Determining factors of transmission and evolution of SARS-CoV-2 in populations at risk

National Institute Of Allergy And Infectious Diseases

Investigators

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Abstract

The major aspects of this project involve characterizing SARS-CoV-2 genetic diversity and microbial communities in the respiratory tract during infection. This involves analyzing samples from COVI19 positive subjects, and from model animal infections. Whole genome sequencing of SARS-CoV-2 has become crucial for epidemiology studies and to determine how the virus sweeps through various populations, with the transmission potential of new emerging variants. We have 2 ongoing genomic epidemiology studies: one is specifically a surveillance project of SARS-CoV-2 in the NIH worker population, where more than 800 asymptomatic and symptomatic positive cases have been identified. The second is a new set of collaborations with clinical and public health teams in the Dominican Republic and Haiti. For the NIH study, we currently have full genomes on >400 viruses for which we have detailed contact tracing, and a large proportion of the samples are from asymptomatics. We are also now receiving positive samples from breakthrough infections post-vaccination. For the DR/Haiti study, we will combine phylogenetics with travel history data, and use the viral diversity information to determine the number of independent introductions into each of these countries that shutdown their borders and airports early in the pandemic. We will also be able to ascertain how the virus evolves in a relative closed population, and the dynamics of new variant introduction when they re-opened their borders. From a public health perspective, it will also enable an evaluation of how efficient border closings are in limiting the introduction of new variants. Since the first reported US introduction of SARS-CoV2 in Washington state on January 19, 2020, hotspots of the virus have arisen in all major US cities and areas. Sequencing of virus isolates from infected patients in these cities has helped to determine the number and origin of introduction events, and key amino acid changes that differentiate clades of the virus in circulation. While identification of these clades and the associated viral consensus changes helps in tracking spread of the virus, few studies have been done on the minority variants present in infected individuals. These minority variants could be seeding the emergence of new clades, thus identifying them early is of relevance for preparedness and to track transmission events. Errors made during replication that are not deleterious or lethal to the virus can lead to the generation of these minority variants. However, the identification of minority variants in SARS-CoV-2 sequence data is complicated by errors introduced during amplification and sequencing of the genome. To help delineate minority variants from introduced errors, we used simulated data to test the ability of 6 software packages to accurately call variants at a range of allele frequencies and coverage cutoffs. Using the results of these tests, we analyzed minority variants within the SARS-CoV-2 data in a sample set from the early outbreak in New York City and in more recent sequence data from clusters of transmission. Our data indicate that even with a small transmission bottleneck, the probability of heterogeneous virion populations is likely. Our data suggest that analysis of shared minority variants could help identify regions of the SARS-CoV-2 genome that are under increased selective pressure, as well as inform transmission chains and give insight into possible variant strain emergence. In a separate study we are examining SARS-CoV-2 virus genetic diversity over the course of the infection. We have analyzed the within-host evolution of SARS-CoV-2 in a patient with B cell depletion. Persistent viral replication occurs in immunosuppressed patients with SARS-CoV-2 and viral persistence in this setting has raised concern for viral evolution and the emergence of variants. While a few studies have reported SARS-CoV-2 genomic information in immunocompromised hosts, this is the first study to describe viral evolution in a patient with nearly year-long infection. We have characterized the same virus infection in a patient that was infected early on in the pandemic and followed the progress of this patient until the virus was cleared over 330 days later, the longest SARS-CoV-2 infection reported to date. Sequencing revealed the emergence of a unique in-frame deletion in the amino-terminal domain of the spike protein, and a complete deletion of ORF7b and ORF8, the first report of its kind in an immunocompromised patient. These mutations could potentially induce resistance against NTD-directed antibodies. In our first study of the airway microbiome of COVID19 patients, we focused on the metagenomic and metatranscriptomic analysis of cross-sectional BAL samples collected from mechanically ventilated patients during the first wave of the pandemic in NYC. However, while these patients all had severe disease requiring intubation, the mortality rate was much lower in this cohort because only stable patients could undergo bronchoscopy. In a follow-up study, we are analyzing longitudinal samples from the first wave and from the second wave with approximately 70 patients for which 1-5 samples were collected up to 6 weeks follow-up. Samples from the first wave are from BAL, while samples from the 2nd wave are primarily tracheal aspirates, which allows us to analyze the microbiome for critically ill patients who could not undergo bronchoscopies.