Influenza A virus’s (IAV’s) frequent genetic changes challenge vaccine strategies and engender resistance to current drugs. We sought to identify conserved and essential RNA secondary structures within IAV’s genome that are predicted to have greater constraints on mutation in response to therapeutic targeting. We identified and genetically validated an RNA structure (packaging stem–loop 2 (PSL2)) that mediates in vitro packaging and in vivo disease and is conserved across all known IAV isolates. A PSL2-targeting locked nucleic acid (LNA), administered 3 d after, or 14 d before, a lethal IAV inoculum provided 100% survival in mice, led to the development of strong immunity to rechallenge with a tenfold lethal inoculum, evaded attempts to select for resistance and retained full potency against neuraminidase inhibitor-resistant virus. Use of an analogous approach to target SARS-CoV-2, prophylactic administration of LNAs specific for highly conserved RNA structures in the viral genome, protected hamsters from efficient transmission of the SARS-CoV-2 USA_WA1/2020 variant. These findings highlight the potential applicability of this approach to any virus of interest via a process we term ‘programmable antivirals’, with implications for antiviral prophylaxis and post-exposure therapy.

甲型流感病毒 (IAV) 频繁的基因变化对疫苗策略提出了挑战，并导致对现有药物产生耐药性。我们试图鉴定 IAV 基因组内保守且必需的 RNA 二级结构，预计这些结构对响应治疗靶向的突变具有更大的限制。我们鉴定并基因验证了介导体外包装和体内疾病的 RNA 结构（包装茎环 2 (PSL2)），并且在所有已知的 IAV 分离株中都是保守的。在致命 IAV 接种物后 3 天或之前 14 天施用 PSL2 靶向锁定核酸 (LNA)，可在小鼠中提供 100% 的存活率，导致对十倍致命接种物的再攻击产生强大的免疫力，从而避免了选择抗性并保留对抗神经氨酸酶抑制剂抗性病毒的全部效力。使用类似的方法来靶向 SARS-CoV-2，即预防性施用针对病毒基因组中高度保守的 RNA 结构的 LNA，可以保护仓鼠免受 SARS-CoV-2 USA_WA1/2020 变体的有效传播。这些发现强调了这种方法通过我们称之为“可编程抗病毒药物”的过程对任何感兴趣的病毒的潜在适用性，对抗病毒预防和暴露后治疗具有影响。