ARS | Publication request: Not so fast on recombination analysis of Newcastle disease virus

Submitted to: Journal of Virology
Publication Type: Other
Publication Acceptance Date: July 8, 2008
Publication Date: September 2, 2008
Citation: Afonso, C.L. 2008. Not so fast on recombination analysis of Newcastle disease virus. Journal of Virology. 82(18):9303.

Technical Abstract: Regarding the letter published in the Journal of Virology Vol. 82 No. 13 p. 6782 indicating that ¿powerful evidence¿ of recombination is a call for caution in the use of Newcastle Disease Virus (NDV) based vaccines, I would like to suggest that evidence for recombination is still weak. The authors cite three reports that suggest the existence of recombination, but a closer look reveals the possibility of oversight in the interpretation of the data (1, 2, 3). There is evidence of recombination in the existing GenBank NDV sequences, but unfortunately the vast majority of available Newcastle disease virus sequence has been obtained by PCR amplification of RNAs from crude field samples grown in eggs. In these samples the possibility of artificially reporting recombination caused by polymerase template switching need to be considered. With widespread use of live vaccines in poultry and with extensive presence of non virulent endemic NDV viruses in live bird markets and in wildlife (4), the existence of unnoticed mixed infections in field samples is likely. In the particular case of the three publications cited, the Chare and Han results are based on the analysis of Genbank sequences that were obtained without any particular purification. In Qin¿s manuscript, only three plaque purification steps were performed, and no attempts were made to confirm the absence of contaminant viruses in the sequenced samples, or to investigate the possibility of contamination with PCR products, which normally abound in NDV sequencing labs. In fact, despite of the availability of a large number of NDV sequences in GenBank databases, no NDV report exist that describes the generation of a natural progeny of viruses derived from a recombination event. Although I agree with the authors in the need for caution in the use of vaccines, caution in the interpretation of the data is also needed. 1. Han G. Z, He C. Q. , Ding N. Z. , and L. Y. Ma. Identification of a natural multi-recombinant of Newcastle disease virus. 2008.Virology. 371:54-60. 2. Qin Z., Sun L., Ma B, Cui Z., Zhu Y, Kitamura Y., and W. Liu. F gene recombination between genotype II and VII Newcastle disease virus. 2008. Virus Res.131:299-303. 3. Chare E.R., Gould E.A., and E. C. Holmes. Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA viruses. 2003. J. Gen. Virol. 84:2691-703 4. Kim L.M., King D.J., Curry P.E., Suarez D.L., Swayne D.E., Stallknecht D.E., Slemons R.D., Pedersen J.C, Senne D.A., Winker K., and C. L. Afonso. Phylogenetic diversity among low-virulence newcastle disease viruses from waterfowl and shorebirds and comparison of genotype distributions to those of poultry-origin isolates. 2007. J. Virol. 81:12641-12653.