Омикрон за омикроном

[chuka_lis]

В Дании провели исследование, поставившее целью определить возможность заражения омикроном2 после обычного омикрона, в короткий промежуток времени.
Омикронов есть несколько вариантов,  сейчас доминирует везде первый, который и называют "омикроном", но есть еще и BA.1.1, BA.2 (омикрон-2) и  BA.3.
Омикрон и омикрон2 отличаются 40 мутациями (это прилично), часть из которых в РСЧ, и  некоторые- в других важных иммуногенных областях, и иммунный ответ на эти варианты может не совпадать.
Дания  с начала омикроновой волны конкретно переболела омикроном, несмотря на высокую привитость популяции (81% получили 2 дозы вакцины, 62% - с бустером): с 21 ноября по 11 февраля, ковид подхватили более 1.8 млн человек, или 32% популяции страны. Омикрон начал очень быстро доминировать, но вскорости за ним в Дании, одной из первых еврпейских стран, появился  и омикрон-2, который, с начала 2022 года так распространился, что на средину февраля был ответственен за 88% новых случаев ковида в стране.
Тк тестируют в Дании бесплатно и местами даже обязательно (если обратился в больницу, с другим поводом, или на операцию, итп, все равно сделают тест на ковид), и, так же, делают периодически полный сиквенс генома вируса, то, наблюдая картину высокой заболеваемости и реинфекций (особенно в районе Копенгагена), авторы смогли сделать выборку по случаям, когда новый ковид случился в период  межуд 20 и 60 днями после предыдущего, к тому же вирусного материала было достаточно, и, так же, был проведен анализ генома достаточного качества.
Полный  сиквенс, разумеется, там делают не всегда, а только примерно в каждом 15 случае, к тому же, для исследования надо было, чтобы были "пары" (и первый и второй полный сиквенс), но у них все же набралось из примерно 1700 реинфекций за этот период, из них примерно 470 удовлетворяющих случаев,  которые они рандомно выбрали, по их критериям. Дальше чуток подсократилось (до 273 пар из которых только 187 качественных), тк достаточно качественный материал в мазках был не всегда.
Часть из пар была: омикрон после дельты, омикрон-2 после дельты, омикрон после омикрона, но нашлось и 47 пар, когда первый ковид за это время был омикрон, а второй- омикрон-2 (18% пар).
Авторы отмечают,  что все случаи заболевания омикроном2 после омикрона были умеренные и легкие, никто не нуждался в госпитализации или не умер. 70%  из этих случаев- молодые люди, до 20 лет. Медианный возраст 15 лет. Из них привитых было только 13%.
Омикроном (первый ковид) они так же болели легко или умеренно. Средняя симптоматичная продолжительность обоих ковидов была 4 дня. Такая же она была,  если подхватывали омикрон после омикрона. Касательно этого варианта "пары"- то в основном, авторы склоняются к мысли, что это была не новая инфекция, а все еще старый вирус, тк в большинстве случаев было мало генетических отличий между 1м и 2 образцом омикрона, и период выяления "второго омикронового ковида" был короче  (чем для пары "омикрон-омикрон2") - в среднем, 26 дней.
Второй омикроновый ковид вскорости после 1го, таким оразом, переносился в общем и целом средне и легко. Кроме того, вируса при втором ковиде (был ли это омикрон или омикрон2) выделялось меньше чем при первом, впрочем, все попадало в разброс выделения омикрона и омикрона2 по популяции ( при 1м ковиде).
С одной стороны, авторы удивлены, что реинфекции спустя короткое время  случаются именно с молодежью- ведь по предположениям, считается, что иммунный ответ на ковид у молодых более качественный и многовариантный, потому они  должны бы быть лучше защищены от реинфекции,  даже и другим штаммом, тем более спустя такое короткое время.
Так же, авторы поднимают вопрос-  не смотря на то, что случаев реинфекций омикрон-омикрон-2 мало, все же это 2 разные линии вируса (как и дельта-омикрон или дельта-омикрон2), и точно реинфекции, и все они случились до 60 дней после 1 ковида. В то время как сейчас реинфекцией называют и считают только те случаи ковида, когда второй раз ковид случился спустя не менее  60 дней.
Возможно, критерий реинфекции в случае ковида стоит пересмотреть.
