Identifying early routes of SARS-CoV-2 introduction to Los Angeles

By Sally Robertson, B.Sc.Jun 15 2020

Researchers at Cedars-Sinai Medical Center, Los Angeles, have described for the first time, the likely sources of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduction to the Los Angeles community.

The findings suggest the source was mainly New York State, but other likely sources included Washington State and China.

“This study presents a snapshot of the molecular characteristics of SARS-COV-2 early transmission into the Los Angeles area,” writes the team.

Wenjuan Zhang and colleagues say their findings could pave the way for further studies looking at using SARS-CoV-2 sequencing to track local spread within communities.

A preprint version of the paper can be accessed on the server medRxiv*, while the article undergoes peer review.

Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of a cell showing morphological signs of apoptosis, infected with SARS-COV-2 virus particles (orange), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Identifying unique genomic features could guide interventions globally

Since COVID-19 was first identified in Wuhan China late last year, urgent efforts have been made to understand all aspects of its causative agent SARS-CoV-2.

Viral genome sequences that have been deposited in public databases are important resources for assessing key genomic features across populations that might help guide epidemiologic and public health endeavors globally.

Sources of origin indicated so far

Analysis of the Nextstrain database of viral genomes and other sequencing studies have indicated that SARS-CoV-2 spread from China to the U.S. West Coast and European populations.

While the first observed case of transmission from China to the U.S. was in Seattle, the largest epicenter in the country is New York State, and the source of isolates identified there seems to be Europe.

For areas along the U.S. West Coast, Washington State, and Northern California, the origin seems to be China, and within Northern California, early introduction of the virus seems to have involved Washington State.

Los Angeles is the largest city found on the U.S. West Coast and is the second major city to have introduced measures confining people to their households, as deaths started to occur in early March.

So far, Nextstrain has not linked the SARS-CoV-2 genome deposited for Los Angeles with any specific source of introduction.

What did the current study involve?

On 21st March, Cedars Sinai Medical Center adopted an in-house quantitative polymerase chain reaction (PCR) test for SARS-CoV-2 that enabled the rapid identification of patients infected with SARS-CoV-2.  

The team identified 192 positive patients and performed a next-generation sequencing analysis to identify the local community spread within the greater Los Angeles area.

“A broader geographical distribution comparison of these early Southern California with New York State, Washington State, and China isolates was conducted to ascertain possible early transmission pathways of SARS-CoV-2 dissemination into Los Angeles,” write Zhang and colleagues.

What did the study find?

The study identified two main clusters of community spread. Further analysis showed that the two main variants defining these clusters were observed throughout March and April and were present within the community before sample collection was started.

One tight clustering pattern identified eight patients with viral genomes that had one mutation in common.

“This finding directly highlights the precision of contact tracing directly through SARS-CoV-2 genome isolation,” says the team.

Another tight cluster pattern identified 17 patients who shared the same postal code, which only covered 2.37 miles.

No other obvious connections were observed within samples outside of those two clusters, reports the team.

What about the source of the virus?

The researchers say that although the sample size was small, the broader geographical distribution comparison with New York State, Washington State, and China provided useful insights for establishing the source of SARS-CoV-2 introduction to the Los Angeles community.

Less than 10% of viral genomes in samples from the Los Angeles community resembled mutational profiles of genomes from China.

On the other hand, more than half of the community samples closely resembled the mutational profiles of viral genomes from New York State. The remaining community samples resembled Washington State genomes.

What are the study implications?

“Based on these findings, we conclude SARS-CoV-2 was likely introduced into the Los Angeles community predominantly from New York State but also via multiple other independent transmission routes including but not limited to Washington State and China,” writes the team.

The researchers say this is the first comprehensive study of the potential sources of SARS-CoV-2 introduction to a COVID-19 epicenter in the United States.

“Global initiatives to track SARS-CoV-2 throughout the world have proven fruitful in monitoring disease incidence, severity and worldwide spread,” say the researchers. “By examining a cohort within a SARS-CoV-2 US epicenter, Los Angeles, we lay the foundation for further studies into the use of SARS-CoV-2 sequencing to monitor local community spread.”

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources