Coronavirus hit California with 7 different strains early in outbreak when community spread was limited: Study
The new coronavirus entered California several times with travelers and the state missed multiple opportunities to stop further transmission, suggests a new study. At least seven different strains arrived and spread in the state including one strain that was most likely transmitted by a single passenger on the Grand Princess cruise ship, says the analysis by the University of California, San Francisco
For the study, researchers examined viral samples taken from 36 patients spanning nine California counties and who had traveled on the Grand Princess cruise ship during its voyages associated with coronavirus outbreaks. They sequenced the genomes directly from the samples using a new method called “Metagenomic Sequencing with Spiked Primer Enrichment (MSSPE).” The results show how quickly the virus had spread in the Bay Area before it moved across the state and emphasized that northern California’s Covid-19 epidemic resulted from multiple virus strains entering the state.
The team says distinct from virus transmission patterns identified elsewhere, analysis of SARS-CoV-2 (the virus that causes Covid-19) genomes from the small number of California-based patients suggests the virus arrived in northern California through a complex series of introductions, not only from state to state but also from international travel. Based on the full results, it appears no one virus lineage was predominant in northern California, say experts. According to the research team, this indicates that transmission between communities was limited. Instead, virus introductions to the state were likely from people traveling from outside the studied counties and the state. These results emphasize the need for social distancing and travel restrictions to contain the spread of Covid-19 in California and in other states, say the authors.
“The Covid-19 pandemic has resulted in more than 52,000 cases in California as of May 4. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic strains associated with Washington State, with a lack of a predominant lineage and limited transmission between communities. These findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states,” says the study published in Science.
The patient samples included 11 collected from the Grand Princess cruise ship, during its two voyages from San Francisco to Mexico and Hawaii in February and March 2020, three from a Solano County cluster that included the first reported case of community transmission in the US with subsequent spread to two health care workers, seven samples from Santa Clara County from a local outbreak cluster associated with workspace transmission, three from patients who contracted the infection from sick contact, five related to domestic or international travel and seven samples from additional cases of community transmission.
The analysis shows that the 36 genomes included 14 in the Washington State lineage, 10 in a lineage associated with the Santa Clara County outbreak cluster, three from a Solano County cluster of three individuals, five related to lineages circulating in Europe and New York, and four related to early lineages from Wuhan or other regions of China (including two patients from San Benito County with identical genomes). “Sequencing the viral genomes and placing them, along with other publicly available genomes, on a phylogenetic tree, revealed that the genomes from northern California were dispersed across the evolutionary tree of SARS-CoV-2; they included lineages circulating in Europe and New York and related to early lineages from China. The virus in California-based travelers on the Grand Princess likely came from Washington State,” says the study.
According to experts, the multiple points of entry of Covid-19 underscore the importance of improving screening and contact tracing as businesses in states across the US reopen. They explain that public health containment measures such as isolation and contact tracing become more difficult to maintain once a lineage becomes established in the community.
“Social distancing interventions, such as the shelter-in-place directive that was issued by the governor of California on March 20, 2020, may assist in stemming spread from community to community. Interstate dissemination of SARS-CoV-2 lineages has also been demonstrated coast-to-coast between Washington State and Connecticut, and from domestic and international travel into the San Francisco Bay Area in the current study. Suspension of non-essential travel may thus be necessary to prevent ongoing importation of new cases in California and other states,” the team recommends.