Overview

Human parainfluenza viruses (HPIVs) are a type of respiratory RNA virus predominantly obtained from human-human interactions from sneezing, coughing, and touching surfaces with viral particles. Similarly to other viruses, research and case studies have indicated that HPIVs undergo mutation, drastically affecting viral infection and vaccine development. Identifying and recognising viral mutations in parainfluenza is integral to constructing an effective medical and epidemiological anti-viral strategy.

Basics of viral mutation

General mechanism of viral mutation

Mutations are common genetic occurrences that happen during cell division. When viruses replicate, they copy their genetic information, or nucleic acid sequence, which can be mistakenly replicated, resulting in mutation.

There are three types of mutations:¹

• Point mutation – one nucleotide is replaced with another
• Insertion – addition of one or more nucleotides
• Deletion – deletion of one or more nucleotides　　

As DNA is directly responsible for the sequencing of proteins, mutations result in the alteration of protein structure and function, consequently affecting viral mechanisms.

Significance of mutation in viruses

We often hear the word “mutation” in our news, especially related to COVID-19, and we even hear it mentioned in science fiction films. This public awareness is both a positive and a negative, and often can lead to misunderstanding of the term. 

Mutation is a natural part of viral activity, as incorrect copying of nucleotides occurs regularly. Out of those mutations, only a handful influence viral mechanisms.² Therefore, when taking account of all mutations that occur in a cell, the effects on viral activity and infection are relatively low.

Considering this, significant mutations can severely affect pathogenesis and treatment methods. Molecular alteration in structural proteins and receptors affects several steps of the RNA virus cycle, including binding, fusion, uncoating, replication, budding and release. These mutations can increase viral replication and survival, resulting in increased infection and disease severity, or, reduced vaccine efficacy.³ For this reason, viral mutations are a key factor in combating epidemic/pandemic diseases – the most familiar case being the COVID-19 pandemic, where a range of variants such as delta and omicron were formed due to mutations.

Parainfluenza virus

Epidemiology in the UK

HPIVs have 4 subtypes and all are common respiratory viruses found in the UK. The table below summarises a study undertaken from 1998 to 2013, regarding the proportion of cases for each HPIV subtype and their seasonality.³

In the UK, HPIV infections are more commonly found in infants and children than in older age groups, although this trend is gradually reversing.⁴

Genetic composition of parainfluenza virus

The genetic composition of HPIV consists of a genome 14.9 to 17.3 kilobases in size.⁵ To put it into comparison, COVID-19 viruses have 29.8 to 29.9 kilobases.⁶ Typically, viruses with genomes that are smaller have higher mutation rates, as mutation results in loss of genes. HPIV subtypes 1 to 4 share similar biomolecular structures, but their differences arise in the age group they infect and the type of symptoms.⁷

The HPIV genome codes for 6 proteins, including:

• The Nucleocapsid proteins (NP)
• Phosphoprotein (P)
• Fusion Glycoprotein (F)
• The matrix protein (M)
• The haemagglutinin-neuraminidase glycoprotein (HN)
• RNA polymerase (L)⁸

These proteins are important for a range of viral functions, for example, RNA polymerase is used for synthesising new RNA strands for replication, while matrix proteins are important in viral assembly.⁹

Mutation rates in RNA viruses

Typically, mutation rates in RNA viruses are 10^-6 to 10^-4 substitutions per nucleotide per cell infection (s/n/c).¹⁰ This is much faster than DNA viruses (10^-8 to 10^-6 s/n/c), suggesting that RNA viruses such as HPIVs are more likely to develop molecular changes that could be influential in medicine development and pathophysiology.

