ABSTRACT
Background: Objectives were to investigate aspects of the COVID-19 epidemics via testing the individuals who were referred to Aramesh Medical Laboratory in Tehran and to integrate the molecular results with epidemiological data since the beginning of the epidemic. Methods: In this cross-sectional Study 77528 outpatients were referred to Aramesh Medical laboratory by physicians for the diagnosis of SARS-CoV-2 infection between March 2019 and May 2021. Viral acid nucleic extracted from nasal and throat specimens and subsequently amplified using Reverse Transcriptase Real-Time PCR. Laboratory data including Ct values compared with epidemic peaks of COVID-19 countrywide. Statistical Analysis was done by SPSS 21 Software. Results: 14312 (18.46%) tested positive.36.5% of the positive cases were in the 30 to 39 years old age group. The positive result rate was significantly different based on months, ranging from 6% to 28%, compatible with four recognized epidemic peaks encompassing the end of March through the first week of April (first epidemic peak), from June to July 2020 (second epidemic peak), October until mid of November 2020 (third epidemic wave) followed by the end of April to May 2021 (until the end period of study, in the middle of 4th peak). In 37.8% of cases, the Ct value was between 21 and 28. Two separate trends were seen for Ct ≤ 25 and Ct ≤ 20 for the first and fourth epidemic peaks, respectively. There was an association between the number of total monthly positive results and total deaths in the country, especially with the second to third peaks (in the course of summer 2020) and fourth epidemic peak. Conclusion: It might be useful to consider laboratory admission rates as an indicator for changes in the epidemic level in the country to continue the SARS-CoV-2 surveillance in accordance with public decision-makers.
ABSTRACT
The SARS-CoV-2 virus has been rapidly spreading globally since December 2019, triggering a pandemic, soon after its emergence. While Iran was among the first countries confronted with rapid spread of virus in February 2020, no real-time SARS-CoV-2 whole-genome tracking in early phase of outbreak was performed in the country. To address this issue, we provided 50 whole-genome sequences of viral isolates ascertained from different geographical locations in Iran during March-July 2020. The corresponding analysis on origins, transmission dynamics and genetic diversity of SARS-CoV-2 virus, represented at least two introductions of the virus into the country, constructing two major clusters defined as B.4 and B.1*. The first entry of the virus might have occurred around very late 2019/early 2020, as suggested by the time to the most recent common ancestor, followed by a rapid community transmission that led to dominancy of B.4 lineage in early epidemic till the end of June. Gradually, reduction in dominancy of B.4 occurred possibly as a result of other entries of the virus, followed by surge of B.1* lineages, as of mid-May. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. The increase in frequency of D614G mutation and B.1* lineages from mid-May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country.
