The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, with >52,000 cases in California as of May 4, 2020. Here we investigate the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of a predominant lineage and limited transmission between communities. Lineages associated with outbreak clusters in 2 counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain SARS-CoV-2 spread in California and other states.

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Introduction: More than 93,000 cases of coronavirus disease have been reported worldwide. We describe the epidemiology, clinical course, and virologic characteristics of the first 12 U.S. patients with COVID-19. Methods:We collected demographic, exposure, and clinical information from 12 patients confirmed by CDC during January 20-February 5, 2020 to have COVID-19. Respiratory, stool, serum, and urine specimens were submitted for SARS-CoV-2 rRT-PCR testing, virus culture, and whole genome sequencing. Results:Among the 12 patients, median age was 53 years (range: 21-68); 8 were male, 10 had traveled to China, and two were contacts of patients in this series. Commonly reported signs and symptoms at illness onset were fever (n=7) and cough (n=8). Seven patients were hospitalized with radiographic evidence of pneumonia and demonstrated clinical or laboratory signs of worsening during the second week of illness. Three were treated with the investigational antiviral remdesivir. All patients had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset, with lowest rRT-PCR Ct values often detected in the first week. SARS-CoV-2 RNA was detected after reported symptom resolution in seven patients. SARS-CoV-2 was cultured from respiratory specimens, and SARS-CoV-2 RNA was detected in stool from 7/10 patients. Conclusions:In 12 patients with mild to moderately severe illness, SARS-CoV-2 RNA and viable virus were detected early, and prolonged RNA detection suggests the window for diagnosis is long. Hospitalized patients showed signs of worsening in the second week after illness onset.for use under a CC0 license.

An increasing proportion of the U.S. population resides in nursing homes (NHs). No surveillance system exists for infections in these facilities. To determine the incidence and types of infections in NH residents, and to identify predictors of death among residents with infections, we initiated a surveillance system at 13 NHs in California during a 6-month period from October 1989 through March 1990. The study included 1754 residents, among whom 835 infections were identified during the study period. The most common infections were urinary tract infections (UTIs; 286, 34.2%), respiratory tract infections (RTIs; 259, 31%), and skin infections (150, 17.9%). Of the 259 residents with respiratory tract infections, 69 (27%) had pneumonia. Antimicrobials were prescribed for 646 (77%) of the infectious episodes. Residents with pneumonia were more likely to die than residents with other infections (4 of 69 versus 12 of 766; P = 0.04). Symptoms of altered body temperature (fever, hypothermia, chills) and change in mental status also were associated with an increased risk of a fatal outcome (10 of 260 versus 6 of 575; P = 0.01) and (7 of 127 versus 9 of 708; P = 0.004). This study suggests that the most common infections among NH residents are UTIs, RTIs, and skin infections. Pneumonia, symptoms of fever, and mental status changes all were associated with increased mortality. The frequency of infections among NH residents and their impact on resident outcome highlights the need for infectious disease surveillance in this population.