Evidence of mutations in parainfluenza virus

Historical data on parainfluenza virus mutations

The build-up of mutations results in a gradual shift in protein conformation, resulting in the formation of lineages with viral subtypes. A study conducted in China from 2012 to 2018 highlighted that HIPV subtypes give rise to several lineages due to mutation. In this particular case, 1 lineage for HIPV type 1, 2 for HIPV type 2, 19 for HIPV type 3, and 2 for HIPV type 4.⁵ In the same study, the recombinant analysis showed that HIPV type 3 strains in China undergo mutations similar in genetic nature to strains found in the US, although this was specific to HIPV type 3 only and was not recorded in other subtypes of HIPV.⁵

Formation of lineages/variants occurs due to mutations at genes that code for proteins integral to the virus life cycle, for example, mutations in the HN gene sequences give rise to HIPV type 2 lineages.¹¹ 

Recent research and developments

Improvements in genetic sequencing and manipulation techniques have allowed a more efficient identification of mutated nucleotides and the characterisation of their biomolecular and pathophysiological outcomes. For example, in HPIV type 3, mutations in haemagglutinin-neuraminidase (HN) glycoprotein increase receptor binding, allowing the development of resistance to anti-viral medicines that inhibit receptor interaction, such as Zanamivir.¹² 

On the other hand, some mutations were also found to hinder viral activity. For example, point mutations in HPIV type 2 prevent viral replication by inhibiting minigenome replication.¹³ 

Furthermore, mutations in the DI-DII linker in the F protein of HPIV type 3 reduces fusion activity.¹⁴ Understanding the consequences of mutation is important in clarifying the function of the gene in question, which further expands the pool of potential targets for anti-viral drugs.

Implications of parainfluenza virus mutations

Impact on disease epidemiology

As mentioned previously, mutations occur frequently and most do not affect a molecule’s biochemical mechanism. For this reason, mutations rarely affect viral outbreaks.² If mutations that affect viral activity do occur, it is likely to affect the epidemiology of the virus too. Perhaps the change in trend observed in HPIV cases in the UK could be due to mutation, however, there is not enough scientific research to support this. 

Vaccine development and effectiveness

Currently, there are no vaccines against HIPV vaccines to protect from infection (Centers For Disease Control and Prevention). However, multiple live-attenuated HPIV vaccines against HPIV type 1 to 3 are in the testing stage, where vaccines against HPIV type 3 have experienced greater advancements compared to the other two subtypes.¹⁵

Since RNA viruses have high mutation rates compared to DNA viruses, the production of vaccines usually faces major issues. This is due to antigenic drift that is caused by mutation. Antibodies produced in the body following vaccination target viral surface proteins (antigens). Since the antibody produced is sensitive to the antigen’s epitope, any conformational changes caused by mutation leave antibodies, and hence vaccinations, ineffective.¹⁶

Essentially, vaccine development against RNA viruses is a race to keep up with mutations. This is why understanding the biomolecular consequences of mutation is important in successful vaccine development. 

Mutations can be used in the production of live-attenuated vaccines. This involves mutations that reduce viral activity, for example, single substitution of C proteins¹⁷ and replacement of F and HN proteins¹⁸ for HPIV type 1, and mutation of L protein¹⁹ or nucleotide substitution in 3’ extragenic leader region²⁰ for HPIV type 2. All vaccines are still in the preclinical stage, although research appears to be promising and human clinical trials could be conducted in the future.²¹

Summary

HPIVs undergo mutations during their normal virus life cycle, however, only some mutations can significantly modify their biomolecular structure. This gives rise to a range of lineages and variants with differing epidemiology and pathophysiology. Mutations cause antigenic drifts which can block antibody binding, reducing vaccine and treatment efficacy. The high mutation rates of RNA viruses have hindered the production of HIPV vaccines. Mutations are unlikely to alter the course of a particular outbreak, however, they could contribute to a long-term shift in epidemiology due to newly generated virus lineages. Meanwhile, understanding the biomolecular effects of mutation allows the production of live-attenuated vaccines. Mutations are, therefore, a useful genetic mechanism that can be targeted for genetic engineering and study for protein functions in HPIV.