Avian Influenza H7N9 Virus Adaptation to Human Hosts

Abstract

Avian influenza virus A (H7N9), after circulating in avian hosts for decades, was identified as a human pathogen in 2013. Herein, amino acid substitutions possibly essential for human adaptation were identified by comparing the 4706 aligned overlapping nonamer position sequences (1–9, 2–10, etc.) of the reported 2014 and 2017 avian and human H7N9 datasets. The initial set of virus sequences (as of year 2014) exhibited a total of 109 avian-to-human (A2H) signature amino acid substitutions. Each represented the most prevalent substitution at a given avian virus nonamer position that was selectively adapted as the corresponding index (most prevalent sequence) of the human viruses. The majority of these avian substitutions were long-standing in the evolution of H7N9, and only 17 were first detected in 2013 as possibly essential for the initial human adaptation. Strikingly, continued evolution of the avian H7N9 virus has resulted in avian and human protein sequences that are almost identical. This rapid and continued adaptation of the avian H7N9 virus to the human host, with near identity of the avian and human viruses, is associated with increased human infection and a predicted greater risk of human-to-human transmission.

UNIQmin, an alignment-free tool to study viral sequence diversity across taxonomic lineages: a case study of monkeypox virus

“…However, this maximum possible entropy value is theoretical given the need to maintain conservation among related sequences for viability. According to Hu et al (2013), the maximum entropy value of 9.2 was observed for envelope protein of human immunodeficiency virus type 1, clade B subtype (HIV-1 clade B), which is significantly higher than that of avian influenza [10,33,34], dengue [35] and West Nile [36] viruses. Similarly, HIV-1 clade B proteome showed the highest mean nonamer entropy value (1.9 – 4.2) compared to other viruses.…”

“…According to Hu et al (2013), the maximum entropy value of 9.2 was observed for envelope protein of human immunodeficiency virus type 1, clade B subtype (HIV-1 clade B), which is significantly higher than that of avian influenza [10,33,34], dengue [35] and West Nile [36] viruses.…”

Genomic characterization of Rocahepevirus ratti hepatitis E virus genotype C1 in Yunnan province of China

“…However, there were several substitutions in other motifs in RdRp, compared with the Rocahepevirus prototype sequence GU345042. It has been documented that the amino acid substitutions might affect viral replication, viral load, and mortality ( Parvez, 2017 ), and be associated with zoonotic infection ( Tan et al., 2021 ). However, further investigation is required to unveil the specific impacts of amino acid mutations on rat and human HEV-C1.…”

An Alignment-Independent Approach for the Study of Viral Sequence Diversity at Any Given Rank of Taxonomy Lineage

“…The length of nine amino acids is reported to be typical for peptides bound to HLA class I and as the binding core for peptides bound to HLA class II [ 28 , 32 ]. As such, a k -mer size of nine may be considered for immunological or biological applications in general [ 17 , 33 , 34 , 35 ]; however, emphasis should be given to the research question for the relevance of the k -mer size. The length of the longest sequence in the dataset as the largest k -mer size that can be used, is not recommended, as there would be no or limited (potentially, if unique partial sequences are present in the dataset) compression of the initial input set.…”