Bat Influenza A(HL18NL11) Virus in Fruit Bats, Brazil

Abstract

Screening of 533 bats for influenza A viruses showed subtype HL18NL11 in intestines of 2 great fruit-eating bats (Artibeus lituratus). High concentrations suggested fecal shedding. Genomic characterizations revealed conservation of viral genes across different host species, countries, and sampling years, suggesting a conserved cellular receptor and wide-ranging occurrence of bat influenza A viruses.

Keywords: Atlantic forest; Brazil; HL18NL11; bats; influenza; influenza A virus; viruses; zoonoses.

Figure 1

Bat influenza A(HL18NL11) virus detection and genomic characterization, Brazil, 2010–2014. A) Distribution of Artibeus species bats carrying HL18NL11 in Central and South America, according to the Red List of Threatened Species from the International Union for Conservation of Nature (https://www.iucnredlist.org). Orange star indicates the sampling site of an HL18NL11-positive bat in Peru (5); blue star indicates the sampling site of the HL18NL11-positive bats in Brazil for this study. Maps were created using QGIS2.14.3 (http://www.qgis.org) with data freely available from http://www.naturalearthdata.com. B) Top, schematic representation of the genome organization of A/great fruit-eating bat/Brazil/2301/2012 (HL18NL11) and amino acid exchanges (black lines) compared with A/great fruit-eating bat/Brazil/2344/2012 (HL18NL11) and Peru HL18NL11 (GenBank accession nos. CY125942–49). Nucleotide sequence identities between the concatenated HL18NL11 (Brazil), HL17NL10, and HL18NL11 (Guatemala and Peru) sequences were calculated in SSE version 1.2 (http://www.virus-evolution.org/Downloads/Software) with a sliding window of 200 and step size of 100 nt. C) Homology model of the HL protein of A/great fruit-eating bat/Brazil/2301/2012 viewed from the top, modeled on the published crystal structure retrieved from the SWISS-MODEL repository (https://www.swissmodel.expasy.org). The putative RBS is shown in blue, 3 highly conserved residues (W153, H183, and Y195) in HAs and HLs are in purple, and amino acid substitutions between Brazil strains and the Peru prototype strain are in red. D) Homology model of the NL of A/great fruit-eating bat/Brazil/2301/2012 viewed from the top, constructed as in panel C. The putative active site is shown in a blue circle, the 6 residues (R118, W178, S179, R224, E276 and E425) conserved in influenza A virus neuraminidase genes are in purple, and amino acid substitutions between Brazil strains and the Peru prototype strain are in red. HA, hemagglutinin; HL, HA-like; NL, neuraminidase-like; RBS, receptor-binding site.

Figure 2

Phylogenetic relationships between bat influenza A viruses from Brazil and reference viruses. Phylogenetic trees show comparison of the 8 segments of representative influenza A virus genomes (PB2, PB1, PA, HA/HL, NP, NA/NL, M, NS) with A/great fruit-eating bat/Brazil/2301/2012 (HL18NL11a; GenBank accession nos. MH682200–7) and A/great fruit-eating bat/Brazil/2344/2012 (HL18NL11b; GenBank accession nos. MH682208–15), shown in red. Maximum-likelihood trees were inferred using a general time-reversible substitution model with a gamma distribution and invariant sites. Black dots represent bootstrap values >75% (1,000 replicates). Trees were generally rooted using influenza B/Lee/1940 (GenBank accession nos. DQ792894–901) (data not shown). Trees were constructed by using MEGA 6.0 (http://www.megasoftware.net). HA, hemagglutinin; M, matrix; NA, neuraminidase; NS1, nonstructural protein 1; NP, nucleoprotein; PA, polymerase acidic; PB, polymerase basic. Scale bars indicate nucleotide substitutions per site.