In the case of FIV, the approach gives us a 95% confidence interval for the model parameters, in particular for the basic reproductive number R 0 ([0.626, 1.942]), with a maximum likelihood estimate of 1.285. This value appears rather low, meaning that virus transmission is rather rare at the level of the population. This is not surprising, since experimental results indicate that most of the virus present in the saliva is not infectious [39] , suggesting a weak efficiency in disease transmission [7] . Given the high frequency of fights between males in such populations and the low rate at which males acquire the infection (around once every four years in a hypothetical scenario where all males are infected), our results are consistent with the concept of a low probability of virus transmission from bites [9] . Multiplex primer prediction software for divergent targets We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets to amplify all members of large, diverse and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers (∼3700 18-mers or ∼2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus (FMDV), hemagglutinin (HA) and neuraminidase (NA) segments of influenza A virus, Norwalk virus, and HIV-1. We empirically demonstrated the application of the software with a multiplex set of 16 short (10 nt) primers designed to amplify the Poxviridae family to produce a specific amplicon from vaccinia virus. Researchers employ numerous approaches for viral detection and discovery, including metagenomic sequencing (1) (2) (3) , microarrays (4) (5) (6) (7) (8) (9) or multiplex PCR followed by other methods of characterization such as mass spectrometry (10) (11) (12) (13) (14) , suspension arrays (15, 16) or amplicon sequencing (17) . Multiplex PCR followed by analysis of amplified products fills a niche for viral identification when singleplex PCR has failed or there are a few dozen likely candidates but the expense of metagenomic sequencing or high-density microarrays is unwarranted (18) . However, multiplex primer design for many highly divergent targets is challenging since no universally conserved primers may exist, and finding sets of primers likely to function well in multiplex (e.g. isothermal T m 's, no primer dimers) adds to the complexity of finding conserved primer candidates. Primer design software that requires a multiple sequence alignment (MSA) as input can be problematic for diverse target sets, as MSAs can be difficult to construct, exhausting memory or available time before an alignment is completed. Even if an alignment does complete for divergent target sets such as all members of a family of RNA viruses or gene homologues across species, alignments may show little nucleotide sequence conservation, and multiple primers are required to amplify all targets. Considering the challenges of primer design for targets showing sequence variation, it is not surprising that many of the PCR-based assays in the literature are predicted to fail to detect desired targets when compared against available sequence data, and this problem is worst at higher taxonomic levels like family (19) .