Expression profiles of bovine adeno-associated virus and avian adeno-associated virus display significant similarity to that of adeno-associated virus type 5

Distinct infectivity and neutralization antibody responses in the highly homologous AAV Go.1 and AAV5

Introduction

Goat-derived adeno-associated virus (AAV) vectors, such as AAV Go.1, represent a novel platform for gene therapy due to their unique origin and potential advantages in transduction efficiency and immune evasion. However, their therapeutic potential and biological properties remain underexplored.

Methods

In this study, we developed a recombinant AAV (rAAV) Go.1 by replacing the goat AAV rep gene with the standard AAV2-rep gene to improve packaging efficiency. We compared the transduction efficiency of rAAV Go.1 with that of AAV5, a closely related serotype with 95% genome similarity, both in vitro and in vivo. Additionally, we assessed immune evasion properties by evaluating resistance to neutralization using sera from rAAV5-immunized mice and human volunteers. To further enhance transduction efficiency, we introduced site-specific mutations in the VP1 unique (VP1u) region and VP1/2 common region.

Results

The rep gene modification led to a significantly higher packaging efficiency for rAAV Go.1 compared to the original goat AAV. rAAV Go.1 exhibited markedly higher transduction efficiency than AAV5 in both in vitro and in vivo models. Furthermore, rAAV Go.1 demonstrated a 4-fold increase in resistance to neutralization by sera from rAAV5-immunized mice. A study involving 20 healthy volunteers revealed that high-titer neutralizing antibodies had a more pronounced inhibitory effect on rAAV5 compared to rAAV Go.1. Mutagenesis studies identified key modifications that enhanced viral properties: K32R, K91R, and K122R mutations in the VP1u region significantly improved viral production, while K137R (VP1u) enhanced transduction efficiency in vitro and in vivo.

Discussion

Our findings highlight the potential of rAAV Go.1 as an improved gene therapy vector with superior transduction efficiency and enhanced immune evasion. The identified VP1 mutations further optimize viral properties, making rAAV Go.1 a promising candidate for future therapeutic applications.

Role of the membrane-associated accessory protein (MAAP) in adeno-associated virus (AAV) infection

Adeno-associated viruses (AAVs) package a single-stranded (ss) DNA genome of 4.7 kb in their capsid of ~20 nm in diameter. AAV replication requires co-infection of a helper virus, such as adenovirus. During the optimization of recombinant AAV production, a small viral nonstructural protein, membrane-associated accessory protein (MAAP), was identified. However, the function of the MAAP in the context of AAV infection remains unknown. Here, we investigated the expression strategy and function of the MAAP during infection of both AAV2 and AAV5 in human embryonic kidney (HEK)293 cells. We found that AAV2 MAAP2 and AAV5 MAAP5 are expressed from the capsid gene (cap)-transcribing mRNA spliced from the donor to the second splice site that encodes VP2 and VP3. Thus, this AAV cap gene transcribes a multicistronic mRNA that can be translated to four viral proteins, MAAP, VP2, AAP, and VP3 in order. In AAV2 infection, MAAP2 predominantly localized in the cytoplasm, alongside the capsid, near the nuclear and plasma membranes, but a fraction of MAAP2 exhibited nuclear localization. In AAV5 infection, MAAP5 revealed a distinct pattern, predominantly localizing within the nucleus. In the cells infected with an MAAP knockout mutant of AAV2 or AAV5, both viral DNA replication and virus replication increased, whereas virus egress decreased, and the decrease in virus egress can be restored by providing MAAP in trans. In summary, MAAP, a novel AAV nonstructural protein translated from a multicistronic viral cap mRNA, not only facilitates cellular egress of AAV but also likely negatively affects viral DNA replication during infection.

