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Aligos Therapeutics, Inc. (ALGS)·Q3 2025 Earnings Summary

Executive Summary

  • Q3 2025 was operationally constructive (first patients dosed in Phase 2 B-SUPREME and active global enrollment) but financially weak, with a larger net loss driven by higher R&D and a negative warrant fair value adjustment .
  • Revenue from customers was $0.74M, above a thin consensus base, while EPS materially missed: Revenue $0.74M vs $0.50M consensus; EPS $(3.04) vs $(1.90) consensus. Revenue beat; EPS miss due to higher R&D and a $(4.2)M warrant revaluation loss . Estimates marked with * are from S&P Global.
  • Cash, cash equivalents and investments were $99.1M (Sep 30), with runway “into Q3 2026” (tightened from “2H 2026” previously) as the company advances HBV candidate pevifoscorvir (pevy/ALG-000184) through Phase 2; interim readouts expected 1H/2H 2026, topline 2027 .
  • Near-term stock catalysts: AASLD Liver Meeting® presentations (including pevy 96-week and post-treatment data), B-SUPREME enrollment updates, and any partnering progress for ALG-055009 in obesity/MASH .

What Went Well and What Went Wrong

What Went Well

  • Phase 2 B-SUPREME initiated and enrolling across multiple geographies; first subjects dosed in August; management expects interim analyses in 2026. CEO: “Our Phase 2 B-SUPREME study… is enrolling nicely… We maintain our enthusiasm regarding the potential for pevy” .
  • Scientific momentum: eight abstracts accepted for AASLD 2025 (four for pevy), including an oral presentation on Phase 1 monotherapy; 96-week dosing completed with off-treatment data to be presented .
  • Preclinical synergy for ALG-055009 with incretin RAs (semaglutide/tirzepatide) showing “profound” weight-loss synergy and improved lipids in DIO mice, supporting partnering discussions .

What Went Wrong

  • EPS miss vs Street: $(3.04) vs $(1.90)*, driven by higher R&D (pevy Phase 2 costs) and a $(4.2)M loss from change in fair value of 2023 common warrants; YoY loss widened (Q3’25 net loss $(31.5)M vs $(19.3)M Q3’24) .
  • Revenue base remains small and down YoY on customers revenue ($0.74M vs $1.25M in Q3’24), with no collaborations revenue in Q3; visibility on recurring revenue limited .
  • Cash runway narrowed from “2H 2026” (Q2) to “into Q3 2026,” reflecting higher spend cadence as Phase 2 execution ramps and warrant volatility influences P&L optics .

Financial Results

P&L snapshot (USD thousands, except per-share)

MetricQ3 2024Q1 2025Q2 2025Q3 2025
Revenue from customers ($000)1,250 311 965 741
Revenue from collaborations ($000)19 0 0 0
Research & development expense ($000)16,774 14,502 13,976 23,937
General & administrative expense ($000)4,626 5,052 5,556 5,165
Loss from operations ($000)(20,131) (19,243) (18,567) (28,361)
Interest and other income, net ($000)1,068 880 1,207 1,085
Change in FV of 2023 common warrants ($000)(105) 61,494 1,682 (4,205)
Net income (loss) ($000)(19,259) 43,088 (15,863) (31,537)
Net (loss) income per share, basic ($)(3.07) 5.12 (1.53) (3.04)

Actual vs Consensus (S&P Global)

MetricQ3 2025 ActualQ3 2025 ConsensusSurprise
Revenue ($000)741 500*+241; +48.2% (beat)
EPS (GAAP) ($)(3.04) (1.90)*(1.14) miss; significant
  • Coverage depth: EPS estimates (n=4); Revenue estimates (n=4).
  • Values marked with * retrieved from S&P Global.

Balance Sheet and Liquidity

MetricDec 31, 2024Jun 30, 2025Sep 30, 2025
Cash & cash equivalents ($000)36,997 18,661 41,946
Short-term investments ($000)19,942 104,284 57,150
Total current assets ($000)62,141 127,944 103,435
Total assets ($000)70,094 134,706 109,764
Total liabilities ($000)99,067 32,840 37,931
Stockholders’ equity ($000)(28,973) 101,866 71,833
Cash, cash equivalents & investments ($000)56,939 122,945 99,096

Operational KPIs

KPIQ1 2025Q2 2025Q3 2025
B-SUPREME statusPlanned mid-2025 start; global approvals advancing Site activations, screening; dosing “in coming weeks” First subjects dosed Aug; enrolling across U.S., China, HK, Canada
AASLD/EASL presenceAPASL: pevy ≤96w data; 055009 reductions/lipids EASL: pevy 96w; 055009 subgroup/lipids AASLD: 8 abstracts; Phase 1 pevy oral/pst-tx data
055009 partnering“Continuing to evaluate out-licensing” “Continuing to evaluate… out-licensing” “Continued discussions with potential partners”

Guidance Changes

MetricPeriodPrevious GuidanceCurrent GuidanceChange
Cash runwayOperating runway“Sufficient funding… into the second half of 2026” (Q2’25) “Sufficient funding… into the third quarter of 2026” (Q3’25) Narrowed/updated timing
B-SUPREME interim readouts2026Interim data expected in 2026 Interim data in 1H and 2H 2026 Clarified timing (two interims)
B-SUPREME topline2027Topline 2027 Topline 2027 Maintained
ALG-055009 business development2025-26Evaluate options incl. out-licensing Continued discussions with potential partners Progressing discussions

Earnings Call Themes & Trends

Note: No Q3’25 earnings call transcript available in our records.

