Rio Mamore Hantavirus Endemicity, Peruvian Amazon, 2020

Abstract

To explore hantavirus infection patterns in Latin America, we conducted molecular and serologic hantavirus investigations among 3,400 febrile patients from Peru during 2020-2021. Reverse transcription PCR indicated that a patient from Loreto, in the Peruvian Amazon, was positive for Rio Mamore hantavirus (serum, 3.8 × 10³ copies/mL). High genomic sequence identity of 87.0%-94.8% and phylogenetic common ancestry with a rodent-associated Rio Mamore hantavirus from Loreto in 1996 indicated endemicity. In 832 samples from Loreto, hantavirus incidence based on IgM ELISA of pooled Sin Nombre (SNV) and Andes virus (ANDV) nucleoproteins and immunofluorescence assay-based end-point titration using SNV/ANDV/Hantaan/Puumala/Saarema/Dobrava/Seoul hantaviruses was 0.5%. Across 3 ecologically distinct departments in Peru, SNV/ANDV IgG ELISA/IFA-based reactivity was 1.7%, suggesting circulation of antigenically distinct New World hantaviruses. Testing for arboviruses, nonendemic pathogens, and antigen-free ELISA corroborated nonspecific reactivity in 2 IgG and several IgM ELISA-positive serum samples. Hantavirus diagnostics and surveillance should be strengthened in Peru ad across Latin America.

Keywords: Peru; Peruvian Amazon; Rio Mamore virus; ecology; genome; hantaviruses; serology; viruses; zoonoses.

Figure 1

Locations and climate classifications related to study of Rio Mamore hantavirus endemicity in the Peruvian Amazon, 2020. A) Location of Peru (green) in South America. B) Regions in Peru where 3,400 serum samples from febrile patients were collected and stored during a dengue outbreak that overlapped with COVID-19 (24) in 3 diverse ecoregions: Loreto (Amazon; n = 1,972 samples), Lambayeque (coastal desert /dry forest; n = 743 samples), and Lima (coastal desert; n = 685 samples) (One Earth, https://www.oneearth.org). C) Climate classification regions of Peru and distribution of Oligoryzomys microtis small-eared rice rats (white dots) (https://www.gbif.org) (26). All maps were created by using QGIS 3.28.10 (https://hub.arcgis.com) based on freely available maps from Bucknell University.

Figure 2

Phylogenetic relationships between partial concatenate sequences of RIOMV from Peru (RIOMV PER 2020, depicted in red) and reference sequences. The phylogenetic trees were constructed by using MrBayes 3.2.6 (http://mrbayes.csit.fsu.edu) and a general time-reversible substitution model with gamma distribution. Black circles at nodes indicate posterior probability >0.80. Reference sequences are available in Appendix 1. A) Partial sequence of the small segment (1,393 nt). B) Partial sequence of the medium segment (1,914 nt). C) Partial sequence of the large segment (1,617 nt). LAIN, Laibin mobatvirus

Figure 3

Sequence identity plot comparing RIOMV variants from Peru (RIOMV PER 2020 and RIOMV PER 1996) and Brazil (RIOMV BRA 2005). The identity plot was calculated by using SSE (http://www.virus-evolution.org) with partial concatenate sequences for the alignment of RIOMV (Appendix 1 Figure 2), a fragment length of 200 nt, and an increment between fragments of 50 nt. GenBank accession nos., RIOMV 1996 (FJ532244, FJ608550, FJ809772) and RIOMV Brazil 2005 (JX443679, JX443700, JX443697). L, large; M, medium; RIOMV, Rio Mamore virus; S, small.

Figure 4

Investigation of unspecific reactivity in serum positive in hantavirus IgM ELISA, Peru. A) OD₄₅₀ in noncoated ELISA plate. B) Comparison of IgM ELISA reactivity for different arboviruses: Control group, n = 38; hantavirus IgM–positive by ELISA group, n = 12. Tukey-style box plots are given with medians (thick lines within boxes) and interquartile ranges (box top and bottom or left and right edges); whiskers indicate 1.5× interquartile range. CCHFV, Crimean-Congo hemorrhagic fever virus, CHIKV, chikungunya virus, MAYV, Mayaro virus; OD₄₅₀, optical density at 450 nm; OROV, Oropouche virus.

Figure 5

Investigation of unspecific reactivity in serum samples positive in hantavirus IgG ELISA, Peru. A) OD₄₅₀ in noncoated ELISA plate. B) Comparison of IgG ELISA reactivity for different viruses excluding the CMV-positive samples. Control group, n = 38 ; hantavirus IgG IFA-negative samples, n = 7; hantavirus IgG IFA-positive samples, n = 13. Tukey-style box plots are given with medians (thick lines within boxes) and interquartile ranges (box top and bottom or left and right edges); whiskers indicate 1.5 × interquartile range. CCHFV, Crimean-Congo hemorrhagic fever virus, CHIKV, chikungunya virus; CMV, cytomegalovirus; IFA, immunofluorescence assay; MAYV, Mayaro virus; MERS-CoV, Middle East respiratory syndrome coronavirus; neg, negative; pos, positive; OD₄₅₀, optical density at 450 nm; OROV, Oropouche virus.