Omicron carries more than 30 mutations and deletions in the spike gene compared to the original Wuhan strain and is associated with increased transmissibility2 and immune escape 3,4. Studies indicate that the Omicron variant results in less severe disease outcomes than Delta5. Currently, Omicron is subdivided into four subvariants, BA.1, BA.1.1, BA.2 and BA.3, where BA.1 is the dominating Omicron subvariant worldwide (https://outbreak.info), and in Europe Omicron is estimated to account for about 70% of all reported cases6. In Denmark, we have observed a dramatic increase in Omicron BA.2 case number since the beginning of early 2022, and BA.2 now accounts for 88% of all cases. Omicron BA.2 case numbers are also increasing in countries like the United Kingdom, South Africa and Norway currently. Omicron BA.1 and BA.2 differ by up to 40 non-synonymous mutations and deletions7 including key mutations in the N-terminal and the receptor binding domains of the spike gene, both regions that influence the immune response. The diversity between Omicron BA.1 and BA.2 in the spike protein exceeds the variation between the Wuhan and the Alpha variant. With the surge of both BA.1 and BA.2, a large number of reinfections, as defined by the European Centre for Disease Prevention and Control (ECDC) as two positive tests >60 days apart, has been observed, raising the question if BA.2 can escape the natural immunity acquired shortly after a BA.1 infection, and if so, whether these cases are associated with changes in disease severity. Using whole genome sequencing (WGS), we investigate whether Omicron BA.2 reinfections occurred within 20-60 days following initial infections with BA.1 in the time period when these two subvariants emerged and became dominant in Denmark. Here we present evidence that Omicron BA.2 reinfections indeed do occur relatively shortly after a BA.1 infection, causing mostly mild disease in unvaccinated young individuals.
Between November 21, 2021, and February 11, 2022, a total number of ~1.8 million individuals (32% of the Danish population) tested positive for SARS-CoV-2 in Denmark by PCR. In this period, WGS produced ~140,000 SARS-CoV-2 genomes at the time of analysis. Based on the surveillance-based genome data, we identified 54 cases with high-quality Omicron BA.1 sequences that also had a non-sequenced sample 20-60 days later, and 18 cases with a high-quality Omicron BA.2 sequence and a non-sequenced sample at 20-60 days earlier within this period. Out of a total of 1,739 potential reinfection cases, 984 samples from 492 cases were selected. In total 1,056 samples were subjected to WGS, of which 613 were successfully sequenced and identified 470 Omicron sequences that were used for further data analysis (Figure 1). Combining these Omicron reinfection data, a total of 67 persons had a pair of samples with adequate sequencing quality of which 64 had an Omicron BA.1 sequence identified in the first sample and 47 had a BA.2 sequence identified in the subsequent sample, while only 17 had BA.1 identified also in the subsequent sample paired samples from the BA.1 to BA.1 cases were on average c 191 сollected within a shorter timespan (median: 26 days) compared to samples collected from the BA.2 reinfection cases (median: 36 days) (p=0.002, Supplementary Figure 1A), possibly representing residual virus RNA (Supplementary Figure 2). Accordingly, when comparing the genomes of the BA.1-BA.1 cases (n=17), the vast majority (88%, 15/17) were identical (0-1 SNP) and only two cases showed a larger SNP difference of seven and eight SNPs. The changes were not overall correlated to difference in sampling time. For the three Omicron BA.2 to BA.2 cases, two were identical and one differed by four SNPs.
Examination of viral load showed that the Ct values for Omicron BA.2 reinfections were higher, thus indicating a lower viral concentration as compared to the initial BA.1 infections (p-value=0.006) (Supplementary Figure 1B and Supplementary Table 1). The same tendency was observed for the Omicron BA.1 to BA.1 cases (Supplementary Figure 1C). In order to validate if the reduced viral load of the Omicron BA.2 reinfection cases could be considered as a general feature of BA.2 infections or was specific for this scenario, i.e. a BA.2 infection emerging shortly after a BA.1 infection, we compared Ct values for the majority of Danish BA.1 and BA.2 genomes (n=58,015). This analysis indicated no difference in viral load between BA.1 and BA.2 in general (Supplemental Table 1). The median age of the 47 cases was 15 years, and no cases were older than 38 at the time of the Omicron BA.1 infection and the majority under the age of 20 (70%) (Table 2). The overall vaccination status of cases showed that 42 (89%) were not vaccinated, three (6%) were vaccinated twice, whereas two (4%) only had one vaccination. For the entire population of Denmark, 81% are vaccinated twice and 62% have received the booster. The reinfection cases were observed across Denmark with most occurring in the Greater Copenhagen region that also had the most incidences during the study period (https://www.covid19genomics.dk/statistics). Interestingly, when looking at the number of Delta to Omicron reinfections in the same period, we observed 26 Delta to Omicron BA.1 and 140 Delta to Omicron BA.2 reinfections. The median age for cases with a Delta to BA.2 reinfection was 16 years, and the majority were unvaccinated (68%) (Supplementary Table 2).