TopicPrevious Mentions (Q-2 and Q-1)Current Period (Q3 2025)Trend
HBV: B-SUPREME executionQ1: $100M+ raised; FDA alignment; dosing mid-2025 Q2: global approvals/activation; dosing imminent Q3: first subjects dosed; multi-country enrollment
Regulatory pathway (monotherapy)—Management (conference) emphasizes monotherapy chronic suppression path accepted by FDA/EMA/NMPA; 14 countries approved design Regulatory clarity improving
R&D spend cadenceQ1: R&D $14.5M (down YoY) Q2: R&D $14.0M (down YoY; MASH trial completion) Q3: R&D $23.9M (pevy Phase 2 costs)
055009 partneringQ1: evaluating out-licensing Q2: evaluating out-licensing Q3: in “continued discussions” with potential partners
Scientific visibilityQ1: APASL data Q2: EASL data Q3: AASLD eight abstracts; 96w + off-treatment pevy data

Management Commentary

  • “Our Phase 2 B-SUPREME study of pevifoscorvir sodium (pevy) is enrolling nicely… We maintain our enthusiasm regarding the potential for pevy as well as our entire development pipeline, including ALG-055009, which is in continued discussions with potential partners for obesity and MASH.” — Lawrence Blatt, CEO .
  • “All [regulators] have… given us the green light that we can go forward with monotherapy superiority study for chronic suppression… 14 different countries… given us regulatory approval.” — Management at H.C. Wainwright Liver Disease Conference .
  • “Recently generated preclinical data combining ALG-055009 with incretin RAs… exhibited profound synergistic effects in body weight loss… enhanced antihyperlipidemic effects as compared to monotherapy.” .

Q&A Highlights

  • Regulatory pathway and differentiation: Management underscored a unique monotherapy chronic suppression path for pevy accepted by FDA/EMA/NMPA, supported by 96-week monotherapy data and absence of resistance, opening a route not available to prior CAMs that required NAs .
  • Clinical design and biomarkers: B-SUPREME includes E+/E– cohorts, stringent DNA endpoints, paired biopsies to quantify cccDNA and integration, and crossover to open-label pevy—designed to demonstrate mechanistic differentiation vs TDF .
  • Milestones: First interim (E–, ~12 weeks) guided for 1H 2026; a second interim (E+, ~24 weeks) in 2026; topline in 2027 .
  • Partnering: Management is in active discussions for ALG-055009; indicated potential timing as early 2026 (aspiration to announce 1H next year) depending on negotiations .

Estimates Context

  • Q3 2025 results vs S&P Global consensus: Revenue $0.74M vs $0.50M* (beat); EPS $(3.04) vs $(1.90)* (miss). Coverage depth: 4 estimates for both revenue and EPS*. The EPS shortfall reflects increased R&D tied to Phase 2 execution and a negative $(4.2)M non-cash warrant fair value change in the quarter .
  • Implications: Street models likely raise near-term R&D run-rate assumptions and incorporate warrant mark volatility; revenue remains a secondary driver pending future BD payments. Values marked with * retrieved from S&P Global.

Key Takeaways for Investors

  • Execution de-risks HBV program: dosing initiated and global enrollment underway; interim analyses in 2026 and topline in 2027 define a clear value-creation arc .
  • Scientific differentiation remains the core bull case: durable 96-week monotherapy, antigen reductions, and a monotherapy regulatory path for chronic suppression set pevy apart; upcoming AASLD data are a near-term inflection .
  • Near-term P&L optics pressured: R&D step-up and warrant fair value loss drove a significant EPS miss; expect continued investment through Phase 2 .
  • Liquidity adequate but finite: $99.1M cash & investments and runway into Q3’26 support planned operations through key interims; partnering and potential milestones remain important optionality .
  • 055009 optionality: preclinical obesity synergy with incretins and favorable MASH profile underpin active BD discussions, a potential non-dilutive funding lever .
  • Trading setup: watch AASLD disclosures and any B-SUPREME enrollment cadence updates; positive early signals or BD announcements could re-rate expectations ahead of 2026 interims .

Additional Supporting Details

  • Q3 2025 financial detail: Net loss $(31.5)M (vs $(19.3)M YoY); R&D $23.9M (vs $16.8M YoY) on pevy Phase 2 costs; G&A $5.2M (vs $4.6M YoY); change in FV of 2023 warrants $(4.2)M loss (vs $(0.1)M YoY) .
  • Prior quarter context: Q2 2025 net loss $(15.9)M, R&D $14.0M (down YoY on MASH trial completion), and cash/investments $122.9M with runway into 2H’26 .
  • First patients dosed in B-SUPREME Aug 2025; trial targets ~200 untreated HBV subjects, with rigorous DNA endpoints and extensive biomarker work (cccDNA, antigens, integration) .