In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals. Since age-dependent differences of COVID-19 were identified in humans, we compared the course of SARS-CoV-2 infection in young and aged Syrian hamsters. We show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. However, older hamsters exhibited more pronounced and consistent weight loss. In situ hybridization in the lungs identified viral RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. The latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients.

Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of viral proteins using underrepresented codon pairs. Because viruses replicate exclusively inside living cells, we posited that their codon pair preferences reflect those of their host(s). Analysis of many human viruses showed, however, that the encoding of viruses is influenced only marginally by host codon pair preferences. Furthermore, examination of codon pair preferences of vertebrate, insect, and arthropod-borne viruses revealed that the latter do not utilize codon pairs overrepresented in arthropods more frequently than other viruses. We found, however, that codon pair bias is a direct consequence of dinucleotide bias. We conclude that codon pair bias does not play a major role in the encoding of viral proteins and that virus attenuation by codon pair deoptimization has the same molecular underpinnings as attenuation based on an increase in CpG/TpA dinucleotides.

Highlights d Three closely related dwarf hamster species are susceptible to SARS-CoV-2 infection d The course and outcome of infection vary dramatically between species d Apparent differences in disease progression are independent of the ACE-2 sequence d The Roborovski dwarf hamster is a valuable addition to current SARS-CoV-2 models

22In late 2019, an outbreak of a severe respiratory disease caused by an emerging 23 coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans 1 . 24Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-25 2, requires suitable small animal models, as does the development and evaluation of 26 vaccines and antivirals 2 . Because age-dependent differences of COVID-19 were identified 27 in humans 3 , we compared the course of SARS-CoV-2 infection in young and aged Syrian 28 hamsters. We show that virus replication in the upper and lower respiratory tract was 29 independent of the age of the animals. However, older hamsters exhibited more 30 pronounced and consistent weight loss. In situ hybridization in the lungs identified viral 31 RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. 32Histopathology revealed clear age-dependent differences, with young hamsters launching 33 earlier and stronger immune cell influx than aged hamsters. The latter developed 34 conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, 35we observed rapid lung recovery at day 14 after infection only in young hamsters. We 36propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 37 vaccines and treatments may yield valuable information as this small-animal model 38 appears to mirror age-dependent differences in human patients.

Highlights d Attenuation by codon pair deoptimization is determined by suboptimal codon pairs d Suboptimal codon pairs reduce mRNA stability and throttle or abrogate translation d CpG dinucleotides are dispensable for attenuation by codon pair deoptimization d Codon pairs are important determinants of mRNA stability