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

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications & trials

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 COVID-19 positive subjects, and from model animal infections. As part of this project we tackle different types of studies that include: (a) Molecular epidemiology (b) Virus evolution and genetic diversity within infected hosts (c) Respiratory tract microbiome profiles and host response (a) Molecular epidemiology 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 currently have 3 ongoing genomic epidemiology studies: The first 2 studies are in collaboration with clinical and public health teams in the Dominican Republic and Haiti. For the DR/Haiti study, we are combining phylogenetics with travel history data, and are using 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. From a public health perspective, it will also enable an evaluation of how efficient border closings are in limiting the introduction of new variants. The Caribbean is a populous region (>40 million people in the island states) at the crossroads of many trade routes and visited by tourists from around the world, yet is drastically undersampled relative to Europe and North America. We analyzed samples from Haiti in Spring 2020, making this the biggest collection from a single Caribbean island in this time period studied so far. Although the number of specimens sequenced in this study nearly doubles the number of specimens available for the early pandemic in the region, the absolute number of samples is small compared to the scale of sequencing in other parts of the world. This increase is nevertheless sufficient to demonstrate that covid-19 was spreading among Caribbean islands in early 2020 and to show that at least one lineage was possibly introduced from the Caribbean into North America, where it sustained community submission over a period of several months. These 2 studies will be submitted for publication in the fall. The third study is a collaboration with Dr. Marcel Tongo in Cameroon with samples from 2020, 2021, and 2022 to determine the diversity of what was circulating. (b) Virus evolution and genetic diversity within infected hosts While identification of new clades and lineages, and the associated viral consensus changes help 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. In an ongoing collaboration with Dr. James Musser (Houston Methodist), we used deep sequences of thousands of SARS-CoV-2 clinical samples to explore within-host diversity of the virus from a high-throughput viral surveillance program associated with a large hospital system. This project has required a complete revision of how we tackle opportunistic datasets for deep sequencing analyses and the identification of all the artifacts that can be introduced. We had initially submitted this manuscript for publication but in response to reviewer comments have revisited our approach. The identification of low-level variants, when effectively distinguished from sequencing artifacts, can help shed light on intrahost viral evolution. In our retrospective genomic observational study, we analyzed 35,000 clinical samples from COVID-19 patients in the Houston Methodist Hospital System collected between December 2020 and January 2022. While using intrahost single-nucleotide variants (iSNVs), we investigated the level of molecular artifacts and systematically filtered them using codon positional biases. We introduced a quantitative estimate of viral titers using sequencing coverage metrics to control for its confounding effect on iSNVs levels. Using the >10,000 higher quality samples and rich clinical metadata, we found that clinical factors, such as vaccination and monoclonal antibody use, did not affect selection at the minor variants but did at the de novo major variants. Lastly, we found that iSNVs foreshadowed mutations in Spike that would later appear in the pandemic. In a collaborative study with Dr. Mirella Salvatore (Weill Cornell), we are currently analyzing the within-host evolution of SARS-CoV-2 in immunocompromised patients with mostly B cell defects. 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. We are also analyzing the effects of therapies on viruse evolution in these protracted infections. In another collaborative study, with Dr. Daniel Chertow (VRC/NIAID), we are determining the diversity of SARS-CoV-2 across tissues from an autopsy case from a patient with an inborn genetic disease that leads to immunocompromise. For both studies we have been resequencing all the samples on a different platform (PacBio) in collaboration with Dr. Melissa Smith (University of Louisville). In both of these studies, SARS-CoV-2 mutations of interest were identified and the isolated viruses are being tested in functional assays in the labs of Dr. Diego Diehl (Cornell), and Dr. Mehul Suthar (Emory).. Since immunocompromise has become of particular interest as it allows to see what genetic space the virus can explore, we are also finalizing a study with Dr. Mehul Suthar (Emory) who collected virus from nasal turbinates of CD4CD8 T cell depleted mice. (c) Respiratory tract microbiome profiles and host response 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. From the same cohort, we are doing a parallel study on patients who are immunocompromised. This cohort has rich metadata on therapeutic regimens and symptoms.