Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequenced 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. A phylogenetic analysis including thousands of globally sampled sequences allowed us to infer multiple independent introductions into Israel, followed by local transmission. Returning travelers from the U.S. contributed dramatically more to viral spread relative to their proportion in incoming infected travelers. Using phylodynamic analysis, we estimated that the basic reproduction number of the virus was initially around ~2.0-2.6, dropping by two-thirds following the implementation of social distancing measures. A comparison between reported and model-estimated case numbers indicated high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 1-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings underscore the ability of this virus to efficiently transmit between and within countries, as well as demonstrate the effectiveness of social distancing measures for reducing its spread.

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Background no updated data currently exist regarding Neisseria meningitidis carriage and genomic epidemiology among young Israeli adults. Methods oropharyngeal swabs were collected from 1,801 military recruits at the day of recruitment during 2019. Neisseria meningitidis was detected and identified by culture and qPCR. Confirmed isolates were serotyped by qPCR and encapsulated strains underwent whole genome sequencing. Risk factors for carriage were determined by analyzing focused questionnaires using uni- and multivariate models. Genomic typing was performed by means of core genome multilocus sequence typing. Results carriage rates overall and of encapsulated strains were 20.1% and 6.7%, respectively. Genogroup B (49.2%) and Y (26.7%) were the most common encapsulated strains. Genogroups C, W and X were scarce and genogroup A was absent. The most notable clonal complexes were CC23 (n=30), CC32 (n=16) and CC44/41 (n=9). Carriage was significantly associated with smoking (OR=1.82, CI[1.43-2.33) and boarding school attendance prior to recruitment (OR=1.49, CI[1.14-1.96]). Conclusions the prevalence of meningococcal carriage among young Israeli adults is high, compared to similar studies in other developed countries. This might be due to sociocultural characteristics including smoking and boarding school attendance during and after high school. The dominant genogroups and CCs found were compatible with those implicated in invasive disease in Israel.

In this report, we describe the first national scale multi-laboratory evaluation of commercial quantitative PCR kits for detection of Monkeypox virus (MPXV) DNA. The objective of this study was to assess the performance of two kits by different diagnostic laboratories across Israel. A panel of 10 standardized samples was tested simultaneously using the Novaplex (15 laboratories) and Bio-Speedy (seven laboratories) kits. An in-house assay based on previously published tests was used as reference. Comparison of the results showed high intra-assay consistency between laboratories, with small variations for most samples. The sensitivity of the two kits was similar to that of the in-house assay, with an analytical detection limit of less than ten copies per reaction. Significant differences were observed, however, in the Cq values and relative fluorescence (RF), between the assays. The RF signal of the in-house and Bio-Speedy assay ranged between 5,000 and 10,000 RFU, while the signal in the Novaplex assay was less than 600 RFU. Due to the kit measurement protocol, the Cq values of the Bio-Speedy kit were 5-7.5 cycles lower than those of the In-house assay. On the contrary, the Cq values of the Novaplex kit were significantly higher than those of the in-house assay, with differences of 3-5 cycles per sample. Our results suggest that while all assays were similar in their overall sensitivity, direct comparison of Cq values between them may be misleading. Additionally, the low fluorescence obtained with the Novaplex kit may be problematic with marginal or high-background samples. Diagnostic laboratories should therefore consider all these aspects when choosing a specific MPX detection assay.

No abstract