IMPORTANCE

Recombinant adeno-associated virus (rAAV) has been used as a gene delivery vector in clinical gene therapy. In current gene therapies employing rAAV, a high dose of the vector is required. Consequently, there is a high demand for efficient and high-purity vector production systems. In this study, we demonstrated that membrane-associated accessory protein (MAAP), a small viral nonstructural protein, is translated from the same viral mRNA transcript encoding VP2 and VP3. In AAV-infected cells, apart from its prevalent expression in the cytoplasm with localization near the plasma and nuclear membranes, the MAAP also exhibits notable localization within the nucleus. During AAV infection, MAAP expression increases the cellular egress of progeny virions and decreases viral DNA replication and progeny virion production. Thus, the choice of MAAP expression has pros and cons during AAV infection, which could provide a guide to rAAV production.

The Diversity of Parvovirus Telomeres

Parvoviridae are small viruses composed of a 4–6 kb linear single-stranded DNA protected by an icosahedral capsid. The viral genes coding non-structural (NS), capsid, and accessory proteins are flanked by intriguing sequences, namely the telomeres. Telomeres are essential for parvovirus genome replication, encapsidation, and integration. Similar (homotelomeric) or different (heterotelomeric) at the two ends, they all contain imperfect palindromes that fold into hairpin structures. Up to 550 nucleotides in length, they harbor a wide variety of motifs and structures known to be recognized by host cell factors. Our study aims to comprehensively analyze parvovirus ends to better understand the role of these particular sequences in the virus life cycle. Forty Parvoviridae terminal repeats (TR) were publicly available in databases. The folding and specific DNA secondary structures, such as G4 and triplex, were systematically analyzed. A principal component analysis was carried out from the prediction data to determine variables signing parvovirus groups. A special focus will be put on adeno-associated virus (AAV) inverted terminal repeats (ITR), a member of the genus Dependoparvovirus used as vectors for gene therapy. This chapter highlights the diversity of the Parvoviridae telomeres regarding shape and secondary structures, providing information that could be relevant for virus-host interactions studies.

Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors

Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.

The history of mutational pressure changes during the evolution of adeno-associated viruses: A message to gene therapy and DNA-vaccine vectors designers

The use of virus-associated vectors for gene therapy and vaccination have emerged as safe and effective delivery system. Like all other genetic materials, these vehicles are also prone to spontaneous mutations. To understand what types of nucleotide mutations are expected in the vector, one needs to know distinct characteristics of mutational process in the corresponding virus. In this study we analyzed mutational pressure directions along the length of the genomes of all types of primate adeno-associated viruses (AAV) that are frequently used in gene therapy or DNA-vaccines. We observed clear evidences of transcription-associated mutational pressure in AAV: nucleotide usage biases are changing drastically after each of the three promoters: the higher the rate of transcription, the stronger the bias towards GC to AT mutations. Moreover, the usage of G decreased at the lower transcription rate (after P19 promoter) than the usage of C (after P40 promoter). Since nucleotide usage biases are retrospective indices, we created a scenario of changes in transcriptional map during the AAV evolution. Current mutational pressure directions are different for AAV types, while all of them demonstrate high rates of T to C transitions in the second long ORF. Since transcription rate and cell tropism are the main factors determining the preferable direction of nucleotide mutations in AAV, mutational pressure should be checked experimentally in DNA vectors before their final design with the aim to make the transferred gene more stable against those mutations.

The adeno-associated virus type 5 small rep proteins expressed via internal translation initiation are functional

Although precluded from using splicing to produce multiple small Rep proteins, adeno-associated virus type 5 (AAV5) generates a Rep40-like protein by alternative translation initiation at an internal AUG. A defined region upstream of the internal AUG was both required and sufficient to program internal initiation within AAV5 and may act similarly in heterologous contexts. The internally initiated AAV5 Rep40-like protein was functional and had helicase activity similar to that of AAV2 Rep40. Surprisingly, both the AAV5 Rep40-like protein and Rep52 were able to be translated from the AAV5 upstream P7-generated RNAs; however, the relative level of small to large Rep proteins was reduced compared to that of the wild type. A P19 mutant AAV5 infectious clone generated near-wild-type levels of the double-stranded monomer replicative form (mRF) replicative intermediate but reduced levels of virus, consistent with the previously defined role of Rep40-like proteins in genome encapsidation. Levels of mutant virus were dramatically reduced upon amplification.

