key: cord-0714980-goutkfhr authors: Mok, Bobo Wing-Yee; Cremin, Conor J.; Lau, Siu-Ying; Deng, Shaofeng; Chen, Pin; Zhang, Anna Jinxia; Lee, Andrew Chak-Yiu; Liu, Honglian; Liu, Siwen; Ng, Timothy Ting-Leung; Lao, Hiu-Yin; Lee, Eddie Lam-Kwong; Leung, Kenneth Siu-Sing; Wang, Pui; To, Kelvin Kai-Wang; Chan, Jasper Fuk-Woo; Chan, Kwok-Hung; Yuen, Kwok-Yung; Siu, Gilman Kit-Hang; Chen, Honglin title: SARS-CoV-2 spike D614G variant exhibits highly efficient replication and transmission in hamsters date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.08.28.271635 sha: 333f4628ad4c9b987b5bb5ff9ea556d83943b25c doc_id: 714980 cord_uid: goutkfhr SARS-CoV-2 causes disease varying in severity from asymptomatic infections to severe respiratory distress and death in humans. The viral factors which determine transmissibility and pathogenicity are not yet clearly characterized. We used the hamster infection model to compare the replication ability and pathogenicity of five SARS-CoV-2 strains isolated from early cases originating in Wuhan, China, in February, and infected individuals returning from Europe and elsewhere in March 2020. The HK-13 and HK-95 isolates showed distinct pathogenicity in hamsters, with higher virus titers and more severe pathological changes in the lungs observed compared to other isolates. HK-95 contains a D614G substitution in the spike protein and demonstrated higher viral gene expression and transmission efficiency in hamsters. Intra-host diversity analysis revealed that further quasi species were generated during hamster infections, indicating that strain-specific adaptive mutants with advantages in replication and transmission will continue to arise and dominate subsequent waves of SARS-CoV-2 dissemination. A newly emerged β-coronavirus, SARS-CoV-2, which causes COVID-19 disease in humans, 35 attained cross species transmission through a process yet to be defined in detail (Andersen et (Mahase, 2020) . More than 20 million laboratory-confirmed cases and over 700,000 deaths 40 have been recorded globally to date (https://coronavirus.jhu.edu/map.html) (Dong et al., 2020) . resulted in more widespread human infections since March 2020. As more humans are exposed 66 to the SARS-CoV-2 virus, it is expected that more host adapted phenotypic variants of the virus will emerge. It is important to determine whether some emerging variants may have the 68 potential to go on to become the dominant strain in the coming waves of circulation. Indeed 85 Five isolates were selected to study variability in the pathogenicity of SARS-CoV-2 86 strains and the host response to such variants in a hamster infection model. These strains 87 represent isolates from the early outbreak in China (HK-8, HK-13 and HK-15) and subsequent 88 outbreaks in Europe and elsewhere (HK-92 and HK-95) (Table S1 ). Phylogenetic analysis 89 revealed that these strains belonged to distinctive GISAID phylogenetic clades ( Figure S1 ). 90 The sequences of these five isolates were compared with that of the index isolate (Wuhan-Hu- Figure 2B) . Interestingly, the expression distribution between each of the viral genes for each 120 isolate is very similar across all isolates, with differences in overall expression being due to a 121 proportional change in expression across all genes. This indicates that the observed differences 122 in viral gene expression can be attributed to isolates maintaining different rates of replication. These differences in replication suggest that some viral isolates may be more constrained by 124 host-specific factors and as such are unable to achieve an optimal rate of replication, as is seen which carries spike D614G, may be enhanced compared to two other isolates (HK-8 and HK-13) which lack the D614G substitution ( Figure S5) . Notably, higher virus titers were found in 185 the lung and nasal turbinate tissues of recipient hamsters co-housed with HK-95-infected 186 hamsters than in those secondarily exposed to HK-8 or HK-13 ( Figure 5A) (Table S2) . Interestingly, some genome variants, which were absent 208 in the original strains, developed during hamster infection. The frequencies of these newly 209 arisen variants were generally higher at 5 dpi than at 3 dpi (Table S2) this study could be due to the high replication efficiency of this strain in animals, given that 257 hamsters are highly susceptible to SARS-CoV-2 infection. This is consistent with our 258 transcriptome analysis of lung tissues from infected hamsters, which revealed no significant 259 difference between host responses to infection with 614D or 614G strains (Figure 4 and S4) . Sequences were aligned using MUSCLE, with positions with less than 95% coverage being 388 excluded (Edgar, 2004) . The evolutionary history of IL6 was inferred using the Maximum 389 Likelihood method and Tamura 3-parameter model (Tamura, 1992) . 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