None of the 47 individuals with Omicron BA.1 to BA2 reinfections had been hospitalized or died during the follow-up study period. Detailed information of symptoms was obtained for 33 of the cases, whereof most of them reported symptoms during both infections (Figure 2, Supplementary Table 3). Twenty-eight (85%) had symtoms during the Omicron BA.2 reinfection, though mainly mild disease (symptoms for a few days) (Figure 2A). The mean duration of symptoms were four days for both infection rounds. The distribution of reported symptoms did not differ markedly between the two infections (Figure 2B). For the first infection, the most common indication for testing was exposure as close contact to a person testing positive (53%) while the primary indication for testing for the second infection was experiencing symptoms (47%). The phylogeny of the paired Omicron BA.1 and BA.2 genomes with the randomly sampled Danish BA.1 and BA.2 genomes, did not show any distinct variant(s) causing the reinfection (BA.2) nor any primary Omicron BA.1 clusters that in some way could be related to later reinfections (Figure 3). Despite differences in age group and vaccination status distributions between the paired reinfection data and the randomly sampled data, no clustering of samples by these parameters was evident. In addition, no mutations were observed in the spike protein other than those seen in general among Omicron BA.2 cases. It appears that for the initial Omicron BA.1 infection, the levels of genomic RNA (mapped at nucleotide 55) and for the two mapped subgenomic RNAs for Spike and Nucleoprotein, respectively, did not differ between the study population and the randomly selected BA.1 samples used for comparison (Supplementary Figure 2).In contrast, for the subsequent Omicron BA.2 infection, the findings in the study population indicate a particular dominance of 241 virus genomic RNA and relatively lower/decreased levels of Spike and Nucleoprotein subgenomic RNAs when compared to the random BA.2 samples used for comparison (Supplementary Figure 2). Further, the BA.2 samples, both the study population and the random selected samples, tended to have more virus genomic RNA and lower levels of Spike and Nucleoprotein subgenomic RNA than the included BA.1 study and random samples
The present study confirms the occurrence of Omicron BA.2 reinfection shortly after a previous BA.1 infection. This is to our knowledge the first study that reports aggregated Omicron BA.2 reinfection cases and document a time interval as short as 20 days after initial infection. Among the 1,848,466 million infected individuals in the study period, we identified 1,739 cases that fulfilled the criteria of two positive samples with more than 20 and less than 60 days apart. From a randomly selected group of 263 paired samples that were successfully analyzed by WGS, we found 187 (71%) cases of reinfections and 47 (18%) of these were Omicron BA.1-BA.2 reinfections. The reinfection rate appears to be low given the high number of positive SARS-CoV-2 tests during the study period but still highlights the need for continuous assessment of length of vaccine-induced and/or natural immunity. Given the short time period between infections it could be reasonable to re-evaluate the definition by ECDC that requires two positive samples with more than 60 days apart in order to consider reinfection. Omicron BA.2 reinfections after either Delta or BA.1 initial infections, were mainly observed among young individuals below the age of 30 and the majority of these cases were not vaccinated, further emphasizing the enhanced immunity obtained by the combination of vaccination and infection compared to infection induced immunity only. For the Omicron BA.1 infection to BA.2 reinfection among cases aged 15 or above, only 13% (3/24) had completed the primary vaccination program contrary to the overall vaccination rate in Denmark of >80%. Reinfections were characterized by overall mild symptoms comparable to the initial infection and did lead to neither hospitalization nor death. It is, however, striking that mainly children and adolescents become reinfected, since children to a higher degree than adults develop a sustained cross-reactive immunity16. This may be explained by the very high incidences among children in the chosen study period, whereas adults and elderly had lower incidences. A change in indication for testing was noted between the first and second infection, and this may reflect a general change in why individuals are tested over time. With more widespread infections and restrictions lifted, the urge to test due to exposure to a person testing positive may have been reduced in general, leading to an increase in the proportion of individuals tested because of symptoms. To evaluate if cases of Omicron BA.2 reinfections are caused by a specific subset of BA.2 variants circulating with intrinsically different properties than BA.2 in general, we compared the paired samples with randomly sampled Danish BA.1 and BA.2 genomes. Here we found no sign of clustering among BA.2 or BA.1 variants involved in reinfection compared with the randomly selected BA.1 and BA.2 sequences. The differences in age group and vaccination status between the paired reinfection data and the randomly sampled data did not give rise to any clustering either. This indicates that the capability of Omicron BA.2 to cause reinfections in recently infected Omicron BA.1 cases with low or no vaccination protection may be an intrinsic BA.2 property. For the Omicron BA.1-BA.1 cases, we found the genomes to be near identical (0-1 SNP) in most cases, thus indicating a residual infection. We observed significantly reduced overall viral load in secondary 290 BA.2 infection samples compared to initial infection together with a lower ratio of subgenomic to genomic RNA. Taken together, this may indicate a more superficial and transient secondary infection that could be explained by T cell-mediated immunity obtained during the first infection17. We have previously speculated that infections in the early stage may be associated with the pattern that we see here for the Omicron BA.2 study population18, and it is possible that the BA.2 infection in these individuals, happening within a short window after an initial BA.1 infection, may somehow differ, perhaps by being more superficial or transient than the BA.2 infections observed in the randomly selected samples used for comparison. In conclusion, we provide evidence that Omicron BA.2 reinfections are rare but can occur relatively shortly after a BA.1 infection, causing mostly mild disease in unvaccinated young individuals. The reinfections were identified among SARS-CoV-2 cases testing positive for more than one time in a country with a high PCR test capacity and extensive community transmission.