Introduction
Influenza is still a major cause of health disorders and mortality
worldwide and affects a large portion of the human population each year,
this potential could cause epidemics in humans, such as H1N1 virus
pandemic in 2009. In addition, many species of animals, including birds,
pigs, horses, and dogs, can be infected with influenza
viruses.12
Influenza viruses belong to the Orthomyxoviridae family defined by
viruses that have a negative-sense, single-stranded, and fragmented RNA
genome. There are currently 18 different hemagglutinin subtypes (H1 to
H18) and 11 different neuraminidase subtypes (N1 to N11) for influenza A
viruses.3 Antigenic
changes occur only in the proteins of influenza virus neuraminidase and
hemagglutinin, and hemagglutinin is more important than neuraminidase
because hemagglutinin is more susceptible to such changes.
The history of the first influenza A (H1N1) pandemic in the 21st century
(March 2009) occurred 33 years after the last pandemic of the 20th
century (1976), followed by the detection of cases in the United States
and many other countries. With the spread of the disease to several
continents in April, the sixth phase of the pandemic was announced by
the World Health
Organization.4 On the
other hand, the emergence and pandemic of influenza A (H1N1) virus with
swine-origin occurred so suddenly that apparently the pathogenic stages
in environment (first phase), pathogenicity in pigs (second phase),
transmission from pig to human (third phase), limited human-to-human
transmission in Mexico (fourth Phase), limited human outbreaks in the
Americas (fifth Phase), and widespread epidemics across the continent
(sixth Phase) occurred in less than three months.
With respect to viral epidemics that may emerge, molecular
epidemiological techniques have been useful tools in detecting the
source of epidemics and tracking the spread of regional or global
viruses. In this regard, phylogenetic methods, a kind of mathematical
modeling, provide new opportunities to study the evolutionary history of
pathogens and to reconstruct the spatio-temporal and demographic
dynamics of viral epidemics. Many viruses, such as the influenza virus,
evolve faster than normal transmission, and phylogenetic techniques as
an ideal and objective tool can be used for reconstructing
spatio-temporal dynamics and transmission history.
Phylogeography is the study of historical processes that may have shaped
the current geographical distribution of living species, such as
viruses. Nowadays, these studies are performed according to the
information obtained from the genealogy. Recent advances have made it
possible to integrate the theory of coalescent into phylogeography in
such a way that both demographic and spatial aspects of the epidemic are
inferred simultaneously. This information is used to track the patterns
of viral spread, which in turn can become effective intervention and
prevention strategies and can shed light on the main factors responsible
for the spread and transmission of the
virus.5
One of the limitations of the traditional epidemiological approaches is
their inability to estimate the path of the virus and identify the
estimated time and place of virus entry into a specific geographical
area based on available data. Bayesian phylogeographical approaches
using nucleotide sequences have made it possible to study the path of
the virus and the approximate time and place of virus entry into a
population along with other characteristics such as molecular dynamics
and so on. In this study, we investigate the above gaps using the
Bayesian phylogeographic approach for influenza virus H1N1 serotypes in
Iran and neighboring countries.