Xapuri virus, a novel mammarenavirus: natural reassortment and increased diversity between New World viruses

Figures & data

Rodents captured in three localities from Acre state, Brazil, 2015–2016, by species and locality

Species	Number of captured rodents
	Porto Acre	Rio Branco	Xapuri	Total
Euryoryzomys macconelli	—	—	1	1
Hylaeamys perenensis	—	—	2	2
Hylaeamys yunganus	1	—	1	2
Mesomys hispidus	1	—	1	2
Neacomys musseri	—	—	4	4
Neacomys spinosus	8	3	6	17
Oecomys bicolor	7	2	—	9
Oecomys sp.	—	—	1	1
Oligoryzomys microtis	1	3	—	4
Proechimys brevicauda	2	—	—	2
Proechimys gardneri	1	1	—	2
Proechimys simonsi	—	2	—	2
Rhipidomys leucodactylus	1	—	—	1
	22	11	16	49

Fig. 1 Municipalities of Acre state, Brazil, in which rodents were captured

Fig. 2 Xapuri mammarenavirus genome organization and potential secondary structure of intergenic regions

Nucleotide and amino acid identities of XAPV compared with New World representatives of the genus Mammarenavirus

Virus species	p distance
	L segment (nt)			S segment (nt)
		Z (aa)	L (aa)		NP (aa)	GPC (aa)
Allpahuayo	46.7%	50.7%	56.2%	39.9%	45.0%	44.3%
Amaparí	41.2%	48.0%	48.4%	39.8%	40.5%	53.4%
Bear Canyon	47.4%	53.3%	56.9%	42.1%	46.0%	50.6%
Chapare	41.8%	48.0%	48.7%	37.6%	38.7%	46.2%
Cupixi	42.8%	46.7%	48.9%	40.3%	38.9%	51.5%
Flexal	48.1%	52.0%	57.1%	39.9%	44.6%	42.0%
Guanarito	42.8%	40.0%	48.7%	38.8%	39.5%	52.4%
Junín	43.2%	46.7%	50.7%	38.5%	41.5%	48.5%
Latino	42.6%	50.7%	50.2%	35.2%	38.9%	44.8%
Machupo	43.1%	45.3%	48.7%	38.9%	38.5%	47.3%
Oliveros	42,4%	49.3%	48.6%	34.8%	38.5%	34.8%
Paraná	46.3%	52.0%	56.0%	39.6%	45.6%	45.5%
Pichindé	46.8%	56.0%	57.3%	40.8%	45.4%	44.3%
Pirital	46.7%	58.7%	55.7%	39.7%	44.6%	46.6%
Sabiá	41.9%	46.7%	49.6%	37.6%	40.3%	48.3%
Tacaribe	43.0%	46.7%	49.5%	41.5%	42.8%	48.3%
Tamiami	47.8%	48.0%	56.5%	41.6%	47.0%	51.0%
Whitewater Arroyo	47.3%	54.7%	57.2%	42.0%	47.7%	50.8%

XAPV Xapuri virus

Fig. 3 Phylogenetic tree based on the mammarenavirus complete L segments, with ML and Bayesian methods, using the evolutionary model GTR + G + l

. Numbers (≥0.7/≥70) above branches indicate node probabilities or bootstrap values (MrBayes/ML). Asterisks indicate values below 0.7/70. Sequences from this study are highlighted in bold

Fig. 4 Phylogenetic tree based on the mammarenavirus complete S segments, with ML and Bayesian methods, using the evolutionary model GTR + G + l

. Numbers (≥0.7/≥70) above branches indicate node probabilities or bootstrap values (MrBayes/ML). Asterisks indicate values below 0.7/70. Sequences from this study are highlighted in bold

Fig. 5 Phylogenetic trees based on the complete NP, GPC, Z, and L mammarenavirus proteins, using ML and Bayesian methods, (Z protein) complete Z, using the evolutionary model RtREV + G + I, (RdRp protein) complete L, using the evolutionary model LG + G + I, (GPC protein) complete GPC, using the evolutionary model LG + G + I, and (NP protein) complete NP, using the evolutionary model.

Numbers (≥0.7/≥70) above branches indicate node probabilities or bootstrap values (MrBayes/ML). Asterisks indicate values below 0.7/70. ^†Exhibited a difference between ML and MrBayes tree-building method topologies. Sequences from this study are highlighted in bold