Analysis of the termini of the DNA of bovine parvovirus: demonstration of sequence inversion at the left terminus and its implication for the replication model

Abstract

The distribution of terminal-sequence orientations in the viral DNA of bovine parvovirus (BPV), an autonomous parvovirus, was studied by end labeling and restriction enzyme digestion and also by cloning. The left (3') end of the minus strand of BPV was found in two alternative sequence orientations (designated as flip and flop, which are reverse complements of each other), with a 10-fold excess of flip. This is in contrast to the autonomous rodent parvoviruses which encapsidate'minus-strand DNA with only the flip orientation at this end. The right (5') end of the minus strand of BPV contained both sequence orientations with equal frequencies, as in the rodent parvoviruses. Sequence inversions were also detected'at both ends of the plus strand,'which makes up about 10% of the encapsidated BPV DNA. Each terminus of BPV DNA had a characteristic ratio of flip to flop forms, and this ratio was restored in the progeny DNA resulting from transfection with genomic clones of different defined terminal conformations. Replicative-form DNA showed the same distribution of terminal-sequence orientations as the reannealed plus and minus virion DNAs, suggesting that the distribution of flip and flop forms observed in virion DNA is not due to selective encapsidation, but rather to the specific distribution of replicative forms. The current replication model for autonomous parvoviruses, which was based on the available data for the rodent parvoviruses, cannot account for the observed distribution of BPV DNA. An alternative model is suggested.

In vivo resolution of circular plasmids containing concatemer junction fragments from minute virus of mice DNA and their subsequent replication as linear molecules

“…Such a mechanism is compatible with the observed replication products of parvoviruses, such as the adeno-associated viruses (AAV), which have inverted terminal repeats and can be partially reproduced in vitro with hairpinned AAV termini and infected-cell extracts (40) or purified, virally encoded proteins (25). However, this mechanism is difficult to reconcile with the observed replication products of viruses which have unique termini (1,2,8,18). Parvoviral palindromes contain a number of mispaired bases, and replication by a simple hairpin transfer mechanism must result in the generation of two complementary forms of each palindrome designated "flip" and "flop."…”

Identification and molecular cloning of a novel porcine parvovirus

“…Parvoviruses have been proposed to replicate their genomes via a modified rolling hairpin model that involves a hairpin transfer mechanism [3,5,8]. In this model, two obligatory dimeric genome replicative intermediates (RF) generated via the terminal palindromic sequences are synthesized during viral DNA replication [6]. These dimeric RFs contain a sense-strand and a minusstrand, i.e., a double-stranded genome, that are covalently linked (via terminal palindromic self-priming) either at the left end or right end of the linear genome and give rise to head-to-head or tail-to-tail concatameric molecules.…”

The silent spread of Porcine Bocavirus in Croatian pigs: should we be concerned?

“…Bocaviruses are isometric, non-enveloped, autonomously replicating, single-stranded DNA viruses containing a genome of approximately 5 kb in length. According to some previous findings, bocaviruses are involved in the development of respiratory and enteric infections in humans and animals (Chen et al, 1986;Chen et al, 1988; Acta Veterinaria Hungarica 65, 2017 Schwartz et al, 2002;Allander et al, 2005;Manteufel and Truyen, 2008;Chen et al, 2010;Kapoor et al, 2010a, b).…”