Influenza A virus (IAV) is found in aquatic birds. Over time, the virus became pathogenic due to mutations in the hemagglutinin (HA) cleavage site. This pathogenic virus can have dire consequences if transmitted into poultry, especially economic costs and potential for human infection. Past studies have shown that the transmission of IAV from aquatic birds to poultry can occur.
Ramey et al. published a paper in 2016 that investigated the following three things: source for the mutated IAV H7N3, timeframe when IAV H7N3 was introduced into pheasants, and co-occurrence of internal gene segments with glycoproteins. This study was conducted using various protocols and experiments. First, the researchers isolated the H7N3 strain from a pheasant and used reverse transcriptase to synthesize DNA from RNA. The DNA was then sequenced. The scientists obtained sequences of H7 hemagglutinin and N3 neuraminidase (NA) that were reported in the past 14 years (Group 1) as well as the H7N3 swabbed from blue-winged teal (Group 2). Secondly, maximum-likelihood phylogenies were used to look at the genetic relationships between the H7N3 isolate, Group 1, and Group 2. Thirdly, nucleotide pairwise distance was calculated to determine shared nucleotide sequences. This is helpful in determining the co-occurrence of internal gene segments with glycoprotein.
Using the above study design, the researchers observed the following results for H7 HA. The maximum-likelihood phylogeny showed that the H7 HA segment of the isolate was similar to the H7 HA segment of the viruses from Group 2. This data indicates that a common ancestry occurred back in 2013. Additionally, the H7 HA gene from the isolate had 65 sequences that were similar to the H7 HA sequences from Group 1 and Group 2. The nucleotide pairwise distance results show a high similarity between the H7 HA from the isolate and Group 2.
The following results were obtained for N3 NA. The maximum-likelihood phylogeny showed that the N3 NA segment of the isolate was similar to the N3 NA segment of the viruses from Group 2. This data indicates that a common ancestry occurred back in 2004. Additionally, the N3 NA gene from the isolate had 112 sequences that were similar to the N3 NA sequences from Group 1 and Group 2. The nucleotide pairwise distance results show a low similarity between the N3 NA from the isolate and Group 2.
This study was successful in determining the date for common ancestry for both the H7 HA and N3 NA by comparing the phylogenies of the isolate, Group 1, and Group 2. However, the study was not able to identify the antecedent virus strain. The theme of the paper is viral diversity that exists in aquatic birds, which has the potential to impact poultry by transmission of IAV.
The study mentioned above is valuable in many ways. First, the researchers have assessed the phylogenetic relationships among the isolate with other viruses. This gives us information about the genetics behind the isolate, which can be helpful in carrying out further research projects that aim to develop an antiviral or vaccines. Secondly, the design of the study can be replicated when researching other diseases. For example, a new virus that has recently emerged can be compared with viruses that it may be most common with. If the virus has a specific protein, then the sequences that code for the protein can be compared with sequences from similar viruses. This can be used to identify viruses based on specific properties. Phylogenetic trees can be made to study relationships with other viral species as well.
This research adds a lot to our understanding as aspiring researchers and wildlife disease enthusiasts. After reading this paper, I am more aware about the experiments that can be conducted to analyze the relationships between a new virus and old viruses. These experiments include maximum-likelihood phylogeny and nucleotide pairwise distance. Secondly, the evolution of viruses can be studied to predict future mutations that may occur and how the viruses may evolve in the future. This is also a good way to keep records of emerging viruses.
Ramey AM, Torchetti MK, Poulson RL, Carter D, Reeves AB, Link P, Walther P, Lebarbenchon C, Stallknecht DE. 2016. Evidence for wild waterfowl origin of H7N3 influenza A virus detected in captive-reared New Jersey pheasants. Arch Virol. [Internet]. Retrieved from http://link.springer.com.pitt.idm.oclc.org/article/10.1007%2Fs00705-016-2947-z