Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients

Abstract

49As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 50 million people with more than 300 thousand death as official reports 1,2 . The key to 51 understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of 52 mutation and evolution of this virus at both inter-and intra-host levels. However, despite quite a 53 few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and 54 their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we 55 achieved and characterized consensus genomes and intra-host genomic variants from 32 serial 56 samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the 57 coexistence of different genotypes within the same patient. We further identified 40 intra-host 58 single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten 59 iSNVs were found in at least two patients or identical to consensus variants. Comparison of 60 allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of 61 the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events 62 among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity 63 within GIT, showing an increased population with accumulated mutations developed in the 64 tissue-specific environments. The iSNVs identified here not only show spatial divergence of 65 intra-host viral populations, but also provide new insights into the complex virus-host 66 interactions. 67 68 MAIN 69 From January 25 to February 10 in 2020, we collected a total of 62 serial clinical samples from70 eight hospitalized patients (GZMU cohort) confirmed with SARS-CoV-2 infection using real-time 71 RT-qPCR (Table S1). All patients had direct contacts with confirmed cases during the early 72 stage of the outbreak. Most patients, except P15 and P62, had severe symptoms and received 73 mechanical ventilation in ICU, including the patient P01 who passed away eventually. The 74 4 patient P01 also showed much lower antibody (IgG and IgM) responses (Table S1) compared 75 to other patients. We then deep sequenced the 62 clinical samples using metatranscriptomic 76 and/or hybrid capture methods ( Table S1). The numbers of SARS-CoV-2 reads per million 77 (SARS-CoV-2 RPM) among the metatranscriptomic data correlated well with the corresponding 78 RT-qPCR cycle threshold (Ct), reflecting a robust estimation of viral load (R = 0.71, P = 6.7e-11) 79 ( Fig. 1a). The respiratory tract (RT: Nose, Sputum, Throat) and gastrointestinal tract (GIT: Anus, 80 Feces) samples showed higher SARS-CoV-2 RPMs compared to gastric mucosa and urine 81 samples (Fig. 1b). Furthermore, RT and GIT samples from two patients with mild symptoms 82 showed relatively low viral loads among their respective sample types. The data here may 83 reflect an active replication of SARS-CoV-2 in RT and GIT, especially in patients with severe 84 sympto...

Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2

“…The relatively narrow transmission bottleneck sizes is expected to increase the variance of viral variants being circulated between transmission pairs [15]. Even after successful transmission, virions carrying the minor variants are likely to be purged out due to the frequent stochastic dynamics within the respiratory tract [7], which is also consistent with the low diversity and instable iSNV observed among the RT samples.…”

“…Using both metatranscriptomic and hybrid-capture based techniques, we newly deep sequenced respiratory tract (RT) samples of seven COVID-19 patients in Guangdong, China, including two pairs of patients from the same households, respectively (P03 and P11; P23 and P24). The data were then combined with those of 23 RT samples used in our previous study [7], yielding a combined data set of 30 RT samples from 13 COVID-19 patients (Table S1).…”

“…Recently, we investigated the intra-host evolution of SARS-CoV-2 and revealed genetic differentiation among tissue-specific populations [7]. However, it is still not clear how the intra-host variants circulate…”

Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

“…The identification of iSNVs in fecal samples as well as in throat swab and bronchoalveolar lavage fluid, suggest ongoing evolution of SARS-CoV-2 in the human body (19)(20)(21)(22). However, the possibility of infection of multiple strains cannot be entirely ruled out.…”

“…Thus, iSNVs are more likely to represent spontaneous mutations rather than infection of multiple strains. A recent study proposed that SARS-CoV-2 in GI had a relatively higher genomic diversity compared to that in the respiratory tract (20), suggesting that the mutation rate may vary among different tissues. Thus, the fast-evolving of the viral genome in GI observed in our study may not be applicable to other organs.…”