No abstract

State and local health departments established the California Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Respiratory Virus Sentinel Surveillance System to conduct enhanced surveillance for SARS-CoV-2 and other respiratory pathogens at sentinel outpatient testing sites in 10 counties throughout California, USA. We describe results obtained during May 10, 2020‒June 12, 2021, and compare persons with positive and negative SARS-CoV-2 PCR results by using Poisson regression. We detected SARS-CoV-2 in 1,696 (19.6%) of 8,662 specimens. Among 7,851 specimens tested by respiratory panel, rhinovirus/enterovirus was detected in 906 (11.5%) specimens and other respiratory pathogens in 136 (1.7%) specimens. We also detected 23 co-infections with SARS-CoV-2 and another pathogen. SARS-CoV-2 positivity was associated with male participants, an age of 35–49 years, Latino race/ethnicity, obesity, and work in transportation occupations. Sentinel surveillance can provide useful virologic and epidemiologic data to supplement other disease monitoring activities and might become increasingly useful as routine testing decreases.

As of August 2022, cases of acute severe hepatitis of unknown etiology in children have been reported from 35 countries, including the United States. Here we used PCR testing, viral enrichment based sequencing, and agnostic metagenomic sequencing to analyze 27 samples, including nasopharyngeal swab, stool, plasma, and/or whole blood, from 16 such cases from 6 states (Alabama, California, Florida, Illinois, North Carolina, and South Dakota) presenting from October 1, 2021 to May 22, 2022, in parallel with whole blood samples from 45 controls. Among the 13 cases for whom whole blood was available, adeno-associated virus 2 (AAV2) sequences were detected in 92% (12 of 13) (p<0.001), while adenovirus sequences were detected in 100%, of which 11 (84.6%) were genotyped as human adenovirus type 41 (HAdV-41), one as HAdV-40, and one as HAdV-2. Co-infections of herpesviruses, Epstein-Barr virus (EBV) or human herpesvirus 6 (HHV-6), and/or enterovirus A71 (EV-A71) were also detected in all 13 cases. In contrast, AAV2 and HAdV-41 were not detected in any control, and EBV, HHV-6, or EV-A71 were each only detected in one or two of 45 controls (p<0.001). Analysis of assembled AAV2 viral genome sequences identified 35 coding mutations relative to the AAV2 reference genome, predominantly located in the VP1 capsid and assembly-activating protein (AAP) proteins, and AAV2 genomes from cases clustered together by phylogenetic analysis. Our findings of a distinct AAV2 strain in nearly all cases of acute severe hepatitis of unknown etiology in conjunction with one or more infecting helper viruses suggest that disease pathogenesis and/or severity may be related to co-infection with AAV2.

Klebsiella spp. are opportunistic pathogens with clinical, veterinary and plant-associated isolates. A previous study showed that bacterial ooze from wetwood of severely declined ironwood trees in Guam contained Ralstonia solanacearum, Klebsiella variicola and K. oxytoca. In this study, Loop-Mediated Isothermal Amplification (LAMP) detected K. variicola and K. oxytoca specifically, using unique primer sets designed individually for each organism. Each LAMP detected its target specifically, while showing negative results for non-target bacteria and negative controls. LAMP detected Klebsiella in inoculated-ironwood stem tissues and bacterial ooze. Due to the presence of plant inhibitors, different sampling protocols were tested. Soaking plant tissue samples to allow diffusion of bacteria into solution, followed by boiling, provided optimum detection of Klebsiella directly from plant samples. False negatives obtained when using crushed plant samples were eliminated by including an enrichment step, involving plating and 12-h incubation. DGGE (denaturing gradient gel electrophoresis) and a colony-blot immunoassay using a Klebsiella-specific antibody also detected Klebsiella in inoculated ironwood. DGGE bands and antibody crossreactions from closely related enterobacters showed the potential for false positive results. The nature of LAMP makes it ideal for point-of-care testing, and when combined with the specificity of the LAMP primers developed in this study, demonstrates its potential as a routine field test for Klebsiella in ironwood in Guam, as well as clinical and veterinary diagnosis of Klebsiella infection. Additionally, the regions targeted for detection in this study have application across all forms of molecular-based diagnostics.

N orovirus is the leading cause of acute gastroenteritis worldwide (1). The virus can be transmitted through person-to-person contact, aerosolized vomitus, contaminated food or water, or fomites (2). Noroviruses are divided into 10 genogroups; viruses in genogroups GI, GII, GIV, GVIII, and GIX cause illness in humans. Norovirus GIX was first identified in fecal samples collected in 1990 from US troops deployed to Saudi Arabia (3). This genogroup was previously known as GII.15 and was reclassified recently (4).