahost viral variants with the host immune system are highly complex and nonlinear (22) and were subjects of mathematical modeling with the goal to understanding the mechanisms that lead to chronic infection. Previously developed mathematical models of interaction between HIV (23–25) or HCV (22) and the immune system showed that immune escape is associated with increase in diversity of the viral population. However, the continuous immune escape predicted by these models is inconsistent with the aforementioned observations, particularly for HCV. Unlike HIV, HCV lacks the ability to induce systemic immune suppression, suggesting a different mechanism of immune adaptation. Here, we develop a model that takes into consideration broad CR among viral variants (18, 19, 26–28) and disparity between CR and neutralization (19, 29). The model predicts antigenic cooperation (AC) among HCV variants that results in protection rather than continuous escape of the HCV population from the neutralizing Ab, thus suggesting a mechanism of intrahost evolution that leads to chronic infection.