The transcription strategy of bovine adeno-associated virus (B-AAV) combines features of both adeno-associated virus type 2 (AAV2) and type 5 (AAV5)

The parvoviruses bovine adeno-associated virus (B-AAV) and adeno-associated virus type 5 (AAV5) have similar transcription maps. However, while the AAV5 capsid gene promoter P41 possesses a high basal level in 293 cells, and is further activated only poorly by Rep during adenovirus type 5 (Ad5) infection, the B-AAV P41 promoter has a low basal activity within RepCap constructs in these cells and can be strongly activated by its Rep protein in the presence of Ad5 when a Rep-binding element (RBE) is included in cis at either end of the molecule. These differences are not due to differences in the intrinsic activating capability of the individual Rep proteins. Both viral promoters contain AP1 and CRE elements that contribute to their basal activity; however, the nature of the B-AAV P41 promoter itself and the surrounding sequences contribute to its relatively lower basal activity. In addition, the B-AAV upstream transcription units themselves also are activated in the presence of Ad5 and Rep. Thus, although the transcription map of B-AAV is much more closely related to AAV5, activation of its promoters is functionally more like the prototype AAV2.

The transcription profile of the bocavirus bovine parvovirus is unlike those of previously characterized parvoviruses

The Bocavirus bovine parvovirus generated a single pre-mRNA from a promoter at its left-hand end; however, the pattern of its alternative polyadenylation and splicing was different from that of other parvoviruses. A large left-hand-end open reading frame (ORF) encoded a nonstructural protein of approximately 95 kDa. An abundant, spliced, internally polyadenylated transcript encoded the viral NP1 protein from an ORF in the center of the genome. Transcripts encoding the capsid proteins were polyadenylated in the right-hand terminal palindrome. This is the first published transcription map of a member of the Bocavirus genus of the Parvovirinae.

Quantification of human bocavirus in lower respiratory tract infections in China

A quantitative PCR method was established to quantify human bocavirus (HBoV) genomic copies in clinical specimens from children with lower respiratory tract infections (LRTI) in China. A total of 257 respiratory tract specimens were tested, and 7 (2.7%) of these (all sputum samples) were positive, with genomic copies that ranged from 8.0 × 10³ to 8.0 × 10⁹ in the samples. The main clinical symptom of patients who were positive for HBoV DNA was a pneumonia-like syndrome represented by high fever and cough. Our results suggest that HBoV may be an important etiological agent of LRTI in children in China.

Upstream AP1- and CREB-binding sites confer high basal activity on the adeno-associated virus type 5 capsid gene promoter

In contrast to the prototype adeno-associated virus type 2 (AAV2), the capsid gene P41 promoter of AAV5, within viral constructs that lack inverted terminal repeat sequences, displays a high basal level of expression in 293 cells in the absence of coinfecting adenovirus. Here we demonstrate that this was due to differences in the relative strengths of the core promoter elements and to the presence of active binding sites for the transcription factors CREB and AP1 within the upstream region of P41 that are absent from the AAV2 capsid gene promoter P40. These differences also governed the relative basal activity of the AAV capsid gene promoters within near-full-length viral genomes.

Molecular characterization of caprine adeno-associated virus (AAV-Go.1) reveals striking similarity to human AAV5

The complete genome of the caprine adeno-associated virus (AAV-Go.1) was sequenced, and the expression profile of AAV-Go.1 was determined following virus infection in primary lamb kidney cells. A remarkable similarity between the Rep coding region, the ITR sequence and the central intron of AAV-Go.1, and the human derived AAV5 was observed. The transcription profile of AAV-Go.1 was also quite similar to that of AAV5. AAV-Go.1 was able to efficiently infect human cell lines, following co-infection of human adenovirus, and in reciprocal experiments, AAV5 also was able to efficiently infect primary lamb cells and bovine cell lines. Recombinant AAV5 and AAV-Go.1 expressing the beta-gal gene flanked by AAV5 ITRs, showed similar transduction efficiency in various human and animal cells. Studies of AAV-Go.1 may expand our understanding of the evolutionary relationship between the AAV-5-like group of AAVs, which, in addition to human derived AAV5, includes AAV viruses from bovine, caprine, and avian species.