Wild aquatic birds are considered the natural hosts of 16 HA (H1–H16) and 9 NA (N1–N9) subtypes of influenza A viruses (FLUAV) found in different combinations. H14 FLUAVs are rarely detected in nature. Since 2011, H14 FLUAVs have been consistently detected in Guatemala, leading to the largest collection of this subtype from a single country. All H14 FLUAVs in Guatemala were detected from blue-winged teal samples. In this report, 17 new full-length H14 FLUAV genome sequences detected from 2014 until 2019 were analyzed and compared to all published H14 sequences, including Guatemala, North America, and Eurasia. The H14 FLUAVs identified in Guatemala were mostly associated with the N3 subtype (n = 25), whereas the rest were paired with either N4 (n = 7), N5 (n = 4), N6 (n = 1), and two mixed infections (N3/N5 n = 2, and N2/N3 n = 1). H14 FLUAVs in Guatemala belong to a distinct H14 lineage in the Americas that is evolving independently from the Eurasian H14 lineage. Of note, the ORF of the H14 HA segments showed three distinct motifs at the cleavage site, two of these containing arginine instead of lysine in the first and fourth positions, not previously described in other countries. The effects of these mutations on virus replication, virulence, and/or transmission remain unknown and warrant further studies.

Information on Influenza A virus (IAV) prevalence in shorebird populations in Guatemala is scarce, and no live captures of shorebirds have been made for this purpose. The only reported case of Influenza A in shorebirds in Guatemala corresponded to a harvested individual. To update and obtain information of IAV in shorebirds, a transversal study was made on the South Coast of Guatemala. The main objective of this study was to evaluate presence of Influenza A among migratory shorebirds in stopover areas in the country. Captures and sampling took place in three sites during migration (October–April) over three migratory periods (2016–2017, 2017–2018, and 2018–2019). In total, 127 shorebirds belonging to 14 species of genera Calidris, Charadrius, Tringa, and Actitis were captured using mist nets. Tracheal and cloacal swabs were collected from each bird using a cotton swab, then tested with RT-PCR techniques targeting Influenza A. Blood samples were taken from the jugular or basilic vein to obtain serum that later was tested using a commercial ELISA Kit for detection of antibodies against Influenza A. Birds were released after sampling. All samples were PCR negative (0/127).One sandpiper specimen (Calidris minutilla) tested sero-positive to Influenza A through the ELISA test (1/122). These results suggest that IAV infection in this region may be minimal, as other studies have reported; nevertheless, it is important to consider that sample size was small in this study, and that the species included may not be the best indicators.