To reconstruct the evolutionary dynamics of the 2019 novel‐coronavirus recently causing an outbreak in Wuhan, China, 52 SARS‐CoV‐2 genomes available on 4 February 2020 at Global Initiative on Sharing All Influenza Data were analyzed. The two models used to estimate the reproduction number (coalescent‐based exponential growth and a birth‐death skyline method) indicated an estimated mean evolutionary rate of 7.8 × 10⁻⁴ subs/site/year (range, 1.1 × 10⁻⁴‐15 × 10⁻⁴) and a mean tMRCA of the tree root of 73 days. The estimated R value was 2.6 (range, 2.1‐5.1), and increased from 0.8 to 2.4 in December 2019. The estimated mean doubling time of the epidemic was between 3.6 and 4.1 days. This study proves the usefulness of phylogeny in supporting the surveillance of emerging new infections even as the epidemic is growing.

This report describes the isolation, molecular characterization, and phylogenetic analysis of the first three complete genomes of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) isolated from three patients involved in the first outbreak of COVID‐19 in Lombardy, Italy. Early molecular epidemiological tracing suggests that SARS‐CoV‐2 was present in Italy weeks before the first reported cases of infection.

Chikungunya virus is a mosquito-transmitted alphavirus that causes chikungunya fever, a febrile illness associated with severe arthralgia and rash. Chikungunya virus is transmitted by culicine mosquitoes; Chikungunya virus replicates in the skin, disseminates to liver, muscle, joints, lymphoid tissue and brain, presumably through the blood. Phylogenetic studies showed that the Indian Ocean and the Indian subcontinent epidemics were caused by two different introductions of distinct strains of East/Central/South African genotype of CHIKV. The paraphyletic grouping of African CHIK viruses supports the historical evidence that the virus was introduced into Asia from Africa. Phylogenetic analysis divided Chikungunya virus isolates into three distinct genotypes based on geographical origins: the first, the West Africa genotype, consisted of isolates from Senegal and Nigeria; the second contained strains from East/Central/South African genotype, while the third contained solely Asian. The most recent common ancestor for the recent epidemic, which ravaged Indian Ocean islands and Indian subcontinent in 2004 - 2007, was found to date in 2002. Asian lineage dated about 1952 and exhibits similar spread patterns of the recent Indian Ocean outbreak lineage, with successive epidemics detected along an eastward path. Asian group splitted into two clades: an Indian lineage and a south east lineage. Outbreaks of Chikungunya virus fever in Asia have not been associated necessarily with outbreaks in Africa. Phylogenetic tools can reconstruct geographic spread of Chikungunya virus during the epidemics wave. The good management of patients with acute Chikungunya virus infection is essential for public health in susceptible areas with current Aedes spp activity.

Background: Immunocompromised patients show prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. We report a case of prolonged persistence of viable SARS-CoV-2 associated with clinical relapses of coronavirus disease 2019 (COVID-19) in a patient with mantle cell lymphoma who underwent treatment with rituximab, bendamustine, cytarabine with consequent lymphopenia and hypogammaglobulinemia. Methods: Nasopharyngeal swabs and blood samples were tested for SARS-CoV-2 by real-time polymerase chain reaction (RT-PCR). On 5 positive nasopharyngeal swabs, we performed viral culture and next-generation sequencing. We analyzed the patient’s adaptive and innate immunity to characterize T- and NK-cell subsets. Results: SARS-CoV-2 RT-PCR on nasopharyngeal swabs samples remained positive for 268 days. All 5 performed viral cultures were positive, and genomic analysis confirmed a persistent infection with the same strain. Viremia resulted positive in 3 out of 4 COVID-19 clinical relapses and cleared each time after remdesivir treatment. The T- and NK-cell dynamic was different in aviremic and viremic samples, and no SARS-CoV-2-specific antibodies were detected throughout the disease course. Conclusions: In our patient, SARS-CoV-2 persisted with proven infectivity for >8 months. Viremia was associated with COVID-19 relapses, and remdesivir treatment was effective in viremia clearance and symptom remission, although it was unable to clear the virus from the upper respiratory airways. During the viremic phase, we observed a low frequency of terminal effector CD8+ T lymphocytes in peripheral blood; these are probably recruited in inflammatory tissue for viral eradication. In addition, we found a high level of NK-cell repertoire perturbation with relevant involvement during SARS-CoV-2 viremia.