Rodent Virus Diversity and Differentiation across Post-Katrina New Orleans

Abstract

Concern about elevated disease risk following disasters has been growing with the progression of global trends in urbanization and climate, in part because shifts in socioecological conditions can promote greater human contact with pathogen reservoirs in cities. Remarkably little is known, however, about the diversity and distributions of pathogens carried by commensal reservoirs across disaster-affected urban landscapes. To address this deficit, we characterized the assemblage structure of viruses in the serum of three widespread commensal rodents (Rattus norvegicus, Rattus rattus, and Mus musculus) that were trapped in New Orleans (LA, USA) following Hurricane Katrina. We assessed virus diversity and differentiation according to host species identity, co-occurrence and abundance, as well as prevailing landscape features known to shape urban rodent assemblages. We detected ≥34 viruses in total, including several pathogens of concern, through metagenomic analysis of serum taken from ≥149 individuals of each host species. We found that virus richness as well as assemblage composition and spatial differentiation differed by host species. Notably, we detected associations with host species co-occurrence and abundance, and while we found that assemblage structure varied by study area, we did not detect strong associations with landscape features known to influence rodent hosts. Evidence that virus diversity and assemblage structure reflect host identity more so than other factors indicates that biotic benchmarks might serve as prognostic indicators of post-disaster pathogen exposure risk in cities worldwide.

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

“…During the lifetime of an animal, the virome varies in response to changes in the environment such as exposure to a new pathogen or changes in diet and individual characteristics, such as immune response or age 7,32 . Proper specimen collection is vital.…”

“…This would help determine viral tissue tropism and provide insight into routes of transmission 7 . The identification of viruses in environmental samples raises the question of whether these viruses are harbored by the host animal and cause infection, or merely infect insects, fungi, plants, or other environmental sources associated with the host's life habits 32 .…”

The ratting of North America: A 350-year retrospective on Rattus species compositions and competition

“…In that context, we believe that the transition between taxa represents a real change in species distribution, at least for the areas most intensively sampled here (i.e., those with denser human populations near North America's eastern coastlines), in which black rats became and then remained comparatively scarce following the surge in brown rat populations. At the same time, it is worth bearing in mind that both historical sources (6,11,47,48,59) and contemporary ecological research (60) indicate spatiotemporal heterogeneity in the disappearance and reappearance of black rat populations in North America. While published research of the contemporary distribution of black and brown rats in North America is limited, there are clear examples of sympatric populations [e.g., (60,61)].…”

“…At the same time, it is worth bearing in mind that both historical sources (6,11,47,48,59) and contemporary ecological research (60) indicate spatiotemporal heterogeneity in the disappearance and reappearance of black rat populations in North America. While published research of the contemporary distribution of black and brown rats in North America is limited, there are clear examples of sympatric populations [e.g., (60,61)]. Our data do not necessarily suggest that black rats disappeared entirely-a number of our samples confirm that they maintained a foothold in at least some areas (e.g., Virginia and Louisiana)-but rather that they became less common to the point where they were rarely incorporated into the archaeological records we have examined.…”