key: cord-0939176-2fj6moa0 authors: Ramírez, Juan D.; Castañeda, Sergio; Ballesteros, Nathalia; Muñoz, Marina; Hernández, Matthew; Banu, Radhika; Shrestha, Paras; Chen, Feng; Shi, Huanzhi; van Bakel, Harm; Simon, Viviana; Cordon‐Cardo, Carlos; Sordillo, Emilia M.; Paniz‐Mondolfi, Alberto E. title: Hotspots for SARS‐CoV‐2 Omicron variant spread: Lessons from New York City date: 2022-03-14 journal: J Med Virol DOI: 10.1002/jmv.27691 sha: 7933a1ce6d659eab4f536326a569a9db8fbb8b74 doc_id: 939176 cord_uid: 2fj6moa0 The coronavirus disease‐2019 (COVID‐19) pandemic is still challenging public health systems worldwide, particularly with the emergence of novel SARS‐CoV‐2 variants with mutations that increase their transmissibility and immune escape. This is the case of the variant of concern Omicron that rapidly spread globally. Here, using epidemiological and genomic data we compared the situations in South Africa as the epicenter of emergence, United Kingdom, and with particular interest New York City. This rapid global dispersal from the place of first report reemphasizes the high transmissibility of Omicron, which needed only two weeks to become dominant in the United Kingdom and New York City. Our analyses suggest that as SARS‐CoV‐2 continues to evolve, global authorities must prioritize equity in vaccine access and continued genomic surveillance. Future studies are still needed to fully unveil the biological properties of Omicron, but what is certain is that vaccination, large‐scale testing, and infection prevention efforts are the greatest arsenal against the COVID‐19 pandemic. Omicron has attracted the attention of global authorities due to recent reports of incomplete immune escape (41 times reduction in neutralizing titers) from healthy, uninfected individuals who received (2 or 3) vaccine doses (Pfizer-BioNtech). In addition, neutralizing activity was decreased in sera from patients vaccinated with two doses of Pfizer-BioNtech or Moderna or heterologous AstraZeneca/ BioNTech among others. 4, 5 These findings may correlate with the observation that Omicron appears to be more contagious, but not more lethal. Recent evidence from South Africa suggests a reduced risk of hospitalization and a reduced risk of severe disease when compared to patient populations infected with the earlier Delta VOC. Given these features, we studied the number of cases, deaths, the effective reproduction number (R t is the average number of new infections caused by a single infected individual at time t in the partially susceptible population) and phylogenomic characteristics of Omicron viruses in NYC compared to UK and SA using publicly available epidemiological and genomic data until January 30, 2022. [6] [7] [8] [9] [10] Following identification of the first Omicron case in NYC at the Icahn School of Medicine at Mount Sinai on December 2, 2021 from a specimen collected on November 27, there has been a dramatic increase in new detections, reaching approximately 42 000 cases per day for NYC alone ( Figure 1A ). 6 Notably, the number of deaths has not increased at the rate seen during earlier waves, consistent with data from SA and the UK ( Figure 1B 12-year old have increased, highlighting the vulnerability of this highrisk unvaccinated population to serious illness due to COVID-19, as well the potential to jeopardize transmission dynamics. 11, 12 It is likely that high transmissibility and large numbers of infected persons has enabled the Omicron VOC to diversify rapidly into three The authors thank and acknowledge all authors and laboratories around the globe contributing their genomes on GISAID. All used genomes in these analyses are listed on Table S1 . This publication is Global Initiative on Sharing All Influenza Data-from vision to reality An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by therapeutic monoclonal antibodies mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant Neutralizing potency of COVID-19 vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant COVID-19 Daily Counts of Cases, Hospitalizations, and Deaths | NYC Open Data COVID-19) Cases -Our World in Data COVID-19 South African Coronavirus News And Information Cases in the UK | Coronavirus in the UK. Accessed COVID-19 Data in New York | Department of Health COVID-19: Data on Vaccines -NYC Health. Accessed Accessed COVID-19) Vaccinations -Humanitarian Data Exchange The authors declare no conflicts of interest.