Andes Hantavirus (ANDV) Genome Analysis - Independent Research Report

Target strain: ANDV/Switzerland/Hu-3337/2026
Reference strains: PV808476.1 (S), PV808477.1 (M), PV808478.1 (L)
Analysis date: May 12, 2026

1. Materials and Methods

1.1 Data Sources

Target sequences were obtained from the NCBI database, including the S, M, and L segments of ANDV/Switzerland/Hu-3337/2026. Reference sequences are PV808476.1 (S segment, 1861bp), PV808477.1 (M segment, 3659bp), PV808478.1 (L segment, 6555bp), all from the Chilean isolate CHI-Hu13724_P2.

1.2 Analysis Methods

• Sequence alignment: Global alignment using BioPython PairwiseAligner, gap open penalty -10, gap extension penalty -1
• Mutation analysis: Identification of single nucleotide variations (SNVs), insertions/deletions (Indels), calculation of transition/transversion ratio
• Frameshift detection: Analysis of whether Indels in coding regions cause reading frame shifts (net Indel length not divisible by 3)
• Amino acid analysis: Translation of CDS regions using the standard genetic code, identification of synonymous/non-synonymous mutations
• Phylogenetic analysis: Calculation of genetic distances between target and reference sequences, construction of neighbor-joining trees
• SEIR model: Simulation of epidemic transmission dynamics using ordinary differential equations, parameter sensitivity analysis

2. Results

2.1 Genome Mutation Overview

Whole genome comparison between the target and reference strains detected 300 nucleotide variations, distributed as follows:

Figure 1: Mutation count and mutation rate for each genome segment

2.2 Transition/Transversion Analysis

The transition/transversion ratio is an important indicator for assessing selection pressure. This study found an extremely high ratio:

Figure 2: Distribution of transition and transversion mutations

2.3 Insertion/Deletion (Indel) and Frameshift Analysis

Indel analysis is crucial for assessing viral genome integrity. The following is the Indel distribution for each segment:

2.4 Impact of Frameshifts on Protein Structure

If the net length of Indels within coding regions is not a multiple of 3, it will cause a frameshift mutation, altering all downstream amino acid sequences. The analysis results are as follows:

2.5 Amino Acid Level Variations

In the regions before frameshifts occur, amino acid level variations are as follows:

*Note: A182X in the L segment indicates an unreliable amino acid call at position 182, which may stem from insufficient sequencing quality, local alignment shifts due to indels, or assembly errors. This site should not be interpreted as a definitive non-synonymous mutation without further verification through Sanger sequencing or long-read sequencing.

2.6 SEIR Model Parameter Sensitivity Analysis

The SEIR model was used to simulate epidemic transmission dynamics under different parameter settings. Key findings include:

Figure 3: SEIR model simulation results under different R0 values

Figure 4: Final attack rate as a function of R0

3. Discussion

3.1 Evolutionary Characteristics

The extremely high transition/transversion ratio (11.5:1) observed in this study suggests a biased mutation spectrum, which may be related to RNA editing, replication error biases, or sequencing/alignment artifacts. Combined with the low dN/dS ratio (0.002), this supports strong purifying selection and functional constraints on protein-coding regions. It should be noted that hantaviruses, as negative-sense RNA viruses, are not known to possess proofreading mechanisms similar to the nsp14/nsp10 exoribonuclease complex in coronaviruses. Therefore, the observed low dN/dS should be interpreted as effective elimination of non-synonymous mutations during evolution, rather than attributed to polymerase proofreading. The current dN/dS estimates should be further validated using standard codon-based models such as HyPhy or PAML.

3.2 Frameshift Implications

The correction of the S segment frameshift conclusion is important. The previous analysis incorrectly included the 1bp deletion at position 1861 (located in the 3' UTR) in the CDS analysis. The correct analysis shows that the net CDS Indel is -3bp, which is divisible by 3, thus not causing a frameshift. This means the nucleoprotein reading frame remains intact.

The M segment frameshift affects only 0.2% of the glycoprotein C-terminal sequence, which may have minimal impact on protein function. However, further experimental validation is needed to confirm this.

3.3 Epidemiological Implications

The SEIR model results highlight the importance of early intervention. When R0 is reduced below 1 through measures such as isolation and social distancing, the epidemic can be controlled with minimal impact. However, when R0 exceeds 1.5, the attack rate increases dramatically, emphasizing the need for rapid response.

4. Conclusions

1. The ANDV genome shows an average sequence divergence of 24.84/1000bp with a transition/transversion ratio of 11.5:1, suggesting a biased mutation spectrum; preliminary dN/dS estimates well below 1 (0.002) indicate strong purifying selection, though further validation with standard codon-based models is needed.
2. The S segment does NOT have a frameshift mutation in the CDS (net -3bp, mod 3 = 0).
3. The M segment has a frameshift mutation affecting 0.2% of the glycoprotein C-terminal sequence.
4. The L segment reading frame is intact with no frameshift mutations.
5. SEIR modeling demonstrates theoretical sensitivity under different R0 assumptions; however, since ANDV human-to-human transmission is typically limited to close, prolonged contact scenarios, the homogeneous mixing SEIR model may overestimate transmission efficiency in general social contact settings. These results should be interpreted as sensitivity analysis under closed-environment and high-contact-rate assumptions, not as general population transmission predictions.