The transmission dynamics and diversity of human metapneumovirus in Peru

Abstract

BackgroundThe transmission dynamics of human metapneumovirus (HMPV) in tropical countries remain unclear. Further understanding of the genetic diversity of the virus could aid in HMPV vaccine design and improve our understanding of respiratory virus transmission dynamics in low‐ and middle‐income countries.Materials & MethodsWe examined the evolution of HMPV in Peru through phylogenetic analysis of 61 full genome HMPV sequences collected in three ecologically diverse regions of Peru (Lima, Piura, and Iquitos) during 2008‐2012, comprising the largest data set of HMPV whole genomes sequenced from any tropical country to date.ResultsWe revealed extensive genetic diversity generated by frequent viral introductions, with little evidence of local persistence. While considerable viral traffic between non‐Peruvian countries and Peru was observed, HMPV epidemics in Peruvian locales were more frequently epidemiologically linked with other sites within Peru. We showed that Iquitos experienced greater HMPV traffic than the similar sized city of Piura by both Bayesian and maximum likelihood methods.ConclusionsThere is extensive HMPV genetic diversity even within smaller and relatively less connected cities of Peru and this virus is spatially fluid. Greater diversity of HMPV in Iquitos compared to Piura may relate to higher volumes of human movement, including air traffic to this location.

Pediatric burden and seasonality of human metapneumovirus over 5 years in Managua, Nicaragua

“…A2c and A2b genetic groupings were more common, 6 than samples derived from Europe, multiple lineages circulating in a specific season are common and found globally 3,6,10,15,16,30,31,38,45,47,[53][54][55][56][57] without substantial changes to their yearly seasonal dynamics.…”

Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia

“…Nasopharyngeal and oropharyngeal (NP-OP) swab samples were collected from children (1–59 months) hospitalized with pneumonia, four of whom were enrolled in the PERCH study [18] in 2012. The fifth sample was collected from a child enrolled in the routine pneumonia surveillance study at Kilifi County Hospital, Kenya, in 2015.…”

“…PCR approaches for targeted whole genome sequencing, in contrast to random amplification, can preferentially amplify the target virus over host or environmental nucleic acids [16, 17] potentially focusing sequencing on the virus of interest. To date, the largest dataset of HMPV whole genomes ( n = 61 ) sequenced from any tropical country is from three Peruvian cities, Lima, Piura and Iquitos [18]. In Africa, apart from one metapneumovirus genome identified from a wild mountain gorilla in Rwanda (GenBank accession number HM197719), there are no HMPV genomes reported according to the NIAID Virus Pathogen Database and Analysis Resource (ViPR, http://www.viprbrc.org/, accessed April 30, 2019).…”

Pediatric burden and seasonality of Human Metapneumovirus over five years in Managua, Nicaragua.

“…It is therefore unlikely that changes in lineage effect the number of severe ALRI outcomes. While specific genetic groupings are globally more common in specific regions, for example in Asian countries after 2005 A2c and A2b genetic groupings were more common 6 , than samples derived from Europe, multiple lineages circulating in a specific season are common and found globally 3,6,10,15,16,28,29,36,40,42,[48][49][50][51][52] without substantial changes to their yearly seasonal dynamics.…”